|
2d_auto_threshold |
ip_threshold |
Automatic thresholding |
2019-01-22 |
https://github.com/bmcv |
0.25.0 |
scikit-image |
|
To update |
Imaging |
Image analysis, Image annotation, Visualisation, Data handling |
Image analysis, Image annotation, Visualisation, Data handling |
Imaging, Software engineering, Literature and language |
Imaging, Software engineering, Literature and language |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold |
scikit-image |
scikit-image |
Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. |
scikit-image |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
130 |
154 |
3302 |
8913 |
5 |
5 |
29 |
29 |
12 |
12 |
607 |
607 |
0 |
0 |
0 |
0 |
9549 |
3938 |
171 |
147 |
https://usegalaxy.eu/published/workflow?id=035f85c1615e0b7b, https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=50c47c5b285f7c00, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=7f8ff64c5ea03a9b, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=cf196794bbd365d8, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.eu/published/workflow?id=e87e726b57f1a875, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/1508?version=1, https://workflowhub.eu/workflows/1517?version=1, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1526?version=1, https://workflowhub.eu/workflows/1532?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/771?version=2 |
imaging/hela-screen-analysis, imaging/imaging-introduction, imaging/parameter-tuning, imaging/process-image-bioimageio, imaging/voronoi-segmentation |
|
2d_feature_extraction |
ip_2d_feature_extraction |
2D feature extraction |
2019-01-08 |
https://github.com/bmcv |
0.18.1 |
scikit-image |
|
To update |
Imaging |
Image analysis, Image annotation, Visualisation, Data handling |
Image analysis, Image annotation, Visualisation, Data handling |
Imaging, Software engineering, Literature and language |
Imaging, Software engineering, Literature and language |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction |
scikit-image |
scikit-image |
Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. |
scikit-image |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
52 |
67 |
2130 |
15217 |
0 |
0 |
0 |
0 |
4 |
4 |
167 |
167 |
0 |
0 |
0 |
0 |
15384 |
2297 |
71 |
56 |
https://usegalaxy.eu/published/workflow?id=035f85c1615e0b7b, https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=2571f7d13686efb2, https://usegalaxy.eu/published/workflow?id=50c47c5b285f7c00, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=cf196794bbd365d8, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/1508?version=1, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/1848?version=1 |
imaging/electrophoresis-gel-bands-image-analysis, imaging/hela-screen-analysis, imaging/voronoi-segmentation |
|
2d_filter_segmentation_by_features |
ip_2d_filter_segmentation_by_features |
filter segmentation by rules |
2019-07-19 |
https://github.com/bmcv |
0.0.1-4 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
34 |
49 |
514 |
7009 |
0 |
0 |
0 |
0 |
3 |
3 |
165 |
165 |
0 |
0 |
0 |
0 |
7174 |
679 |
52 |
37 |
https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=50c47c5b285f7c00, https://usegalaxy.eu/published/workflow?id=cf196794bbd365d8, https://workflowhub.eu/workflows/1508?version=1 |
imaging/hela-screen-analysis |
|
2d_histogram_equalization |
ip_histogram_equalization |
2d histogram equalization |
2019-07-23 |
https://github.com/bmcv |
0.18.1 |
scikit-image |
|
To update |
Imaging |
Image analysis, Image annotation, Visualisation, Data handling |
Image analysis, Image annotation, Visualisation, Data handling |
Imaging, Software engineering, Literature and language |
Imaging, Software engineering, Literature and language |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization |
scikit-image |
scikit-image |
Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. |
scikit-image |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
100 |
122 |
2565 |
2669 |
5 |
5 |
24 |
24 |
15 |
15 |
284 |
284 |
0 |
0 |
0 |
0 |
2977 |
2873 |
142 |
120 |
https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=751e3e2c338949c0, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/1517?version=1, https://workflowhub.eu/workflows/1528?version=1, https://workflowhub.eu/workflows/1532?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/1840?version=1, https://workflowhub.eu/workflows/771?version=2 |
imaging/2D-spot-detection, imaging/imaging-introduction, imaging/parameter-tuning, imaging/yolo-segmentation-training |
|
2d_simple_filter |
ip_filter_standard |
2d simple filter |
2019-01-22 |
https://github.com/bmcv |
1.12.0 |
scipy |
|
To update |
Imaging |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter |
|
|
|
scipy |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
107 |
131 |
2596 |
8178 |
5 |
5 |
23 |
23 |
15 |
15 |
484 |
484 |
0 |
0 |
0 |
0 |
8685 |
3103 |
151 |
127 |
https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=50c47c5b285f7c00, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=7f8ff64c5ea03a9b, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=cf196794bbd365d8, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/1508?version=1, https://workflowhub.eu/workflows/1517?version=1, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1532?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/771?version=2 |
imaging/hela-screen-analysis, imaging/imaging-introduction, imaging/parameter-tuning, imaging/voronoi-segmentation |
|
2dnmrannotation |
2DNmrAnnotation |
[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra |
2020-02-04 |
http://workflow4metabolomics.org |
2.0.0+galaxy3 |
r-batch |
1.1_4 |
To update |
Metabolomics |
|
|
|
|
marie-tremblay-metatoul |
https://github.com/workflow4metabolomics/tools-metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
12 |
59 |
60 |
60 |
59 |
12 |
11 |
|
|
|
Ensembl-REST |
get_feature_info, get_genetree, get_sequences |
A suite of Galaxy tools designed to work with Ensembl REST API. |
2015-10-02 |
https://rest.ensembl.org |
1.0.0 |
python |
|
To update |
Data Source |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/Ensembl-REST |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/Ensembl-REST |
|
|
|
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
62 |
87 |
322 |
2959 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2959 |
322 |
87 |
62 |
https://usegalaxy.eu/published/workflow?id=d22dac11eba8c5a3 |
|
|
abacas |
abacas |
Order and Orientate Contigs |
2019-11-20 |
https://github.com/phac-nml/abacas |
1.1 |
mummer |
3.23 |
To update |
Assembly |
|
|
|
|
nml |
https://github.com/phac-nml/abacas |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
3 |
3 |
3 |
3 |
2 |
2 |
|
|
|
anisotropic_diffusion |
ip_anisotropic_diffusion |
Anisotropic image diffusion |
2018-12-04 |
https://github.com/bmcv |
0.4.0 |
medpy |
0.4.0 |
Up-to-date |
Imaging |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
3 |
924 |
964 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
964 |
924 |
3 |
2 |
|
|
|
apoc |
apoc |
Large-scale structural comparison of protein pockets |
2017-07-04 |
https://sites.gatech.edu/cssb/apoc/ |
1.0+galaxy1 |
apoc |
1b16 |
To update |
Computational chemistry |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/apoc/ |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/apoc |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
6 |
6 |
9 |
9 |
3 |
3 |
26 |
26 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
35 |
35 |
9 |
9 |
|
|
|
apollo |
create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism |
Access an Apollo instance from Galaxy |
2017-06-12 |
https://github.com/galaxy-genome-annotation/python-apollo |
|
apollo |
4.2.13 |
To update |
Web Services |
|
|
|
|
gga |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo |
|
|
|
|
0 |
0 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
9 |
393 |
403 |
5757 |
6363 |
3 |
3 |
9 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6372 |
5766 |
406 |
396 |
https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=3c233cc56d4df8b0, https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=44189803f223acd1, https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6, https://workflowhub.eu/workflows/1554?version=1, https://workflowhub.eu/workflows/749?version=1 |
genome-annotation/apollo, genome-annotation/apollo-euk |
|
askomics |
askomics_integrate |
Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/ |
2017-08-11 |
https://github.com/askomics/ |
|
askocli |
0.5 |
To update |
Web Services |
|
|
|
|
gga |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
askor_de |
askor_de |
AskoR links EdgeR and AskOmics |
2018-04-06 |
https://github.com/askomics/askoR |
0.2 |
bioconductor-limma |
3.62.1 |
To update |
Transcriptomics |
|
|
|
|
genouest |
https://github.com/genouest/galaxy-tools/tree/master/tools/askor |
https://github.com/genouest/galaxy-tools/tree/master/tools/askor |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
3 |
3 |
3 |
3 |
1 |
1 |
|
|
|
assemblystats |
assemblystats |
Summarise an assembly (e.g. N50 metrics) |
2017-10-13 |
https://github.com/phac-nml/galaxy_tools |
1.1.0 |
perl-bioperl |
1.7.8 |
To update |
Assembly |
|
|
|
|
nml |
https://github.com/phac-nml/galaxy_tools |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
background_removal |
background_removal |
Background removal filters using scikit-image |
2024-07-12 |
https://github.com/bmcv |
0.24.0 |
scikit-image |
|
To update |
Imaging |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tools/background_removal |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
763 |
763 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
763 |
763 |
4 |
4 |
|
|
|
bam2mappingstats |
bam2mappingstats |
Generates mapping stats from a bam file. |
2017-10-13 |
https://github.com/phac-nml/galaxy_tools |
1.1.0 |
perl |
|
To update |
Assembly |
|
|
|
|
nml |
https://github.com/phac-nml/galaxy_tools |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
bamclipper |
bamclipper |
Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. |
2020-04-28 |
https://github.com/tommyau/bamclipper |
1.0.0 |
bamclipper |
1.0.0 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/tommyau/bamclipper |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
baric_archive |
baric_archive_rennes, baric_archive_toulouse |
A data source tool to fetch data from a BARIC Archive server. |
2022-03-03 |
https://www.cesgo.org/catibaric/ |
1.1.0 |
|
|
To update |
Data Source |
|
|
|
|
genouest |
https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive |
https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive |
|
|
|
|
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
16 |
16 |
16 |
16 |
4 |
4 |
|
|
|
batched_lastz |
batched_lastz |
Galaxy wrapper for the batching Lastz runs |
2024-04-30 |
https://github.com/galaxyproject/KegAlign |
1.04.22 |
lastz |
1.04.52 |
To update |
Next Gen Mappers |
|
|
|
|
richard-burhans |
https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz |
https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
37 |
37 |
313 |
313 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
313 |
313 |
37 |
37 |
https://usegalaxy.org/published/workflow?id=ca68ad0d7420c615 |
|
|
bfconvert |
ip_convertimage |
Convert image |
2019-07-22 |
https://github.com/bmcv |
6.7.0 |
bftools |
8.0.0 |
To update |
Imaging, Convert Formats |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert |
|
|
|
python-bioformats |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
120 |
146 |
2087 |
2237 |
13 |
13 |
48 |
48 |
23 |
23 |
482 |
482 |
0 |
0 |
0 |
0 |
2767 |
2617 |
182 |
156 |
https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/1337?version=2, https://workflowhub.eu/workflows/1514?version=1, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/771?version=2 |
imaging/multiplex-tissue-imaging-TMA, imaging/voronoi-segmentation |
|
binary2labelimage |
ip_binary_to_labelimage |
Binary 2 label image |
2017-02-11 |
https://github.com/bmcv |
0.6 |
giatools |
0.4.1 |
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
97 |
117 |
2363 |
3402 |
6 |
6 |
23 |
23 |
10 |
10 |
299 |
299 |
0 |
0 |
0 |
0 |
3724 |
2685 |
133 |
113 |
https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=50c47c5b285f7c00, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/1508?version=1, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1526?version=1, https://workflowhub.eu/workflows/1532?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/771?version=2 |
imaging/2D-spot-detection, imaging/hela-screen-analysis, imaging/imaging-introduction, imaging/process-image-bioimageio, imaging/voronoi-segmentation |
|
binaryimage2points |
ip_binaryimage_to_points |
Binary Image to Points |
2017-10-30 |
https://github.com/bmcv |
0.1-2 |
numpy |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2 |
729 |
758 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
758 |
729 |
2 |
1 |
|
|
|
bioformats2raw |
bf2raw |
Convert image to OME-Zarr |
2023-11-02 |
https://github.com/Euro-BioImaging |
0.7.0 |
|
|
To update |
Imaging, Convert Formats |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
109 |
109 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
109 |
109 |
7 |
7 |
|
|
|
biohansel |
biohansel |
Heidelberg and Enteritidis SNP Elucidation |
2018-08-01 |
https://github.com/phac-nml/biohansel |
2.4.0 |
bio_hansel |
2.6.1 |
To update |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/biohansel |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
biohansel_bionumeric_converter |
bionumeric_convert |
Convert BioHansel output data to a Bionumerics friendly form |
2019-03-15 |
https://github.com/phac-nml/galaxy_tools |
0.2.0 |
pandas |
|
To update |
Text Manipulation |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
blast_parser |
blast_parser |
Convert 12- or 24-column BLAST output into 3-column hcluster_sg input |
2015-08-06 |
https://github.com/TGAC/earlham-galaxytools/ |
0.2.0 |
python |
|
To update |
Phylogenetics |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/blast_parser |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/blast_parser |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
133 |
146 |
769 |
942 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
942 |
769 |
146 |
133 |
https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09 |
|
|
braker |
braker |
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . |
2021-10-05 |
https://github.com/Gaius-Augustus/BRAKER |
2.1.6 |
|
|
To update |
Genome annotation |
|
|
|
|
genouest |
https://github.com/genouest/galaxy-tools/tree/master/tools/braker |
https://github.com/genouest/galaxy-tools/tree/master/tools/braker |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
96 |
96 |
287 |
287 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
9 |
9 |
296 |
296 |
97 |
97 |
|
|
|
braker3 |
braker3 |
BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . |
2023-06-13 |
https://github.com/Gaius-Augustus/BRAKER |
3.0.8 |
|
|
To update |
Genome annotation |
Genome annotation, Gene prediction |
Genome annotation, Gene prediction |
RNA-Seq, Genomics, Structure prediction, Sequence analysis |
RNA-Seq, Genomics, Structure prediction, Sequence analysis |
genouest |
https://github.com/genouest/galaxy-tools/tree/master/tools/braker |
https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 |
braker3 |
BRAKER3 |
BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
711 |
711 |
5354 |
5354 |
0 |
0 |
0 |
0 |
135 |
135 |
987 |
987 |
26 |
26 |
275 |
275 |
6616 |
6616 |
872 |
872 |
https://workflowhub.eu/workflows/1509?version=1, https://workflowhub.eu/workflows/1746?version=1 |
genome-annotation/braker3, genome-annotation/comparison-braker-helixer-annotation |
|
bundle_collections |
bundle_collection |
Tool to bundle up list collection into a single zip to be download |
2015-11-20 |
|
1.3.0 |
perl-getopt-long |
2.58 |
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections |
|
|
|
|
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
78 |
93 |
1733 |
1894 |
41 |
41 |
2107 |
2107 |
4003 |
3842 |
135 |
120 |
https://workflowhub.eu/workflows/373?version=2, https://workflowhub.eu/workflows/374?version=1, https://workflowhub.eu/workflows/375?version=1 |
|
|
camera |
abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos, CAMERA_findAdducts, CAMERA_findIsotopes, CAMERA_groupCorr, CAMERA_groupFWHM |
|
2023-05-25 |
|
1.48.0 |
r-snow |
0.4_1 |
To update |
Metabolomics |
|
|
|
|
workflow4metabolomics |
|
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera |
|
|
|
|
0 |
2 |
2 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
2 |
2 |
159 |
178 |
551 |
882 |
48 |
48 |
105 |
105 |
28 |
33 |
730 |
938 |
846 |
885 |
15960 |
16852 |
18777 |
17346 |
1144 |
1081 |
https://usegalaxy.fr/published/workflow?id=06fa7dd6eea42350, https://usegalaxy.fr/published/workflow?id=15275ba7c23028ed, https://usegalaxy.fr/published/workflow?id=180744a2f8dca6eb, https://usegalaxy.fr/published/workflow?id=19e99a5c09c01bb7, https://usegalaxy.fr/published/workflow?id=26a3e5741d66982a, https://usegalaxy.fr/published/workflow?id=26bdb32c017d798c, https://usegalaxy.fr/published/workflow?id=2ee479308227a926, https://usegalaxy.fr/published/workflow?id=3c41c4c5a6332c25, https://usegalaxy.fr/published/workflow?id=57748aa2cecf0405, https://usegalaxy.fr/published/workflow?id=5964606a3836cbdf, https://usegalaxy.fr/published/workflow?id=5ec8a143f82a8c90, https://usegalaxy.fr/published/workflow?id=6895bf9cff915ba1, https://usegalaxy.fr/published/workflow?id=7a790b0acf8ba14d, https://usegalaxy.fr/published/workflow?id=7cc77d6cdd8de027, https://usegalaxy.fr/published/workflow?id=98bb6a831a2b399d, https://usegalaxy.fr/published/workflow?id=b6311795ae10032b, https://usegalaxy.fr/published/workflow?id=bb69fa998b900cb8, https://usegalaxy.fr/published/workflow?id=bcd348178335a19b, https://usegalaxy.fr/published/workflow?id=dc17a87057dec748, https://usegalaxy.fr/published/workflow?id=e6a55d00f1364794, https://usegalaxy.fr/published/workflow?id=e6f26a543c3e044a, https://usegalaxy.fr/published/workflow?id=f49e102f63d3e2bb, https://usegalaxy.org.au/published/workflow?id=f9e5caaf08a450ec, https://usegalaxy.org.au/published/workflow?id=fa0243ff9b5ca997, https://usegalaxy.org/published/workflow?id=650f3eb7647b4508, https://usegalaxy.org/published/workflow?id=aeeaf3e06a13bc22, https://workflowhub.eu/workflows/1584?version=1, https://workflowhub.eu/workflows/677?version=2 |
metabolomics/lcms, metabolomics/lcms-preprocessing |
|
cfmid |
cfmid |
Competitive Fragmentation Modeling (CFM) |
2019-03-07 |
https://sourceforge.net/p/cfm-id/ |
33 |
cfm |
33 |
Up-to-date |
Metabolomics |
|
|
|
|
computational-metabolomics |
https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm |
https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
chado |
analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree |
Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado |
2018-06-11 |
https://github.com/galaxy-genome-annotation/python-chado |
|
python-chado |
2.3.9 |
To update |
Web Services |
|
|
|
|
gga |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
collapse_collections |
collapse_dataset |
Collection tool that collapses a list of files into a single datasset in order of appears in collection |
2015-12-10 |
|
5.1.0 |
gawk |
|
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
4683 |
4989 |
95465 |
101118 |
4256 |
5158 |
26570 |
32872 |
972 |
1042 |
5860 |
6266 |
181 |
190 |
3579 |
3597 |
143853 |
131474 |
11379 |
10092 |
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assembly/ERGA-post-assembly-QC, assembly/assembly-with-preprocessing, assembly/ecoli_comparison, assembly/vgp_genome_assembly, computational-chemistry/cheminformatics, computational-chemistry/covid19-docking, ecology/phylogeny-data-prep, evolution/mtb_transmission, galaxy-interface/collections, galaxy-interface/workflow-automation, genome-annotation/gene-centric, genome-annotation/secondary-metabolite-discovery, imaging/hela-screen-analysis, imaging/parameter-tuning, introduction/galaxy-intro-ngs-data-managment, microbiome/clinical-mp-3-verification, microbiome/mgnify-amplicon, microbiome/mothur-miseq-sop-short, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/clinical-mp-3-verification, proteomics/neoantigen-fragpipe-discovery, single-cell/bulk-deconvolution-evaluate, variant-analysis/aiv-analysis, variant-analysis/baculovirus-isolate-variation |
|
color_deconvolution |
ip_color_deconvolution |
Color-deconvolution methods |
2024-09-30 |
https://github.com/bmcv |
0.9 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
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0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
7 |
9 |
132 |
135 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
135 |
132 |
9 |
7 |
https://usegalaxy.eu/published/workflow?id=035f85c1615e0b7b |
|
|
colorize_labels |
colorize_labels |
Colorize label map |
2024-03-12 |
https://github.com/bmcv |
3.2.1 |
networkx |
|
To update |
Imaging |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
16 |
257 |
257 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
257 |
257 |
16 |
16 |
https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1730?version=1 |
imaging/voronoi-segmentation |
|
combine_assemblystats |
combine_stats |
Combine multiple Assemblystats datasets into a single tabular report |
2017-11-08 |
https://github.com/phac-nml/galaxy_tools |
1.0 |
perl-getopt-long |
2.58 |
To update |
Assembly |
|
|
|
|
nml |
https://github.com/phac-nml/galaxy_tools |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
combine_json |
combine_json |
JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array. |
2018-03-02 |
|
0.1 |
|
|
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
combine_tabular_collection |
combine |
Combine Tabular Collection into a single file |
2017-02-06 |
|
0.1 |
|
|
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
concat_channels |
ip_concat_channels |
Concatenate images |
2017-10-30 |
https://github.com/bmcv |
0.3-1 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
12 |
15 |
43 |
87 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
87 |
43 |
15 |
12 |
|
|
|
concat_paired |
concat_fastqs |
Concatenate paired datasets |
2019-12-16 |
https://github.com/phac-nml/concat |
0.2 |
|
|
To update |
Text Manipulation |
|
|
|
|
nml |
https://github.com/phac-nml/concat |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
coordinates_of_roi |
ip_coordinates_of_roi |
Coordinates of ROI |
2019-01-08 |
https://github.com/bmcv |
0.0.4-2 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
13 |
14 |
15194 |
17323 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
17323 |
15194 |
14 |
13 |
https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc |
|
|
correlation_analysis |
correlation_analysis |
[Metabolomics][W4M] Metabolites Correlation Analysis |
2020-12-08 |
http://workflow4metabolomics.org |
1.0.1+galaxy2 |
r-batch |
1.1_4 |
To update |
Metabolomics |
|
|
|
|
workflow4metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
57 |
57 |
241 |
241 |
241 |
241 |
57 |
57 |
|
|
|
count_objects |
ip_count_objects |
Count Objects |
2019-01-08 |
https://github.com/bmcv |
0.0.5-2 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
79 |
96 |
1176 |
1241 |
8 |
8 |
24 |
24 |
7 |
7 |
183 |
183 |
0 |
0 |
0 |
0 |
1448 |
1383 |
111 |
94 |
https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1532?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/771?version=2 |
imaging/imaging-introduction, imaging/voronoi-segmentation |
|
crop_image |
ip_crop_image |
Crop image |
2025-06-06 |
https://github.com/bmcv |
0.4.1 |
giatools |
0.4.1 |
Up-to-date |
Imaging |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image |
giatools |
giatools |
Tools required for Galaxy Image Analysis |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
|
|
|
cryptogenotyper |
CryptoGenotyper |
CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA (18S) and gp60 markers. |
2020-10-14 |
https://github.com/phac-nml/CryptoGenotyper |
1.5.0 |
cryptogenotyper |
1.5.0 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/CryptoGenotyper |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
31 |
31 |
12430 |
12430 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12430 |
12430 |
31 |
31 |
https://usegalaxy.eu/published/workflow?id=07865c770825c54a, https://usegalaxy.eu/published/workflow?id=280877e42b09f49f, https://usegalaxy.eu/published/workflow?id=3d7659452e3af984, https://usegalaxy.eu/published/workflow?id=4ba4da05a7696923, https://usegalaxy.eu/published/workflow?id=aefe927f13bc9374, https://usegalaxy.eu/published/workflow?id=f7558edf450e781f |
|
|
csvtk |
csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq |
Rapid data investigation and manipulation of csv/tsv files |
2019-08-23 |
https://bioinf.shenwei.me/csvtk/ |
0.20.0 |
csvtk |
0.31.0 |
To update |
Text Manipulation |
|
|
|
|
nml |
https://github.com/shenwei356/csvtk |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk |
|
|
|
|
0 |
6 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
20 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
350 |
350 |
18 |
18 |
130 |
130 |
480 |
480 |
25 |
25 |
|
|
|
curve_fitting |
ip_curve_fitting |
Polynomial curve fitting to data points |
2021-07-22 |
https://github.com/BMCV/galaxy-image-analysis |
0.0.3-2 |
numpy |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
4 |
4 |
30 |
30 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
30 |
30 |
4 |
4 |
https://usegalaxy.eu/published/workflow?id=ffa80e0637d079f2, https://workflowhub.eu/workflows/1499?version=1 |
imaging/detection-of-mitoflashes |
|
detection_viz |
ip_detection_viz |
Detection Visualization |
2017-10-30 |
https://github.com/bmcv |
0.3-2 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
6 |
9 |
6 |
49 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
49 |
6 |
9 |
6 |
|
|
|
ectyper |
ectyper |
EC-Typer - in silico serotyping of Escherichia coli species |
2018-12-21 |
https://github.com/phac-nml/ecoli_serotyping |
2.0.0 |
ectyper |
2.0.0 |
Up-to-date |
Sequence Analysis |
Sequence assembly, Read pre-processing, Variant calling |
Sequence assembly, Read pre-processing, Variant calling |
Whole genome sequencing, Public health and epidemiology, Sequence assembly, Genotype and phenotype, Workflows |
Whole genome sequencing, Public health and epidemiology, Sequence assembly, Genotype and phenotype, Workflows |
nml |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper |
ectyper |
ECTyper |
Ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats. (Galaxy Version 1.0.0) |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
218 |
218 |
30463 |
30463 |
1 |
1 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
30473 |
30473 |
219 |
219 |
https://usegalaxy.eu/published/workflow?id=b90585626a793502 |
|
|
ete |
ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator |
Analyse phylogenetic trees using the ETE Toolkit |
2016-06-01 |
https://etetoolkit.org/ |
3.1.3 |
ete3 |
3.1.1 |
To update |
Phylogenetics |
Phylogenetic analysis, Phylogenetic tree editing |
Phylogenetic tree editing |
Phylogenetics |
Phylogenetics |
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete |
ete |
ete |
The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org |
|
0 |
0 |
7 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
30 |
39 |
279 |
1030 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
13 |
13 |
1043 |
292 |
41 |
32 |
|
|
|
export_to_cluster |
export_to_cluster |
Export datasets to cluster |
2016-01-18 |
https://github.com/TGAC/earlham-galaxytools/ |
0.1.0 |
python |
|
To update |
Data Export |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/export_to_cluster/ |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/export_to_cluster |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
fasta2bed |
fasta2bed |
Convert multiple fasta file into tabular bed file format |
2017-10-11 |
https://github.com/phac-nml/galaxy_tools |
1.0.0 |
perl-bioperl |
1.7.8 |
To update |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/galaxy_tools |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
fasta_extract |
fa-extract-sequence |
extract single fasta from multiple fasta file |
2016-10-26 |
https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract |
1.1.0 |
perl-bioperl |
1.7.8 |
To update |
Sequence Analysis |
|
|
|
|
nml |
https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
10 |
0 |
0 |
0 |
0 |
107 |
181 |
923 |
1827 |
0 |
0 |
0 |
0 |
1837 |
923 |
182 |
107 |
|
|
|
fastqc_stats |
FastQC_Summary |
Summary multiple FastQC into a single tabular line report |
2017-10-11 |
https://github.com/phac-nml/galaxy_tools |
1.2 |
perl-bioperl |
1.7.8 |
To update |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/galaxy_tools |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
feelnc2asko |
feelnc2asko |
Convert FeelNC GTF to GFF3 |
2018-04-11 |
https://github.com/tderrien/FEELnc |
0.1 |
perl-bioperl |
1.7.8 |
To update |
Convert Formats |
|
|
|
|
genouest |
https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko |
https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
feht |
feht |
Automatically identify makers predictive of groups. |
2017-10-11 |
https://github.com/phac-nml/galaxy_tools |
0.1.0 |
feht |
1.1.0 |
To update |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/galaxy_tools |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
filter_spades_repeats |
filter_spades_repeat |
Remove short and repeat contigs/scaffolds |
2017-10-12 |
https://github.com/phac-nml/galaxy_tools/ |
1.0.1 |
perl-bioperl |
1.7.8 |
To update |
Assembly |
|
|
|
|
nml |
https://github.com/phac-nml/galaxy_tools/ |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gafa |
gafa |
Gene Align and Family Aggregator |
2016-12-15 |
https://github.com/TGAC/Aequatus |
0.4.1 |
python |
|
To update |
Visualization |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/GAFA/ |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/GAFA |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
4 |
6 |
5 |
47 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
47 |
5 |
6 |
4 |
https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09 |
|
|
gblocks |
gblocks |
Gblocks |
2018-04-11 |
https://www.biologiaevolutiva.org/jcastresana/Gblocks/Gblocks_documentation.html |
0.91b |
gblocks |
0.91b |
Up-to-date |
Sequence Analysis |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/gblocks |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/gblocks |
|
|
|
|
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
87 |
87 |
661 |
661 |
6 |
6 |
36 |
36 |
697 |
697 |
93 |
93 |
|
|
|
gcms2isocor |
gcms2isocor |
Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs |
2023-03-15 |
https://github.com/p2m2/p2m2tools |
0.2.1 |
|
|
To update |
Metabolomics |
|
|
|
|
workflow4metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gcms2isocor |
gcms2isocor |
Conversion from GCMS PostRun Analysis to Isocor |
2021-09-16 |
|
0.1.0 |
openjdk |
|
To update |
Metabolomics |
|
|
|
|
genouest |
|
https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
genenotebook |
genenotebook_build |
Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io |
2021-09-17 |
https://genenotebook.github.io |
0.4.18 |
genoboo |
0.4.18 |
Up-to-date |
Web Services |
|
|
|
|
gga |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
9 |
354 |
354 |
362 |
362 |
13 |
13 |
|
|
|
genform |
genform |
genform: generation of molecular formulas by high-resolution MS and MS/MS data |
2019-09-12 |
https://sourceforge.net/projects/genform/ |
|
genform |
r8 |
To update |
Metabolomics |
|
|
|
|
workflow4metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
4 |
3 |
68 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
68 |
3 |
4 |
2 |
|
|
|
get_pairs |
get_pairs |
Separate paired and unpaired reads from two fastq files |
2018-09-10 |
|
0.3 |
python |
|
To update |
Fastq Manipulation |
|
|
|
|
genouest |
https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs |
https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
getmlst |
getmlst |
Download MLST datasets by species from pubmlst.org |
2015-12-03 |
|
0.1.4.1 |
srst2 |
0.2.0 |
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gnali |
gnali |
A tool to find nonessential, loss-of-function gene variants |
2020-03-30 |
https://github.com/phac-nml/gnali/ |
1.1.0 |
gnali |
1.1.0 |
Up-to-date |
Variant Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/gnali/ |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gstf_preparation |
gstf_preparation |
GeneSeqToFamily preparation converts data for the workflow |
2017-03-15 |
https://github.com/TGAC/earlham-galaxytools/ |
0.4.3 |
python |
|
To update |
Convert Formats |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/gstf_preparation |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/gstf_preparation |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
14 |
20 |
21 |
404 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
404 |
21 |
20 |
14 |
|
|
|
hcluster_sg |
hcluster_sg |
Hierarchically clustering on a sparse graph |
2015-08-05 |
https://github.com/douglasgscofield/hcluster |
0.5.1.1 |
hcluster_sg |
0.5.1 |
To update |
Phylogenetics |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/hcluster_sg |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/hcluster_sg |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
59 |
69 |
147 |
303 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
303 |
147 |
69 |
59 |
https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09 |
|
|
hcluster_sg_parser |
hcluster_sg_parser |
Converts hcluster_sg 3-column output into lists of ids |
2015-08-12 |
https://github.com/TGAC/earlham-galaxytools/ |
0.3.0 |
python |
|
To update |
Phylogenetics |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/hcluster_sg_parser |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/hcluster_sg_parser |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
19 |
27 |
41 |
298 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
298 |
41 |
27 |
19 |
https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09 |
|
|
helixer |
helixer |
Gene calling with Deep Neural Networks |
2023-06-14 |
https://github.com/weberlab-hhu/Helixer |
0.3.3 |
|
|
To update |
Genome annotation |
Gene prediction, Genome annotation |
Gene prediction, Genome annotation |
Sequence analysis, Gene transcripts |
Sequence analysis, Gene transcripts |
genouest |
https://github.com/genouest/galaxy-tools/tree/master/tools/helixer |
https://github.com/genouest/galaxy-tools/tree/master/tools/helixer |
helixer |
Helixer |
Deep Learning to predict gene annotations |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
161 |
161 |
1024 |
1024 |
56 |
56 |
184 |
184 |
51 |
51 |
385 |
385 |
25 |
25 |
363 |
363 |
1956 |
1956 |
293 |
293 |
https://usegalaxy.eu/published/workflow?id=31bc2a44fb89aa89, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=6550f72070b24082, https://usegalaxy.eu/published/workflow?id=8976041ef89e4548, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org.au/published/workflow?id=dd9272826e6dd98d, https://usegalaxy.org.au/published/workflow?id=e263fcb6c98e231b, https://usegalaxy.org.au/published/workflow?id=ec7efff3d3249177, https://usegalaxy.org/published/workflow?id=4605309321799e9b, https://usegalaxy.org/published/workflow?id=80a7124c40438cc9, https://usegalaxy.org/published/workflow?id=f4111a169255535c, https://workflowhub.eu/workflows/1255?version=3, https://workflowhub.eu/workflows/1500?version=1, https://workflowhub.eu/workflows/1746?version=1 |
genome-annotation/comparison-braker-helixer-annotation, genome-annotation/helixer |
|
hivtrace |
hivtrace |
An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. |
2015-12-10 |
|
1.0.1 |
hivtrace |
1.5.0 |
To update |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
image_info |
ip_imageinfo |
Extracts image metadata |
2019-07-19 |
https://github.com/bmcv |
5.7.1 |
bftools |
8.0.0 |
To update |
Imaging |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info |
|
|
|
python-bioformats |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
100 |
122 |
436 |
887 |
0 |
0 |
0 |
0 |
16 |
16 |
206 |
206 |
0 |
0 |
0 |
0 |
1093 |
642 |
138 |
116 |
https://usegalaxy.eu/published/workflow?id=2571f7d13686efb2, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://workflowhub.eu/workflows/1532?version=1, https://workflowhub.eu/workflows/1848?version=1 |
imaging/electrophoresis-gel-bands-image-analysis, imaging/imaging-introduction, imaging/voronoi-segmentation |
|
image_math |
image_math |
Process images using arithmetic expressions |
2024-03-09 |
https://github.com/bmcv |
1.26.4 |
numpy |
|
To update |
Imaging |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
16 |
380 |
380 |
0 |
0 |
0 |
0 |
1 |
1 |
11 |
11 |
0 |
0 |
0 |
0 |
391 |
391 |
17 |
17 |
https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1526?version=1, https://workflowhub.eu/workflows/1730?version=1 |
imaging/process-image-bioimageio, imaging/voronoi-segmentation |
|
image_registration_affine |
ip_image_registration |
Intensity-based Image Registration |
2020-12-29 |
https://github.com/bmcv |
0.0.3-2 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
5 |
5 |
17 |
17 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
17 |
17 |
5 |
5 |
|
|
|
imagecoordinates_flipaxis |
imagecoordinates_flipaxis |
Flip coordinate axes |
2019-03-08 |
https://github.com/bmcv |
0.1-2 |
pandas |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
11 |
14 |
19734 |
21898 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
21898 |
19734 |
14 |
11 |
https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc |
|
|
influx_si |
influx_si |
metabolic flux estimation based on [in]stationary labeling |
2020-04-17 |
https://github.com/sgsokol/influx |
7.0.1 |
influx_si |
7.4.1 |
To update |
Metabolomics |
|
|
|
|
workflow4metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
18 |
18 |
18 |
18 |
2 |
2 |
https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac |
|
|
influx_si_data_manager |
influx_data_manager |
Handling influx_si data inputs in Galaxy workflows |
2024-02-09 |
https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/ |
1.0.2 |
influx-si-data-manager |
1.1.1 |
To update |
Metabolomics |
|
|
|
|
workflow4metabolomics |
https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
9 |
9 |
9 |
9 |
1 |
1 |
https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac |
|
|
intensity_checks |
intens_check |
Statistical measures, number of missing values and mean fold change for metabolomics data. |
2025-05-14 |
https://workflow4metabolomics.org/ |
2.0.1 |
r-base |
|
To update |
Metabolomics |
|
|
|
|
melpetera |
https://github.com/workflow4metabolomics/tools-metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/intensity_check |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
43 |
46 |
229 |
233 |
22 |
22 |
76 |
76 |
0 |
0 |
0 |
0 |
372 |
376 |
8696 |
8857 |
9166 |
9001 |
444 |
437 |
https://usegalaxy.eu/published/workflow?id=3e2718f1ba1a22be, https://usegalaxy.fr/published/workflow?id=15275ba7c23028ed, https://usegalaxy.fr/published/workflow?id=180744a2f8dca6eb, https://usegalaxy.fr/published/workflow?id=18b2f77f2915adc7, https://usegalaxy.fr/published/workflow?id=26a3e5741d66982a, https://usegalaxy.fr/published/workflow?id=26bdb32c017d798c, https://usegalaxy.fr/published/workflow?id=3c41c4c5a6332c25, https://usegalaxy.fr/published/workflow?id=49e59327f299e9f7, https://usegalaxy.fr/published/workflow?id=57748aa2cecf0405, https://usegalaxy.fr/published/workflow?id=5964606a3836cbdf, https://usegalaxy.fr/published/workflow?id=5bfbe77fd6b37c45, https://usegalaxy.fr/published/workflow?id=6895bf9cff915ba1, https://usegalaxy.fr/published/workflow?id=7a790b0acf8ba14d, https://usegalaxy.fr/published/workflow?id=7cc77d6cdd8de027, https://usegalaxy.fr/published/workflow?id=7e9dcb13f95f9567, https://usegalaxy.fr/published/workflow?id=bb69fa998b900cb8, https://usegalaxy.fr/published/workflow?id=dc17a87057dec748, https://usegalaxy.fr/published/workflow?id=e3d00bdef9addd7c, https://usegalaxy.fr/published/workflow?id=e6f26a543c3e044a, https://usegalaxy.fr/published/workflow?id=f49e102f63d3e2bb, https://usegalaxy.org/published/workflow?id=650f3eb7647b4508, https://usegalaxy.org/published/workflow?id=aeeaf3e06a13bc22, https://workflowhub.eu/workflows/677?version=2 |
metabolomics/lcms-dataprocessing, metabolomics/lcms-preprocessing |
|
ipo |
ipo4retgroup, ipo4xcmsSet |
[W4M][LC-MS] IPO |
2019-10-02 |
https://github.com/rietho/IPO |
1.10.0 |
bioconductor-ipo |
1.32.0 |
To update |
Metabolomics |
|
|
|
|
lecorguille |
https://github.com/rietho/IPO |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
isoplot |
isoplot |
Isoplot is a software for the visualisation of MS data from C13 labelling experiments |
2021-07-12 |
https://github.com/llegregam/Isoplot |
1.3.1 |
jinja2 |
|
To update |
Metabolomics, Visualization |
|
|
|
|
workflow4metabolomics |
https://github.com/llegregam/Isoplot/tree/main |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
3 |
3 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
11 |
132 |
132 |
137 |
137 |
14 |
14 |
https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac |
|
|
jbrowse_to_container |
jbrowse_to_container |
A tool allowing to export a JBrowse dataset into a JBrowse docker container |
2016-11-08 |
https://jbrowse.org |
|
python |
|
To update |
Web Services |
|
|
|
|
gga |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
kaptive |
kaptive |
Kaptive reports information about capsular (K) loci found in genome assemblies. |
2017-04-10 |
|
0.3.0 |
kaptive |
3.1.0 |
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
kat_filter |
kat_@EXECUTABLE@ |
Filtering kmers or reads from a database of kmers hashes |
2017-03-13 |
|
2.3 |
kat |
2.4.2 |
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
kat_sect |
kat_@EXECUTABLE@ |
SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file. |
2017-02-06 |
|
2.3 |
kat |
2.4.2 |
To update |
|
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
kegalign |
kegalign |
A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. |
2024-08-29 |
https://github.com/galaxyproject/KegAlign |
0.1.2.7 |
kegalign-full |
0.1.2.7 |
Up-to-date |
Next Gen Mappers |
|
|
|
|
richard-burhans |
https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign |
https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
52 |
52 |
228 |
228 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
228 |
228 |
52 |
52 |
https://usegalaxy.org/published/workflow?id=ca68ad0d7420c615 |
|
|
kmd_hmdb_data_plot |
kmd_hmdb_data_plot |
retrieves data from KMD HMDB API and produce plot and csv file |
2023-07-10 |
https://github.com/workflow4metabolomics/tools-metabolomics |
1.0.0 |
click |
|
To update |
Metabolomics |
|
|
|
|
workflow4metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
label_to_binary |
label_to_binary |
Convert label map to binary image |
2024-03-13 |
https://github.com/bmcv |
1.26.4 |
numpy |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
104 |
104 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
104 |
104 |
1 |
1 |
|
|
|
labelimage2points |
ip_labelimage_to_points |
Label Image to Points |
2017-10-30 |
https://github.com/bmcv |
0.2-2 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
3 |
106 |
142 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
142 |
106 |
3 |
2 |
|
|
|
landmark_registration |
ip_landmark_registration |
Landmark Registration |
2019-02-04 |
https://github.com/bmcv |
0.1.0-2 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
16 |
19 |
871 |
1035 |
6 |
6 |
7 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1042 |
878 |
25 |
22 |
https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=1eaff95bfeb13890, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc |
|
|
logol |
logol_wrapper |
Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence |
2018-06-06 |
http://logol.genouest.org/web/app.php/logol |
1.7.8 |
logol |
1.7.8 |
Up-to-date |
Sequence Analysis |
|
|
|
|
genouest |
https://github.com/genouest/galaxy-tools/tree/master/tools/logol |
https://github.com/genouest/galaxy-tools/tree/master/tools/logol |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
lotus2 |
lotus2 |
LotuS2 OTU processing pipeline |
2021-05-13 |
https://lotus2.earlham.ac.uk/ |
2.32 |
lotus2 |
2.34.1 |
To update |
Metagenomics |
Sequence feature detection, DNA barcoding |
Sequence feature detection, DNA barcoding |
Metagenomics, Taxonomy, Microbial ecology |
Metagenomics, Taxonomy, Microbial ecology |
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/lotus2 |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/lotus2 |
lotus2 |
lotus2 |
LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
249 |
249 |
1979 |
1979 |
0 |
0 |
0 |
0 |
22 |
22 |
417 |
417 |
2 |
2 |
5 |
5 |
2401 |
2401 |
273 |
273 |
https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://workflowhub.eu/workflows/1460?version=1 |
microbiome/lotus2-identifying-fungi, microbiome/mgnify-amplicon |
|
mahotas_features |
ip_mahotas_features |
Compute image features using mahotas. |
2024-09-30 |
https://github.com/luispedro/mahotas |
0.7-2 |
mahotas |
|
To update |
Imaging |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features |
|
|
|
mahotas-feature-computation |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
6 |
7 |
10 |
45 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
45 |
10 |
7 |
6 |
|
|
|
mauve_contig_mover |
mauve_contig_mover |
Order a draft genome relative to a related reference genome |
2019-11-19 |
https://github.com/phac-nml/mauve_contig_mover |
1.0.10 |
mauve |
2.4.0.r4736 |
To update |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/mauve_contig_mover |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
meneco |
meneco |
Meneco computes minimal completions to your draft network with reactions from a repair network |
2018-06-11 |
http://bioasp.github.io/meneco/ |
1.5.2 |
meneco |
1.5.2 |
Up-to-date |
Systems Biology |
|
|
|
|
genouest |
https://github.com/genouest/galaxy-tools/tree/master/tools/meneco |
https://github.com/genouest/galaxy-tools/tree/master/tools/meneco |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
mergeneighboursinlabelimage |
ip_merge_neighbours_in_label |
Merge Neighbours in Label Image |
2019-01-08 |
https://github.com/bmcv |
0.3-2 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3 |
1 |
25 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
25 |
1 |
3 |
1 |
|
|
|
metfrag |
metfrag |
[Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity) |
2018-03-25 |
https://github.com/computational-metabolomics/metfrag-galaxy |
2.4.5+galaxy3 |
metfrag |
2.4.5 |
To update |
Metabolomics |
|
|
|
|
computational-metabolomics |
https://github.com/computational-metabolomics/metfrag-galaxy |
https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
22 |
25 |
109 |
206 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
87 |
88 |
452 |
457 |
663 |
561 |
113 |
109 |
https://usegalaxy.fr/published/workflow?id=bcd348178335a19b |
|
|
metfrag-vis |
metfrag_vis |
[Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag |
2020-06-30 |
https://github.com/computational-metabolomics/metfrag-galaxy |
2.4.5+galaxy0 |
metfrag |
2.4.5 |
To update |
Metabolomics |
|
|
|
|
computational-metabolomics |
https://github.com/computational-metabolomics/metfrag-galaxy |
https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
16 |
16 |
64 |
64 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
64 |
64 |
16 |
16 |
|
|
|
miranda |
miranda |
Finds potential target sites for miRNAs in genomic sequences |
2015-10-30 |
https://github.com/hacktrackgnulinux/miranda |
3.3a+galaxy1 |
miranda |
3.3a |
To update |
RNA |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/miranda |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/miranda |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
100 |
123 |
2555 |
7459 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
23 |
23 |
27 |
27 |
7486 |
2582 |
146 |
123 |
|
|
|
miranda2asko |
miranda2asko |
Converts miRanda output into AskOmics format |
2018-04-12 |
|
0.2 |
perl |
|
To update |
Convert Formats |
|
|
|
|
genouest |
https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko |
https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
mixmodel4repeated_measures |
mixmodel4repeated_measures |
[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model |
2022-05-16 |
http://workflow4metabolomics.org |
3.1.0+galaxy1 |
r-lme4 |
|
To update |
Metabolomics |
|
|
|
|
workflow4metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
39 |
39 |
368 |
368 |
369 |
369 |
40 |
40 |
|
|
|
mob_suite |
mob_recon, mob_typer |
MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies |
2018-04-30 |
https://github.com/phac-nml/mob-suite |
3.1.9 |
mob_suite |
3.1.9 |
Up-to-date |
Sequence Analysis |
Clustering, Sequence analysis |
Clustering, Sequence analysis |
Metagenomics, Sequence assembly, Genotype and phenotype, Mobile genetic elements, Genomics |
Metagenomics, Sequence assembly, Genotype and phenotype, Mobile genetic elements |
nml |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob-suite |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite |
mob_suite |
mob_suite |
MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assembliesThe MOB-suite depends on a series of databases which are too large to be hosted in git-hub. They can be downloaded or updated by running mob_init or if running any of the tools for the first time, the databases will download and initialize automatically if you do not specify an alternate database location. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
620 |
620 |
162457 |
162457 |
1 |
1 |
42 |
42 |
199 |
199 |
66525 |
66525 |
12 |
12 |
58 |
58 |
229082 |
229082 |
832 |
832 |
https://workflowhub.eu/workflows/407?version=1 |
|
|
morphological_operations |
morphological_operations |
Apply morphological operations to images |
2024-03-08 |
https://github.com/bmcv |
1.12.0 |
scipy |
|
To update |
Imaging |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations |
|
|
|
scipy |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
298 |
298 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
298 |
298 |
1 |
1 |
|
|
|
mrbayes |
mrbayes |
A program for the Bayesian estimation of phylogeny. |
2015-12-04 |
|
1.0.2 |
mrbayes |
3.2.7 |
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
4 |
4 |
18 |
18 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
18 |
18 |
4 |
4 |
|
|
|
ms2snoop |
ms2snoop |
[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. |
2022-03-15 |
http://workflow4metabolomics.org |
2.2.1 |
r-base |
|
To update |
Metabolomics |
|
|
|
|
workflow4metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
157 |
157 |
157 |
157 |
10 |
10 |
|
|
|
msPurity |
mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching |
[Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data |
2019-05-24 |
https://github.com/computational-metabolomics/mspurity-galaxy |
1.28.0 |
bioconductor-mspurity |
1.32.0 |
To update |
Metabolomics |
|
|
|
|
computational-metabolomics |
https://github.com/computational-metabolomics/mspurity-galaxy |
https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity |
|
|
|
|
0 |
0 |
10 |
11 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
20 |
21 |
591 |
900 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
147 |
148 |
11336 |
11552 |
12452 |
11927 |
169 |
167 |
https://usegalaxy.fr/published/workflow?id=6babfa7409467035, https://usegalaxy.fr/published/workflow?id=bcd348178335a19b, https://usegalaxy.fr/published/workflow?id=cca13353d553319e |
|
|
msp_split |
msp_split |
[Metabolomics][LC-MS][DIMS][MS/MS] msPurity - R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data |
2019-09-24 |
https://github.com/computational-metabolomics/mspurity-galaxy |
0.0.2 |
|
|
To update |
Metabolomics |
|
|
|
|
tomnl |
https://github.com/computational-metabolomics/mspurity-galaxy |
https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
mykrobe_parser |
mykrobe_parseR |
RScript to parse the results of mykrobe predictor. |
2018-09-28 |
https://github.com/phac-nml/mykrobe-parser |
0.1.4.1 |
r-base |
|
To update |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/mykrobe-parser |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
mzxmlshaper |
mzxmlshaper |
Convert mzML, mzXML or netCDF files to mzML or mzXML |
2024-09-20 |
https://rdrr.io/bioc/mzR/ |
1.0.0+galaxy1 |
r-base |
|
To update |
Metabolomics |
|
|
|
|
workflow4metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
2721 |
2721 |
2721 |
2721 |
8 |
8 |
|
|
|
ncbi_egapx |
ncbi_egapx |
Eukaryotic Genome Annotation Pipeline - External (EGAPx) |
2024-08-19 |
https://github.com/ncbi/egapx |
0.4.1 |
|
|
To update |
Genome annotation |
|
|
|
|
richard-burhans |
https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx |
https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
7 |
7 |
49 |
49 |
1037 |
1037 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1044 |
1044 |
51 |
51 |
https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=951575e9a352301c, https://usegalaxy.org/published/workflow?id=ce488732866ba48f, https://usegalaxy.org/published/workflow?id=e93a0522ec3a35e6 |
|
|
ncbi_fcs_adaptor |
ncbi_fcs_adaptor |
FCS-adaptor detects adaptor and vector contamination in genome sequences. |
2024-02-23 |
https://github.com/ncbi/fcs |
0.5.0 |
|
|
To update |
Sequence Analysis |
|
|
|
|
richard-burhans |
https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor |
https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
12 |
12 |
374 |
374 |
9268 |
9268 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9280 |
9280 |
375 |
375 |
|
sequence-analysis/ncbi-fcs |
|
nmr_annotation |
NmrAnnotation |
[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation |
2019-07-30 |
http://workflow4metabolomics.org |
3.0.0+galaxy1 |
libgfortran |
|
To update |
Metabolomics |
|
|
|
|
marie-tremblay-metatoul |
https://github.com/workflow4metabolomics/nmr_annotation |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
5 |
6 |
14 |
51 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
48 |
51 |
479 |
508 |
559 |
493 |
57 |
53 |
|
|
|
nmr_preprocessing |
NMR_Preprocessing, NMR_Read |
[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction |
2019-07-29 |
http://workflow4metabolomics.org |
|
r-ggplot2 |
2.2.1 |
To update |
Metabolomics |
|
|
|
|
marie-tremblay-metatoul |
https://github.com/workflow4metabolomics/nmr_preprocessing |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing |
|
|
|
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
5 |
6 |
87 |
146 |
0 |
0 |
0 |
0 |
5 |
5 |
343 |
429 |
92 |
96 |
2370 |
2469 |
3044 |
2800 |
107 |
102 |
|
|
|
normalization |
normalization |
[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data |
2019-07-30 |
http://workflow4metabolomics.org |
1.0.7+galaxy2 |
r-batch |
1.1_4 |
To update |
Metabolomics |
|
|
|
|
marie-tremblay-metatoul |
https://github.com/workflow4metabolomics/normalization |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
50 |
53 |
182 |
242 |
0 |
0 |
0 |
0 |
14 |
15 |
243 |
289 |
315 |
329 |
3350 |
3424 |
3955 |
3775 |
397 |
379 |
https://usegalaxy.eu/published/workflow?id=3e2718f1ba1a22be, https://usegalaxy.fr/published/workflow?id=7e9dcb13f95f9567 |
metabolomics/lcms-dataprocessing |
|
openlabcds2csv |
openlabcds2csv |
Creates a summary of several "Internal Standard Report" OpenLabCDS results. |
2021-10-28 |
|
0.1.0 |
openjdk |
|
To update |
Metabolomics |
|
|
|
|
genouest |
|
https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
orientationpy |
orientationpy |
Compute image orientation |
2024-03-12 |
https://github.com/bmcv |
0.2.0.4 |
orientationpy |
0.2.0.4 |
Up-to-date |
Imaging |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy |
|
|
|
orientationj |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
105 |
105 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
105 |
105 |
2 |
2 |
|
|
|
overlay_images |
ip_overlay_images |
Overlay two images |
2022-02-26 |
https://github.com/BMCV/galaxy-image-analysis |
0.0.4 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
56 |
56 |
466 |
466 |
4 |
4 |
19 |
19 |
2 |
2 |
303 |
303 |
0 |
0 |
0 |
0 |
788 |
788 |
62 |
62 |
https://usegalaxy.eu/published/workflow?id=1ffacb28226460ac, https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=6fbd9b2274c62ebe, https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae, https://usegalaxy.org.au/published/workflow?id=8e28c3b252062b3b, https://usegalaxy.org/published/workflow?id=a8e39acc103c3d6b, https://usegalaxy.org/published/workflow?id=d47cddc372c88094, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1526?version=1, https://workflowhub.eu/workflows/1528?version=1, https://workflowhub.eu/workflows/1532?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/771?version=2 |
imaging/2D-spot-detection, imaging/imaging-introduction, imaging/process-image-bioimageio, imaging/voronoi-segmentation |
|
pangolin |
pangolin |
Phylogenetic Assignment of Named Global Outbreak LINeages |
2020-05-01 |
https://github.com/hCoV-2019/pangolin |
1.1.14 |
pangolin |
4.3.1 |
To update |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/hCoV-2019/pangolin |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
595 |
595 |
7737 |
7737 |
416 |
416 |
9068 |
9068 |
277 |
277 |
3099 |
3099 |
12 |
12 |
603 |
603 |
20507 |
20507 |
1300 |
1300 |
https://usegalaxy.eu/published/workflow?id=0189bab68f828d86, https://usegalaxy.eu/published/workflow?id=1d1ebdeddf23bdb9, https://usegalaxy.eu/published/workflow?id=3f046b416b10b871, https://usegalaxy.eu/published/workflow?id=4c75ab0be3c56494, https://usegalaxy.eu/published/workflow?id=5c15f251642bfa1f, https://usegalaxy.eu/published/workflow?id=74f19aff1b9cdd6b, https://usegalaxy.eu/published/workflow?id=9feebfc6c34da287, https://usegalaxy.fr/published/workflow?id=2345fad7dac13daa, https://usegalaxy.fr/published/workflow?id=591c57173e259ca6, https://usegalaxy.fr/published/workflow?id=e4735d214a68b790, https://usegalaxy.fr/published/workflow?id=feb57548b3ce914d, https://usegalaxy.org.au/published/workflow?id=7563b3ef697a69fd, https://usegalaxy.org.au/published/workflow?id=af12a3ec85859563, https://usegalaxy.org/published/workflow?id=0fa2ce12c2874b1d, https://usegalaxy.org/published/workflow?id=426e3951dac0704e, https://usegalaxy.org/published/workflow?id=4b41a8247f52c463, https://usegalaxy.org/published/workflow?id=8b81b9a3b49bbf98, https://usegalaxy.org/published/workflow?id=d96bd5c9fb553f2c, https://workflowhub.eu/workflows/1391?version=1, https://workflowhub.eu/workflows/155?version=6 |
galaxy-interface/workflow-automation, variant-analysis/sars-cov-2-variant-discovery |
|
patrist |
patrist |
Extract Patristic Distance From a Tree |
2019-12-14 |
https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 |
0.1.2 |
python |
|
To update |
Phylogenetics |
|
|
|
|
nml |
https://github.com/phac-nml/patrist |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
peptimapper |
peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag |
Proteogenomics workflow for the expert annotation of eukaryotic genomes |
2021-11-03 |
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9 |
2.1 |
|
|
To update |
Proteomics |
|
|
|
|
genouest |
https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper |
https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper |
|
|
|
|
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
6 |
6 |
6 |
6 |
1 |
1 |
|
|
|
permutate_axis |
ip_permutate_axis |
Permutates axes |
2017-10-30 |
https://github.com/bmcv |
0.2-2 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
2 |
0 |
42 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
42 |
0 |
2 |
0 |
|
|
|
physiofit |
physiofit |
PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes |
2022-09-26 |
physiofit.readthedocs.io |
3.4.0 |
physiofit |
3.4.0 |
Up-to-date |
Metabolomics |
|
|
|
|
workflow4metabolomics |
https://github.com/MetaSys-LISBP/PhysioFit |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
28 |
28 |
28 |
28 |
2 |
2 |
https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac |
|
|
physiofit_manager |
physiofit_data_manager |
Handling of physiofit input files |
2022-11-03 |
physiofit.readthedocs.io |
1.0.1 |
physiofit_data_manager |
1.0.1 |
Up-to-date |
Metabolomics |
|
|
|
|
workflow4metabolomics |
https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
9 |
9 |
9 |
9 |
1 |
1 |
https://usegalaxy.fr/published/workflow?id=7ae6ad6f74a50fac |
|
|
plantseg |
plantseg |
Tool for cell instance aware segmentation in densely packed 3D volumetric images |
2024-06-19 |
https://github.com/bmcv |
1.8.1 |
plant-seg |
|
To update |
Imaging |
Network analysis, Quantification, Microscope image visualisation |
Network analysis, Quantification, Microscope image visualisation |
Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy |
Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg |
plantseg |
PlantSeg |
Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
plasmid_profiler |
plasmid_profiler |
Explores plasmid content in WGS data |
2016-11-07 |
|
0.1.6 |
r |
|
To update |
|
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
plasmidspades |
plasmidspades |
Genome assembler for assemblying plasmid |
2016-06-06 |
|
1.1 |
spades |
4.2.0 |
To update |
Assembly |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
plotheatmap |
plotheatmap |
Plot heatmap of gene expression data |
2017-07-04 |
https://github.com/TGAC/earlham-galaxytools/ |
1.0 |
bioconductor-preprocesscore |
1.68.0 |
To update |
Computational chemistry |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/plotheatmap |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
pneumocat |
pneumocat |
Pneumococcal Capsular Typing of illumina fastq reads |
2020-03-24 |
https://github.com/phe-bioinformatics/PneumoCaT |
1.2.1 |
pneumocat |
1.2.1 |
Up-to-date |
Variant Analysis |
|
|
|
|
nml |
https://github.com/phe-bioinformatics/PneumoCaT |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
points2labelimage |
ip_points_to_label |
Points to label image |
2017-10-30 |
https://github.com/bmcv |
0.4.1 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
3 |
46 |
77 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
77 |
46 |
3 |
2 |
https://usegalaxy.eu/published/workflow?id=2571f7d13686efb2, https://workflowhub.eu/workflows/1528?version=1, https://workflowhub.eu/workflows/1848?version=1 |
imaging/2D-spot-detection, imaging/electrophoresis-gel-bands-image-analysis |
|
points_association_nn |
ip_points_association_nn |
Association of points in consecutive frames |
2021-07-22 |
https://github.com/BMCV/galaxy-image-analysis |
0.0.3-2 |
numpy |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
6 |
6 |
47 |
47 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
47 |
47 |
6 |
6 |
https://usegalaxy.eu/published/workflow?id=e25f3ca3a1b4e4d8, https://usegalaxy.eu/published/workflow?id=ffa80e0637d079f2, https://workflowhub.eu/workflows/1499?version=1 |
imaging/detection-of-mitoflashes |
|
projective_transformation |
ip_projective_transformation |
Projective transformation |
2018-12-07 |
https://github.com/bmcv |
0.1.2 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
3 |
6 |
21 |
86 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
86 |
21 |
6 |
3 |
https://usegalaxy.eu/published/workflow?id=1eaff95bfeb13890 |
|
|
projective_transformation_points |
ip_projective_transformation_points |
Projective transformation of ROIs defined by pixel (point) coordinates |
2018-12-07 |
https://github.com/bmcv |
0.1.1 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
15 |
20 |
19258 |
21493 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
21493 |
19258 |
20 |
15 |
https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc |
|
|
promer |
promer4_substitutions |
Aligns two sets of contigs and reports amino acid substitutions between them |
2019-12-14 |
https://github.com/phac-nml/promer |
1.2 |
python |
|
To update |
Assembly |
|
|
|
|
nml |
https://github.com/phac-nml/promer |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
pseudogenome |
pseudogenome |
Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. |
2018-04-06 |
https://github.com/phac-nml/galaxy_tools |
1.0.0 |
perl-bioperl |
1.7.8 |
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
qiime2 |
qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats |
|
2022-08-26 |
https://github.com/biocore/deblur |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
40 |
40 |
225 |
225 |
24 |
24 |
78 |
78 |
9 |
9 |
177 |
177 |
1 |
1 |
8 |
8 |
488 |
488 |
74 |
74 |
|
|
|
qiime2 |
qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac |
|
2022-08-26 |
https://github.com/qiime2/q2-diversity-lib |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
12 |
12 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
0 |
4 |
4 |
33 |
33 |
8 |
8 |
47 |
47 |
6 |
6 |
2850 |
2850 |
2 |
2 |
3 |
3 |
2933 |
2933 |
20 |
20 |
https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927 |
|
|
qiime2 |
qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads |
|
2022-08-26 |
https://github.com/qiime2/q2-quality-control |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
6 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
0 |
4 |
4 |
6 |
6 |
11 |
11 |
105 |
105 |
4 |
4 |
11 |
11 |
0 |
0 |
0 |
0 |
122 |
122 |
19 |
19 |
|
|
|
qiime2 |
qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds |
|
2022-08-26 |
https://github.com/qiime2/q2-phylogeny |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
12 |
12 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
0 |
167 |
167 |
880 |
880 |
93 |
93 |
338 |
338 |
66 |
66 |
373 |
373 |
13 |
13 |
91 |
91 |
1682 |
1682 |
339 |
339 |
https://usegalaxy.eu/published/workflow?id=7c07e87c77dcee05 |
|
|
qiime2 |
qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate |
|
2022-08-26 |
https://github.com/qiime2/q2-metadata |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
331 |
331 |
2227 |
2227 |
292 |
292 |
1317 |
1317 |
94 |
94 |
744 |
744 |
39 |
39 |
269 |
269 |
4557 |
4557 |
756 |
756 |
https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4, https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3, https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d, https://usegalaxy.org/published/workflow?id=517f307db25e4715, https://usegalaxy.org/published/workflow?id=8bb471c28e1a30a3, https://usegalaxy.org/published/workflow?id=a382adce80293f0d, https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf, https://workflowhub.eu/workflows/892?version=3 |
|
|
qiime2 |
qiime2__quality_filter__q_score |
|
2022-08-26 |
https://github.com/qiime2/q2-quality-filter |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
25 |
25 |
55 |
55 |
16 |
16 |
39 |
39 |
7 |
7 |
90 |
90 |
13 |
13 |
21 |
21 |
205 |
205 |
61 |
61 |
|
|
|
qiime2 |
qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp |
|
2022-08-26 |
https://github.com/qiime2/q2-fragment-insertion |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
16 |
16 |
81 |
81 |
7 |
7 |
59 |
59 |
1 |
1 |
6 |
6 |
2 |
2 |
2 |
2 |
148 |
148 |
26 |
26 |
https://usegalaxy.eu/published/workflow?id=6ad6d87618c4e405 |
|
|
qiime2 |
qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__normalize, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose |
|
2022-08-26 |
https://github.com/qiime2/q2-feature-table |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
17 |
17 |
17 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
17 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
17 |
0 |
298 |
298 |
5335 |
5335 |
203 |
203 |
1938 |
1938 |
95 |
95 |
2932 |
2932 |
28 |
28 |
591 |
591 |
10796 |
10796 |
624 |
624 |
https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3, https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d, https://usegalaxy.org/published/workflow?id=517f307db25e4715, https://usegalaxy.org/published/workflow?id=8bb471c28e1a30a3, https://usegalaxy.org/published/workflow?id=a382adce80293f0d, https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf, https://workflowhub.eu/workflows/892?version=3 |
|
|
qiime2 |
qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global |
|
2022-08-26 |
https://github.com/qiime2/q2-feature-classifier |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
10 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
0 |
325 |
325 |
3046 |
3046 |
232 |
232 |
1256 |
1256 |
88 |
88 |
1282 |
1282 |
28 |
28 |
178 |
178 |
5762 |
5762 |
673 |
673 |
https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927 |
|
|
qiime2 |
qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask |
|
2022-08-26 |
https://github.com/qiime2/q2-alignment |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
67 |
67 |
390 |
390 |
35 |
35 |
78 |
78 |
16 |
16 |
114 |
114 |
14 |
14 |
69 |
69 |
651 |
651 |
132 |
132 |
|
|
|
qiime2 |
qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap |
|
2022-08-26 |
https://github.com/qiime2/q2-diversity |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
21 |
22 |
21 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
22 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
21 |
0 |
135 |
135 |
3770 |
3770 |
88 |
88 |
2286 |
2286 |
60 |
60 |
1211 |
1211 |
26 |
26 |
360 |
360 |
7627 |
7627 |
309 |
309 |
https://usegalaxy.eu/published/workflow?id=457a3de5c1512707, https://usegalaxy.eu/published/workflow?id=6e5fad1de09af683, https://usegalaxy.eu/published/workflow?id=a91c46b9e0c1d635, https://usegalaxy.org.au/published/workflow?id=543001c51567b438, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=c6b6524108f53688, https://usegalaxy.org/published/workflow?id=ef28b1c267b5a318 |
|
|
qiime2 |
qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__ancombc2, qiime2__composition__ancombc2_visualizer, qiime2__composition__da_barplot, qiime2__composition__tabulate |
|
2022-08-26 |
https://github.com/qiime2/q2-composition |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
4 |
4 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
26 |
26 |
388 |
388 |
31 |
31 |
256 |
256 |
8 |
8 |
325 |
325 |
9 |
9 |
89 |
89 |
1058 |
1058 |
74 |
74 |
|
|
|
qiime2 |
qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single |
|
2022-08-26 |
https://github.com/qiime2/q2-cutadapt |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
4 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
73 |
73 |
364 |
364 |
69 |
69 |
273 |
273 |
7 |
7 |
213 |
213 |
3 |
3 |
31 |
31 |
881 |
881 |
152 |
152 |
|
|
|
qiime2 |
qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single |
|
2022-08-26 |
http://benjjneb.github.io/dada2/ |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
4 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
319 |
319 |
2670 |
2670 |
253 |
253 |
1230 |
1230 |
79 |
79 |
843 |
843 |
29 |
29 |
182 |
182 |
4925 |
4925 |
680 |
680 |
https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5223c9554718114d, https://usegalaxy.eu/published/workflow?id=851b97ea3d1de9f7, https://usegalaxy.eu/published/workflow?id=b3d48f81329926fc, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=da17a4d690eb0ff3, https://usegalaxy.eu/published/workflow?id=e1f08a63fbc8e173, https://usegalaxy.org.au/published/workflow?id=2d16ed86414f23b3, https://usegalaxy.org.au/published/workflow?id=fb517ec08b571a2d, https://usegalaxy.org/published/workflow?id=517f307db25e4715, https://usegalaxy.org/published/workflow?id=8bb471c28e1a30a3, https://usegalaxy.org/published/workflow?id=a382adce80293f0d, https://usegalaxy.org/published/workflow?id=d32392a39c4d6fbf, https://workflowhub.eu/workflows/892?version=3 |
|
|
qiime2 |
qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts |
|
2022-08-26 |
https://github.com/qiime2/q2-demux |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
6 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
0 |
289 |
289 |
1358 |
1358 |
251 |
251 |
1071 |
1071 |
91 |
91 |
1146 |
1146 |
28 |
28 |
127 |
127 |
3702 |
3702 |
659 |
659 |
https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=5528702f49c33d83, https://usegalaxy.eu/published/workflow?id=5d401d357500617f, https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41, https://usegalaxy.eu/published/workflow?id=b1f68ff8158d0b85, https://usegalaxy.eu/published/workflow?id=b2975bb705d3e851, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=c0b5b499b149005f, https://usegalaxy.eu/published/workflow?id=c58941443cec9380, https://usegalaxy.eu/published/workflow?id=ca5da5179cefec8b, https://usegalaxy.eu/published/workflow?id=fb96000c99db2fa8, https://usegalaxy.org.au/published/workflow?id=19b0f96df6d09b4e, https://usegalaxy.org.au/published/workflow?id=3c1bf73067334071, https://usegalaxy.org.au/published/workflow?id=57aa23f4f0418a07, https://usegalaxy.org.au/published/workflow?id=cddd668a29b1488a, https://usegalaxy.org.au/published/workflow?id=f946d722f7c27479, https://usegalaxy.org/published/workflow?id=0dc387dc861bdb61, https://usegalaxy.org/published/workflow?id=4ca9319c98be08f8, https://usegalaxy.org/published/workflow?id=685b0de4c31f6695, https://usegalaxy.org/published/workflow?id=76b2c4762dd61d03, https://usegalaxy.org/published/workflow?id=7aa87e7f9cfdae78, https://usegalaxy.org/published/workflow?id=a7cc1038b14f2201, https://usegalaxy.org/published/workflow?id=b335f75495dab9b4, https://usegalaxy.org/published/workflow?id=b92e0ee710d167b2, https://workflowhub.eu/workflows/893?version=3 |
|
|
qiime2 |
qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility |
|
2022-08-26 |
https://github.com/qiime2/q2-longitudinal |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
11 |
11 |
11 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
0 |
12 |
12 |
63 |
63 |
7 |
7 |
60 |
60 |
6 |
6 |
142 |
142 |
2 |
2 |
8 |
8 |
273 |
273 |
27 |
27 |
|
|
|
qiime2 |
qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot |
|
2022-08-26 |
http://biocore.github.io/emperor/build/html/index.html |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
42 |
42 |
142 |
142 |
34 |
34 |
198 |
198 |
15 |
15 |
195 |
195 |
9 |
9 |
27 |
27 |
562 |
562 |
100 |
100 |
|
|
|
qiime2 |
qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize |
|
2022-08-26 |
https://github.com/qiime2/q2-sample-classifier |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
15 |
15 |
15 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
15 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
15 |
0 |
5 |
5 |
30 |
30 |
17 |
17 |
47 |
47 |
5 |
5 |
6 |
6 |
1 |
1 |
4 |
4 |
87 |
87 |
28 |
28 |
|
|
|
qiime2 |
qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table |
|
2022-08-26 |
https://github.com/qiime2/q2-taxa |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
4 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
266 |
266 |
2747 |
2747 |
159 |
159 |
1008 |
1008 |
78 |
78 |
690 |
690 |
22 |
22 |
236 |
236 |
4681 |
4681 |
525 |
525 |
https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=e2af8c661e98f4f4 |
|
|
qiime2 |
qiime2__vizard__boxplot, qiime2__vizard__heatmap, qiime2__vizard__lineplot, qiime2__vizard__scatterplot_2d |
|
2024-10-30 |
https://github.com/qiime2/q2-vizard |
0.0.1.dev0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
20 |
20 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
20 |
20 |
5 |
5 |
|
|
|
qiime2 |
qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_bv_brc_genome_features, qiime2__rescript__get_bv_brc_genomes, qiime2__rescript__get_bv_brc_metadata, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_midori2_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_pr2_data, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_reads, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment |
|
2024-04-25 |
https://github.com/nbokulich/RESCRIPt |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
18 |
18 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
18 |
18 |
6 |
6 |
|
|
|
qiime2 |
qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref |
|
2022-08-26 |
https://github.com/qiime2/q2-vsearch |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
8 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
0 |
31 |
31 |
409 |
409 |
18 |
18 |
280 |
280 |
5 |
5 |
24 |
24 |
10 |
10 |
77 |
77 |
790 |
790 |
64 |
64 |
|
|
|
qiime2 |
qiime2__stats__alpha_group_significance, qiime2__stats__collate_stats, qiime2__stats__facet_across, qiime2__stats__facet_within, qiime2__stats__mann_whitney_u, qiime2__stats__mann_whitney_u_facet, qiime2__stats__plot_rainclouds, qiime2__stats__prep_alpha_distribution, qiime2__stats__wilcoxon_srt, qiime2__stats__wilcoxon_srt_facet |
|
2024-10-30 |
https://github.com/qiime2/q2-stats |
2025.7.0+q2galaxy.2025.7.0 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
qiime2 |
qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq |
|
2022-08-26 |
https://qiime2.org |
2025.7.0+dist.h44bd78f6 |
|
|
To update |
Metagenomics, Sequence Analysis, Statistics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
q2d2 |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools |
https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
2 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
636 |
636 |
61165 |
61165 |
813 |
813 |
58124 |
58124 |
228 |
228 |
10152 |
10152 |
62 |
62 |
2237 |
2237 |
131678 |
131678 |
1739 |
1739 |
https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=457a3de5c1512707, https://usegalaxy.eu/published/workflow?id=5528702f49c33d83, https://usegalaxy.eu/published/workflow?id=5d401d357500617f, https://usegalaxy.eu/published/workflow?id=6e5fad1de09af683, https://usegalaxy.eu/published/workflow?id=86b31ac8a7720e41, https://usegalaxy.eu/published/workflow?id=a91c46b9e0c1d635, https://usegalaxy.eu/published/workflow?id=b1f68ff8158d0b85, https://usegalaxy.eu/published/workflow?id=b2975bb705d3e851, https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34, https://usegalaxy.eu/published/workflow?id=c0b5b499b149005f, https://usegalaxy.eu/published/workflow?id=c58941443cec9380, https://usegalaxy.eu/published/workflow?id=ca5da5179cefec8b, https://usegalaxy.eu/published/workflow?id=fb96000c99db2fa8, https://usegalaxy.org.au/published/workflow?id=19b0f96df6d09b4e, https://usegalaxy.org.au/published/workflow?id=3c1bf73067334071, https://usegalaxy.org.au/published/workflow?id=543001c51567b438, https://usegalaxy.org.au/published/workflow?id=57aa23f4f0418a07, https://usegalaxy.org.au/published/workflow?id=cddd668a29b1488a, https://usegalaxy.org.au/published/workflow?id=f946d722f7c27479, https://usegalaxy.org/published/workflow?id=0dc387dc861bdb61, https://usegalaxy.org/published/workflow?id=4ca9319c98be08f8, https://usegalaxy.org/published/workflow?id=685b0de4c31f6695, https://usegalaxy.org/published/workflow?id=76b2c4762dd61d03, https://usegalaxy.org/published/workflow?id=7aa87e7f9cfdae78, https://usegalaxy.org/published/workflow?id=a7cc1038b14f2201, https://usegalaxy.org/published/workflow?id=b335f75495dab9b4, https://usegalaxy.org/published/workflow?id=b92e0ee710d167b2, https://usegalaxy.org/published/workflow?id=c6b6524108f53688, https://usegalaxy.org/published/workflow?id=ef28b1c267b5a318, https://workflowhub.eu/workflows/893?version=3 |
|
|
quasitools |
aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality |
A collection of tools for analysing Viral Quasispecies |
2017-10-05 |
https://github.com/phac-nml/quasitools |
0.7.0 |
quasitools |
0.7.0 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/quasitools |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools |
|
|
|
|
0 |
12 |
0 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
182 |
183 |
15277 |
15540 |
8 |
8 |
39 |
39 |
15579 |
15316 |
191 |
190 |
|
|
|
rdeval |
rdeval, rdeval_report |
rdeval is a General purpose, multithreaded read analysis and manipulation tool. |
2025-02-17 |
https://github.com/vgl-hub/rdeval |
0.0.7 |
rdeval |
0.0.7 |
Up-to-date |
Assembly |
|
|
|
|
richard-burhans |
https://github.com/vgl-hub/rdeval |
https://github.com/richard-burhans/galaxytools/tree/main/tools/rdeval |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
15 |
15 |
223 |
223 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
223 |
223 |
15 |
15 |
https://usegalaxy.org/published/workflow?id=4b919e575a16d062, https://usegalaxy.org/published/workflow?id=6988c29ae84d2788, https://usegalaxy.org/published/workflow?id=af1f4dba9aaa0b52, https://workflowhub.eu/workflows/632?version=11 |
|
|
rdock |
rdock |
Docking ligands to proteins and nucleic acids |
2016-12-14 |
https://rdock.github.io/ |
1.0 |
rDock |
2013.1 |
To update |
Computational chemistry |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/rdock/ |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/rdock |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
refseq_masher |
refseq_masher_contains, refseq_masher_matches |
Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. |
2018-01-31 |
https://github.com/phac-nml/refseq_masher |
0.1.2 |
refseq_masher |
0.1.2 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/refseq_masher |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher |
|
|
|
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
149 |
149 |
3315 |
3315 |
164 |
164 |
992 |
992 |
0 |
0 |
0 |
0 |
14 |
14 |
4334 |
4334 |
8641 |
8641 |
327 |
327 |
https://usegalaxy.eu/published/workflow?id=0404013d5c27210d, https://usegalaxy.eu/published/workflow?id=3303a04887a47675, https://usegalaxy.eu/published/workflow?id=3d937648809ca4e7, https://usegalaxy.eu/published/workflow?id=4216424f032c055f, https://usegalaxy.eu/published/workflow?id=723e718f37e9ab91, https://usegalaxy.eu/published/workflow?id=7e48134082dab0a3, https://usegalaxy.eu/published/workflow?id=b93333efdab316d8, https://usegalaxy.eu/published/workflow?id=ba1fda2318046543, https://usegalaxy.eu/published/workflow?id=e532d98f4b368666, https://usegalaxy.eu/published/workflow?id=fca458178b3c794a, https://usegalaxy.org/published/workflow?id=0e30324072570abb, https://usegalaxy.org/published/workflow?id=4161cfd67ed94b5d, https://usegalaxy.org/published/workflow?id=4d1279007d0137fa, https://usegalaxy.org/published/workflow?id=524602abe59b18f7, https://usegalaxy.org/published/workflow?id=5cd56232e873beab, https://usegalaxy.org/published/workflow?id=9ac1e4efe310b3b3, https://usegalaxy.org/published/workflow?id=9e5c5ddb60a24889, https://usegalaxy.org/published/workflow?id=b76a9ce44ea019f1, https://usegalaxy.org/published/workflow?id=c454c930ccfb0d3f, https://usegalaxy.org/published/workflow?id=f4d623a19b32370e, https://workflowhub.eu/workflows/1043?version=11 |
|
|
repeat_channels |
repeat_channels |
Convert single-channel to multi-channel image |
2024-04-25 |
https://github.com/bmcv |
1.26.4 |
numpy |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
15 |
15 |
101 |
101 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
101 |
101 |
15 |
15 |
https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1730?version=1 |
imaging/voronoi-segmentation |
|
repeatexplorer2 |
repeatexplorer_clustering |
Tool for annotation of repeats from unassembled shotgun reads. |
2023-11-01 |
https://github.com/repeatexplorer/repex_tarean |
2.3.8 |
|
|
To update |
Genome annotation |
|
|
|
|
gga |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
83 |
83 |
369 |
369 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
369 |
369 |
83 |
83 |
|
|
|
replace_chromosome_names |
replace_chromosome_names |
Replace chromosome names |
2017-05-18 |
https://github.com/dpryan79/ChromosomeMappings/ |
0.1 |
python |
|
To update |
Text Manipulation |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/replace_chromosome_names/ |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/replace_chromosome_names |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
54 |
93 |
582 |
749 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
749 |
582 |
93 |
54 |
|
|
|
rfove |
rfove |
Perform segmentation region-based fitting of overlapping ellipses |
2023-11-12 |
https://sites.google.com/site/costaspanagiotakis/research/cs |
2023.11.12 |
|
|
To update |
Imaging |
Image analysis |
Image analysis |
Cell biology, Biomedical science, Imaging |
Cell biology, Biomedical science, Imaging |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove |
rfove |
RFOVE |
RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
15 |
15 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
15 |
15 |
7 |
7 |
|
|
|
scale_image |
ip_scale_image |
Scale image |
2018-12-07 |
https://github.com/bmcv |
0.18.3 |
scikit-image |
|
To update |
Imaging |
Image analysis, Image annotation, Visualisation, Data handling |
Image analysis, Image annotation, Visualisation, Data handling |
Imaging, Software engineering, Literature and language |
Imaging, Software engineering, Literature and language |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image |
scikit-image |
scikit-image |
Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. |
scikit-image |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
17 |
20 |
751 |
870 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
870 |
751 |
20 |
17 |
https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc |
|
|
segalign |
segalign |
A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. |
2024-04-15 |
https://github.com/gsneha26/SegAlign |
0.1.2.7 |
segalign-galaxy |
0.1.2.7 |
Up-to-date |
Next Gen Mappers |
|
|
|
|
richard-burhans |
https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign |
https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
123 |
123 |
468 |
468 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
468 |
468 |
123 |
123 |
|
|
|
segmetrics |
ip_segmetrics |
Image segmentation and object detection performance measures |
2022-10-07 |
https://github.com/bmcv |
1.4 |
segmetrics |
1.5 |
To update |
Imaging |
Image analysis |
Image analysis |
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics |
segmetrics |
SegMetrics |
Image segmentation and object detection performance measures |
segmetrics |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
3 |
3 |
88 |
88 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
88 |
88 |
3 |
3 |
https://workflowhub.eu/workflows/1517?version=1 |
imaging/parameter-tuning |
|
seqtk_nml |
seqtk_nml_sample |
Tool to downsample fastq reads |
2017-09-19 |
https://github.com/lh3/seqtk |
1.0.1 |
seqtk |
1.5 |
To update |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/snvphyl-galaxy |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
sistr_cmd |
sistr_cmd |
SISTR in silico serotyping tool |
2017-02-20 |
https://github.com/phac-nml/sistr_cmd |
1.1.3 |
sistr_cmd |
1.1.3 |
Up-to-date |
Sequence Analysis |
Genome assembly, Visualisation, Multilocus sequence typing |
Genome assembly, Visualisation, Multilocus sequence typing |
Whole genome sequencing, Immunoproteins and antigens, Sequence assembly, Zoology, Public health and epidemiology |
Whole genome sequencing, Immunoproteins and antigens, Sequence assembly, Zoology, Public health and epidemiology |
nml |
https://github.com/phac-nml/sistr_cmd |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd |
SISTR |
SISTR |
The Salmonella In Silico Typing Resource (SISTR) is an open-source and freely available web application for rapid in silico typing and serovar prediction from Salmonella genome assemblies using cgMLST and O and H antigen gene searching. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
395 |
397 |
5345 |
5466 |
0 |
0 |
0 |
0 |
91 |
95 |
907 |
1010 |
0 |
0 |
0 |
0 |
6476 |
6252 |
492 |
486 |
https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=cbe3769f1abb9fa5, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://workflowhub.eu/workflows/407?version=1 |
|
|
skyline2isocor |
skyline2isocor |
Converting skyline output to IsoCor input |
2024-02-07 |
https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor |
1.0.0 |
skyline2isocor |
1.0.0 |
Up-to-date |
Metabolomics |
|
|
|
|
workflow4metabolomics |
https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
149 |
149 |
150 |
150 |
11 |
11 |
|
|
|
slice_image |
ip_slice_image |
Slice image |
2017-10-30 |
https://github.com/bmcv |
0.3-4 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
3 |
6 |
4 |
104 |
0 |
0 |
0 |
0 |
1 |
1 |
48 |
48 |
0 |
0 |
0 |
0 |
152 |
52 |
7 |
4 |
|
|
|
smalt |
smalt |
SMALT aligns DNA sequencing reads with a reference genome. |
2017-09-19 |
http://www.sanger.ac.uk/science/tools/smalt-0 |
0.7.6 |
smalt |
0.7.6 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://sourceforge.net/projects/smalt/ |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
smart_domains |
smart_domains |
SMART domains |
2017-05-12 |
https://smart.embl.de/ |
0.1.0 |
perl-bioperl |
1.7.8 |
To update |
Sequence Analysis |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/smart_domains |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/smart_domains |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
smina |
smina |
Scoring and Minimization with smina |
2017-07-07 |
https://sourceforge.net/projects/smina/ |
1.0 |
smina |
2017.11.9 |
To update |
Computational chemistry |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/smina/ |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/smina |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
18 |
18 |
501 |
501 |
14 |
14 |
50 |
50 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
551 |
551 |
32 |
32 |
|
|
|
spades_fasta_header_fixer |
spades_header_fixer |
Fixes Spades Fasta ids |
2019-12-18 |
https://github.com/phac-nml/galaxy_tools |
1.1.2+galaxy1 |
sed |
|
To update |
Fasta Manipulation |
|
|
|
|
nml |
https://github.com/phac-nml/galaxy_tools |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
spatyper |
spatyper |
Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file. |
2023-03-16 |
https://github.com/HCGB-IGTP/spaTyper |
0.3.3 |
spatyper |
0.3.3 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
split_image |
ip_split_image |
Split image along axes |
2025-03-07 |
https://github.com/bmcv |
2.2.3 |
numpy |
|
To update |
Imaging |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
17 |
17 |
232 |
232 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
232 |
232 |
17 |
17 |
https://usegalaxy.eu/published/workflow?id=035f85c1615e0b7b, https://usegalaxy.eu/published/workflow?id=2571f7d13686efb2, https://usegalaxy.eu/published/workflow?id=7f8ff64c5ea03a9b, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://workflowhub.eu/workflows/1526?version=1, https://workflowhub.eu/workflows/1730?version=1, https://workflowhub.eu/workflows/1848?version=1 |
imaging/electrophoresis-gel-bands-image-analysis, imaging/process-image-bioimageio |
|
split_labelmap |
ip_split_labelmap |
Split Labelmaps |
2018-12-11 |
https://github.com/bmcv |
0.2-3 |
scikit-image |
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
4 |
113 |
155 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
155 |
113 |
4 |
2 |
|
|
|
spolpred |
spolpred |
A program for predicting the spoligotype from raw sequence reads |
2015-12-14 |
|
1.0.1 |
spolpred |
|
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
spot_detection_2d |
ip_spot_detection_2d |
Spot detection in 2D image sequence |
2021-07-20 |
https://github.com/BMCV/galaxy-image-analysis |
0.1 |
giatools |
0.4.1 |
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Bioinformatics |
Imaging, Bioinformatics |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d |
galaxy_image_analysis |
Galaxy Image Analysis |
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
7 |
7 |
93 |
93 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
93 |
93 |
7 |
7 |
https://usegalaxy.eu/published/workflow?id=e25f3ca3a1b4e4d8, https://usegalaxy.eu/published/workflow?id=ffa80e0637d079f2, https://workflowhub.eu/workflows/1499?version=1, https://workflowhub.eu/workflows/1528?version=1 |
imaging/2D-spot-detection, imaging/detection-of-mitoflashes |
|
srst2 |
srst2 |
Short Read Sequence Typing for Bacterial Pathogens |
2015-12-02 |
|
0.3.7 |
srst2 |
0.2.0 |
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
68 |
68 |
407 |
407 |
1 |
1 |
71 |
71 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
478 |
478 |
69 |
69 |
https://workflowhub.eu/workflows/407?version=1 |
|
|
staramr |
staramr_search |
Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. |
2018-05-10 |
https://github.com/phac-nml/staramr |
0.11.0 |
staramr |
0.11.0 |
Up-to-date |
Sequence Analysis |
Antimicrobial resistance prediction |
Antimicrobial resistance prediction |
Microbiology, Public health and epidemiology, Infectious disease |
Microbiology, Public health and epidemiology, Infectious disease |
nml |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr |
staramr |
staramr |
staramr (*AMR) scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes. The star|* in staramr indicates that it can handle all of the ResFinder, PointFinder, and PlasmidFinder databases. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2921 |
3072 |
31443 |
33124 |
2130 |
2130 |
14763 |
14763 |
1173 |
1182 |
8989 |
9237 |
97 |
97 |
9838 |
9838 |
66962 |
65033 |
6481 |
6321 |
https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=32de10b9de8a999a, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=374797e58377c40f, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a06b1ed5cd25922f, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=d3dc805cd43b2737, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=8, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/1488?version=1, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/470?version=1 |
genome-annotation/amr-gene-detection, microbiome/plasmid-metagenomics-nanopore |
|
stringmlst |
stringmlst |
Rapid and accurate identification of the sequence type (ST) |
2016-10-19 |
|
1.1.0 |
stringMLST |
0.6.3 |
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
suite_plasmid_profiler |
|
Plasmid Profiler suite defining all dependencies for Plasmid Profiler |
2016-11-07 |
|
|
|
|
To update |
Sequence Analysis |
|
|
|
|
nml |
|
https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
suite_qiime2_core |
|
|
2022-08-29 |
|
|
|
|
To update |
Statistics, Metagenomics, Sequence Analysis |
|
|
|
|
q2d2 |
|
https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
superdsm |
ip_superdsm |
Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images |
2023-06-20 |
https://github.com/bmcv |
0.2.0 |
superdsm |
0.4.0 |
To update |
Imaging |
Image analysis |
Image analysis |
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm |
superdsm |
SuperDSM |
SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. |
superdsm |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
5 |
5 |
26 |
26 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
26 |
26 |
5 |
5 |
|
|
|
t_coffee |
t_coffee |
T-Coffee |
2016-12-13 |
https://tcoffee.org/ |
13.45.0.4846264 |
t-coffee |
13.46.0.919e8c6b |
To update |
Sequence Analysis |
|
|
|
|
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/t_coffee |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/t_coffee |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
274 |
311 |
3958 |
9664 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9665 |
3959 |
312 |
275 |
https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09 |
|
|
tree_relabeler |
tree_relabel |
Relabels the tips of a newick formatted tree. |
2019-04-15 |
|
1.1.0 |
perl-bioperl |
1.7.8 |
To update |
Text Manipulation |
|
|
|
|
nml |
https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
treebest_best |
treebest_best |
TreeBeST best |
2015-08-06 |
https://treesoft.sourceforge.net/treebest.shtml |
1.9.2.post0 |
treebest |
1.9.2.post1 |
To update |
Phylogenetics |
Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) |
Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) |
Phylogenetics |
Phylogenetics |
earlhaminst |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/TreeBest |
https://github.com/TGAC/earlham-galaxytools/tree/main/tools/TreeBest |
treebest |
TreeBeST |
TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
45 |
58 |
966 |
1033 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
1034 |
967 |
59 |
46 |
https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09 |
|
|
tripal |
analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync |
Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal |
2017-05-29 |
https://github.com/galaxy-genome-annotation/python-tripal |
|
python-tripal |
3.2.1 |
To update |
Web Services |
|
|
|
|
gga |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal |
https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
unzip |
unzip |
Unzip file |
2019-08-01 |
https://github.com/bmcv |
6.0 |
unzip |
|
To update |
Convert Formats |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1765 |
1918 |
8513 |
9140 |
1 |
1 |
1 |
1 |
382 |
382 |
3072 |
3072 |
47 |
47 |
174 |
174 |
12387 |
11760 |
2348 |
2195 |
https://usegalaxy.eu/published/workflow?id=3dbee72d7c550b0c, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d, https://usegalaxy.eu/published/workflow?id=c5de0b794849e1b1, https://usegalaxy.eu/published/workflow?id=edf7e2128f5aef8d, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=2a1e4de0dc77bbed, https://workflowhub.eu/workflows/115?version=1, https://workflowhub.eu/workflows/1208?version=1, https://workflowhub.eu/workflows/1503?version=1, https://workflowhub.eu/workflows/1528?version=1, https://workflowhub.eu/workflows/1635?version=1, https://workflowhub.eu/workflows/1702?version=1, https://workflowhub.eu/workflows/655?version=1 |
ecology/Ecoregionalization_tutorial, ecology/Obitools-metabarcoding, ecology/ecoregiolifetraits, imaging/2D-spot-detection, imaging/hela-screen-analysis, imaging/imaging-introduction, imaging/object-tracking-using-cell-profiler, imaging/voronoi-segmentation, imaging/yolo-segmentation-training, sequence-analysis/Manage_AB1_Sanger, single-cell/scrna-ncbi-anndata |
|
visceral_evaluatesegmentation |
ip_visceral_evaluatesegmentation |
Visceral Project - Evaluate Segmentation Tool |
2024-09-30 |
https://github.com/bmcv |
0.5-2 |
visceral-evaluatesegmentation |
2021.03.25 |
To update |
Imaging |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation |
|
|
|
evaluatesegmentation-tool |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2 |
10 |
35 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
35 |
10 |
2 |
1 |
|
|
|
voronoi_tesselation |
voronoi_tessellation |
Compute Voronoi tesselation |
2024-03-09 |
https://github.com/bmcv |
0.22.0 |
scikit-image |
|
To update |
Imaging |
Image analysis, Image annotation, Visualisation, Data handling |
Image analysis, Image annotation, Visualisation, Data handling |
Imaging, Software engineering, Literature and language |
Imaging, Software engineering, Literature and language |
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation |
scikit-image |
scikit-image |
Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. |
scikit-image |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
15 |
15 |
148 |
148 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
148 |
148 |
15 |
15 |
https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2, https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://workflowhub.eu/workflows/1522?version=1, https://workflowhub.eu/workflows/1730?version=1 |
imaging/voronoi-segmentation |
|
w4mclassfilter |
w4mclassfilter |
Filter W4M data by values or metadata |
2018-08-06 |
https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper |
0.98.19 |
r-base |
|
To update |
Metabolomics |
|
|
|
|
eschen42 |
https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master |
https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
7 |
10 |
2003 |
2850 |
0 |
0 |
0 |
0 |
4 |
4 |
1500 |
1905 |
0 |
0 |
0 |
0 |
4755 |
3503 |
14 |
11 |
|
|
|
w4mconcatenate |
W4Mconcatenate |
[W4M][Utils] concatenate two Metadata tables |
2024-07-10 |
http://workflow4metabolomics.org |
1.0.0+galaxy1 |
r-base |
|
To update |
Metabolomics |
|
|
|
|
workflow4metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
56 |
56 |
56 |
56 |
4 |
4 |
|
|
|
w4mcorcov |
w4mcorcov |
OPLS-DA Contrasts of Univariate Results |
2018-08-06 |
https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper |
0.98.18 |
r-base |
|
To update |
Metabolomics |
|
|
|
|
eschen42 |
https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master |
https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
12 |
13 |
208 |
382 |
0 |
0 |
0 |
0 |
3 |
3 |
11 |
11 |
0 |
0 |
0 |
0 |
393 |
219 |
16 |
15 |
|
|
|
w4mjoinpn |
w4mjoinpn |
Join positive- and negative-mode W4M datasets |
2018-08-06 |
https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper |
0.98.2 |
coreutils |
8.25 |
To update |
Metabolomics |
|
|
|
|
eschen42 |
https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master |
https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
4 |
7 |
132 |
171 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
7 |
0 |
0 |
0 |
0 |
178 |
132 |
9 |
4 |
|
|
|
wade |
wade |
identify regions of interest |
2019-09-20 |
https://github.com/phac-nml/wade |
0.2.5+galaxy1 |
wade |
0.2.6 |
To update |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/wade |
https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
wsi_extract_top_view |
ip_wsi_extract_top_view |
WSI Extract Top View |
2017-10-30 |
https://github.com/bmcv |
0.2-2 |
scikit-image |
|
To update |
Imaging |
|
|
|
|
imgteam |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ |
https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
4 |
20 |
58 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
58 |
20 |
4 |
1 |
|
|
|
xcms |
abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw |
|
2023-05-24 |
https://github.com/sneumann/xcms |
4.4.0 |
bioconductor-xcms |
4.4.0 |
Up-to-date |
Metabolomics |
Mass spectrum visualisation, Label-free quantification, Validation, Chromatographic alignment, Peak detection, Chromatogram visualisation, Data filtering |
Mass spectrum visualisation, Label-free quantification, Validation, Chromatographic alignment, Peak detection, Chromatogram visualisation |
Biological imaging, Data visualisation, Metabolomics |
Data visualisation, Metabolomics |
workflow4metabolomics |
https://github.com/workflow4metabolomics/tools-metabolomics/ |
https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms |
XCMS |
xcms |
Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling. |
|
0 |
11 |
12 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
10 |
9 |
305 |
327 |
28321 |
44355 |
115 |
115 |
10237 |
10237 |
62 |
68 |
4838 |
6536 |
1306 |
1374 |
2965294 |
3054761 |
3115889 |
3008690 |
1884 |
1788 |
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metabolomics/gc_ms_with_xcms, metabolomics/gcms, metabolomics/lcms, metabolomics/lcms-preprocessing |
|
10x_bamtofastq |
10x_bamtofastq |
Converts 10x Genomics BAM to FASTQ |
2022-05-10 |
https://github.com/10XGenomics/bamtofastq |
1.4.1 |
10x_bamtofastq |
1.4.1 |
Up-to-date |
Convert Formats, Single Cell |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq |
https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
90 |
90 |
328 |
328 |
23 |
23 |
63 |
63 |
5 |
5 |
53 |
53 |
0 |
0 |
0 |
0 |
444 |
444 |
118 |
118 |
|
|
|
Wound healing scratch assay image analysis |
woundhealing_scratch_assay |
Tool to automate quantification of wound healing in high-throughput microscopy scratch assays |
2024-02-29 |
https://git.embl.de/grp-cba/wound-healing-htm-screen |
1.6.1 |
fiji-morpholibj |
1.6.1 |
Up-to-date |
Imaging |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools |
https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
31 |
31 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
31 |
31 |
1 |
1 |
https://workflowhub.eu/workflows/782?version=1 |
|
|
add_line_to_file |
add_line_to_file |
Adds a text line to the beginning or end of a file. |
2020-11-01 |
|
0.1.0 |
coreutils |
8.25 |
To update |
Text Manipulation |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file |
https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file |
|
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0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
516 |
516 |
21338 |
21338 |
327 |
327 |
2254 |
2254 |
81 |
81 |
2317 |
2317 |
0 |
0 |
0 |
0 |
25909 |
25909 |
924 |
924 |
https://usegalaxy.eu/published/workflow?id=1b10ece62e745125, https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e, https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=2c3d05023c02113e, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=6ed1016dfdf9f928, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=ce1712139b4a4273, https://usegalaxy.eu/published/workflow?id=d1357759d0962144, https://usegalaxy.eu/published/workflow?id=dd73bdcbac8649a3, https://usegalaxy.eu/published/workflow?id=e3b0b521ee8f2aef, https://usegalaxy.eu/published/workflow?id=ff2fd4a4bb27d859, https://usegalaxy.org.au/published/workflow?id=5cd804644a34c8fd, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=a335b9c9103b57ad, https://usegalaxy.org/published/workflow?id=195a608c481040de, https://usegalaxy.org/published/workflow?id=28c7e8269d478244, https://usegalaxy.org/published/workflow?id=634bbef1f67a0e30, https://workflowhub.eu/workflows/1199?version=2, https://workflowhub.eu/workflows/1552?version=1, https://workflowhub.eu/workflows/249?version=4, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1, https://workflowhub.eu/workflows/794?version=2 |
microbiome/pathogen-detection-from-nanopore-foodborne-data, single-cell/bulk-music-2-preparescref |
|
add_value |
addValue |
Add a value as a new column. |
2012-12-04 |
|
1.0.1 |
perl |
|
To update |
Text Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value |
|
|
|
|
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
1 |
0 |
1 |
0 |
1 |
1 |
1 |
1593 |
2059 |
56543 |
397436 |
1325 |
6510 |
19244 |
300241 |
239 |
289 |
4331 |
5125 |
40 |
41 |
424 |
434 |
703236 |
80542 |
8899 |
3197 |
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https://usegalaxy.org/published/workflow?id=e3e646407e3f921d, https://usegalaxy.org/published/workflow?id=e4f1cce653812a22, https://usegalaxy.org/published/workflow?id=e50e36a25bae863c, https://usegalaxy.org/published/workflow?id=e5c066644cc7cc07, https://usegalaxy.org/published/workflow?id=e75a7802d2941f31, https://usegalaxy.org/published/workflow?id=e8b1d1e5e889c986, https://usegalaxy.org/published/workflow?id=f18e6fa5270fcd37, https://usegalaxy.org/published/workflow?id=f6ee07c7edf170fb, https://workflowhub.eu/workflows/1057?version=9, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1267?version=1, https://workflowhub.eu/workflows/1369?version=1, https://workflowhub.eu/workflows/1434?version=1, https://workflowhub.eu/workflows/1438?version=1, https://workflowhub.eu/workflows/1550?version=1, https://workflowhub.eu/workflows/1638?version=1, https://workflowhub.eu/workflows/1665?version=1, https://workflowhub.eu/workflows/1688?version=1 |
assembly/ecoli_comparison, ecology/ref-based-rad-seq, proteomics/database-handling, single-cell/scrna-case_cell-cycle, transcriptomics/differential-isoform-expression |
|
agat |
agat |
GTF/GFF analysis toolkit |
2023-05-22 |
https://github.com/NBISweden/AGAT |
1.4.0 |
agat |
1.5.1 |
To update |
Convert Formats, Statistics, Fasta Manipulation |
Data handling, Genome annotation |
Data handling, Genome annotation |
Genomics |
Genomics |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/agat |
https://github.com/bgruening/galaxytools/tree/master/tools/agat |
agat |
AGAT |
Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
516 |
516 |
7064 |
7064 |
220 |
220 |
854 |
854 |
85 |
85 |
1199 |
1199 |
17 |
17 |
228 |
228 |
9345 |
9345 |
838 |
838 |
https://usegalaxy.org/published/workflow?id=951575e9a352301c, https://workflowhub.eu/workflows/1096?version=2 |
|
|
align_back_trans |
align_back_trans |
Thread nucleotides onto a protein alignment (back-translation) |
2014-02-18 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans |
0.0.10 |
biopython |
1.70 |
To update |
Fasta Manipulation, Sequence Analysis |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans |
https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
36 |
42 |
1303 |
1347 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1347 |
1303 |
42 |
36 |
|
|
|
antarna |
antarna |
antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . |
2015-04-30 |
|
1.1 |
antarna |
2.0.1.2 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
4 |
7 |
263 |
307 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
307 |
263 |
7 |
4 |
|
|
|
antismash |
antismash |
Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters |
2015-02-28 |
https://antismash.secondarymetabolites.org |
6.1.1 |
antismash |
8.0.4 |
To update |
Sequence Analysis |
Sequence clustering, Gene prediction, Differential gene expression analysis |
Sequence clustering, Gene prediction, Differential gene expression analysis |
Molecular interactions, pathways and networks, Gene and protein families |
Molecular interactions, pathways and networks, Gene and protein families |
bgruening |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash |
https://github.com/bgruening/galaxytools/tree/master/tools/antismash |
antismash |
antiSMASH |
Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1083 |
1236 |
29269 |
32703 |
1017 |
1017 |
12499 |
12499 |
280 |
280 |
10622 |
10622 |
6 |
6 |
170 |
170 |
55994 |
52560 |
2539 |
2386 |
https://usegalaxy.eu/published/workflow?id=0461bbd1f96292e2, https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=6984990d0ac2e1e6, https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.eu/published/workflow?id=edbaf66c1e97ebdb, https://usegalaxy.eu/published/workflow?id=f141db5179ea8422, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://workflowhub.eu/workflows/1558?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1 |
genome-annotation/secondary-metabolite-discovery |
|
aresite2 |
AREsite2_REST |
AREsite2 REST Interface |
2017-02-01 |
http://rna.tbi.univie.ac.at/AREsite |
0.1.2 |
python |
|
To update |
RNA, Data Source, Sequence Analysis |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
11 |
14 |
36 |
83 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
83 |
36 |
14 |
11 |
https://usegalaxy.eu/published/workflow?id=4e57c5cf750afadd |
|
|
atactk_trim_adapters |
atactk_trim_adapters |
Trim adapters from paired-end HTS reads. |
2018-06-20 |
https://github.com/ParkerLab/atactk/ |
0.1.6 |
atactk |
0.1.9 |
To update |
Fastq Manipulation |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters |
https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
60 |
83 |
148 |
299 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
299 |
148 |
83 |
60 |
|
|
|
bamhash |
bamhash |
Hash BAM and FASTQ files to verify data integrity |
2015-09-17 |
https://github.com/DecodeGenetics/BamHash |
1.1 |
bamhash |
1.1 |
Up-to-date |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/bamhash |
https://github.com/bgruening/galaxytools/tree/master/tools/bamhash |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
48 |
55 |
62 |
194 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
194 |
62 |
55 |
48 |
|
|
|
barcode_collapse |
barcode_collapse |
Paired End randomer aware duplicate removal algorithm |
2016-06-11 |
https://github.com/YeoLab/gscripts |
0.1.0 |
pysam |
0.23.3 |
To update |
RNA, Sequence Analysis |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse |
https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
basecoverage |
gops_basecoverage_1 |
Base Coverage of all intervals |
2014-04-01 |
https://github.com/galaxyproject/gops |
1.0.0 |
bx-python |
0.14.0 |
To update |
Genomic Interval Operations |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3 |
35 |
20 |
308 |
199 |
2294 |
1286 |
45703 |
22 |
36 |
321 |
581 |
1 |
2 |
3 |
13 |
46605 |
1630 |
2367 |
225 |
https://usegalaxy.org/published/workflow?id=6f836f4b71d399e7, https://usegalaxy.org/published/workflow?id=baf01109a1bf8d0d, https://usegalaxy.org/published/workflow?id=e3c1736cca484dda |
|
|
best_regression_subsets |
BestSubsetsRegression1 |
Perform Best-subsets Regression |
2014-04-01 |
|
1.0.0 |
numpy |
|
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
4 |
6 |
4 |
6 |
8 |
74 |
14 |
255 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
261 |
18 |
80 |
12 |
|
|
|
bg_statistical_hypothesis_testing |
bg_statistical_hypothesis_testing |
Tool for computing statistical tests. |
2015-02-28 |
https://github.com/bgruening/galaxytools/tree/master/tools/statistics |
0.3 |
numpy |
|
To update |
Statistics |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/statistics |
https://github.com/bgruening/galaxytools/tree/master/tools/statistics |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
52 |
74 |
218 |
415 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
416 |
219 |
75 |
53 |
|
|
|
bia_download |
bia_download |
Tool to query ftp links for study from bioimage archive |
2023-12-06 |
https://www.ebi.ac.uk/biostudies/bioimages/studies |
0.2.0 |
wget |
|
To update |
Imaging |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools |
https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
13 |
13 |
30 |
30 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
30 |
30 |
13 |
13 |
|
|
|
bigwig_to_bedgraph |
bigwig_to_bedgraph |
Convert from bigWig to bedGraph format |
2015-06-04 |
|
0.1.0 |
ucsc_tools |
|
To update |
Convert Formats |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph |
https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
715 |
873 |
7732 |
9584 |
1 |
1 |
1 |
1 |
1 |
2 |
4 |
7 |
0 |
0 |
0 |
0 |
9592 |
7737 |
876 |
717 |
|
|
|
bioimage_inference |
bioimage_inference |
Load model from BioImage.IO and make inferences |
2024-08-02 |
https://github.com/bgruening/galaxytools |
2.4.1 |
python |
|
To update |
Imaging |
|
|
Machine learning, Computer science |
Machine learning |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging |
https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging |
pytorch |
PyTorch |
PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. |
pytorch |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
9 |
9 |
133 |
133 |
0 |
0 |
0 |
0 |
1 |
1 |
68 |
68 |
0 |
0 |
0 |
0 |
201 |
201 |
10 |
10 |
https://workflowhub.eu/workflows/1526?version=1 |
imaging/process-image-bioimageio |
|
biomodels |
biomodels_biomd0000001066, biomodels_biomd0000001076 |
Wrappers for tools to bring BioModels AI models into Galaxy. |
2023-11-07 |
https://www.ebi.ac.uk/biomodels/ |
1.1 |
|
|
To update |
Machine Learning |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools |
https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
16 |
125 |
125 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
126 |
126 |
17 |
17 |
|
|
|
bionano |
bionano_scaffold |
Bionano Solve is a set of tools for analyzing Bionano data |
2021-05-17 |
https://bionanogenomics.com/ |
3.7.0 |
|
|
To update |
Assembly |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/bionano |
https://github.com/bgruening/galaxytools/tree/master/tools/bionano |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
169 |
169 |
615 |
615 |
63 |
63 |
177 |
177 |
23 |
23 |
898 |
898 |
0 |
0 |
0 |
0 |
1690 |
1690 |
255 |
255 |
https://usegalaxy.eu/published/workflow?id=075c4126e66def01, https://usegalaxy.eu/published/workflow?id=2e6ed783bdf05d16, https://usegalaxy.eu/published/workflow?id=319bc351f7a8e358, https://usegalaxy.eu/published/workflow?id=3d047ed984762ce8, https://usegalaxy.eu/published/workflow?id=45c0933b5c522628, https://usegalaxy.eu/published/workflow?id=5bb7691b176d1010, https://usegalaxy.eu/published/workflow?id=bb13f30a5562d30d, https://usegalaxy.eu/published/workflow?id=f6bd10486a0ba17d, https://usegalaxy.org.au/published/workflow?id=02f2a556e77eed14, https://usegalaxy.org.au/published/workflow?id=11f1564f2bd815d8, https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=53cbacc71790c41b, https://usegalaxy.org.au/published/workflow?id=73565f6cb4136370, https://usegalaxy.org.au/published/workflow?id=87bbf9408b3f2a32, https://usegalaxy.org.au/published/workflow?id=bcb0be4f4a0e369f, https://usegalaxy.org/published/workflow?id=85f521f5c7351406, https://usegalaxy.org/published/workflow?id=b1cfa3c239ef2523, https://usegalaxy.org/published/workflow?id=bff8bc8d0059274f, https://usegalaxy.org/published/workflow?id=ca3f2d9554e9e1c8, https://usegalaxy.org/published/workflow?id=d5183b025d0e78dd, https://workflowhub.eu/workflows/1607?version=1, https://workflowhub.eu/workflows/643?version=5 |
assembly/vgp_genome_assembly |
|
bismark |
bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor |
A tool to map bisulfite converted sequence reads and determine cytosine methylation states |
2015-02-28 |
https://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
0.22.1 |
bismark |
0.25.1 |
To update |
Sequence Analysis, Next Gen Mappers |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/bismark |
https://github.com/bgruening/galaxytools/tree/master/tools/bismark |
|
|
|
|
0 |
4 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
4 |
439 |
543 |
17084 |
20515 |
4 |
4 |
33 |
33 |
41 |
41 |
1423 |
1423 |
7 |
7 |
74 |
74 |
22045 |
18614 |
595 |
491 |
https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=8601a62dbca3082f |
|
|
black_forest_labs_flux |
black_forest_labs_flux |
Using the black forest labs FLUX.1 models to generate image based on user input. |
2024-10-14 |
https://github.com/bgruening/galaxytools/tree/master/tools/flux |
2024 |
|
|
To update |
Machine Learning |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/flux |
https://github.com/bgruening/galaxytools/tree/master/tools/flux |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
38 |
38 |
377 |
377 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
377 |
377 |
38 |
38 |
|
|
|
blat_coverage_report |
generate_coverage_report |
Polymorphism of the Reads |
2014-05-19 |
|
1.0.0 |
|
|
To update |
Next Gen Mappers, Sequence Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
blat_mapping |
blat2wig |
Coverage of the Reads in wiggle format |
2014-05-19 |
|
1.0.0 |
|
|
To update |
Next Gen Mappers, Sequence Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
blobtoolkit |
blobtoolkit |
Identification and isolation non-target data in draft and publicly available genome assemblies. |
2022-11-04 |
https://blobtoolkit.genomehubs.org/ |
4.0.7 |
|
|
To update |
Sequence Analysis, Assembly |
Genome assembly, Scaffolding, Visualisation, Data deposition, Data parsing |
Genome assembly, Scaffolding, Visualisation |
Sequence assembly, Model organisms, Workflows, Phylogenomics, Zoology, Biodiversity |
Sequence assembly, Model organisms, Workflows, Phylogenomics, Zoology, Biodiversity |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit |
https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit |
BlobToolKit |
BlobToolKit |
BlobToolKit Viewer is a genome-scale dataset visualistion tool developed as part of the blobtoolkit project to allow browser-based identification and filtering of target and non-target data in genome assemblies. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
148 |
148 |
3084 |
3084 |
62 |
62 |
237 |
237 |
85 |
85 |
1022 |
1022 |
1 |
1 |
2 |
2 |
4345 |
4345 |
296 |
296 |
https://usegalaxy.eu/published/workflow?id=3069c17b52decab4, https://usegalaxy.eu/published/workflow?id=88f80a31e3ff8663, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=c9a8fba4c56f5c83, https://usegalaxy.org.au/published/workflow?id=0a3fb089674de144, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1641?version=1 |
assembly/ERGA-post-assembly-QC |
|
blockbuster |
blockbuster |
Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. |
2015-02-28 |
http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html |
0.1.2 |
blockbuster |
0.0.1.1 |
To update |
RNA, Sequence Analysis |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster |
https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
96 |
128 |
567 |
3059 |
15 |
15 |
20 |
20 |
11 |
11 |
368 |
394 |
0 |
0 |
0 |
0 |
3473 |
955 |
154 |
122 |
https://usegalaxy.eu/published/workflow?id=2e1feecca56bb0b8, https://usegalaxy.eu/published/workflow?id=4f40ae432d8a4259, https://usegalaxy.eu/published/workflow?id=5ec0d6d108e02e1a, https://usegalaxy.eu/published/workflow?id=667d05ae290d11ea, https://usegalaxy.eu/published/workflow?id=7d343d982f1105bf, https://usegalaxy.eu/published/workflow?id=b36be9100485e6cd, https://usegalaxy.eu/published/workflow?id=c7026cd5578c8678, https://usegalaxy.eu/published/workflow?id=f00b862b06093636, https://usegalaxy.org.au/published/workflow?id=4a7f22081ecde089, https://workflowhub.eu/workflows/1671?version=1 |
transcriptomics/small_ncrna_clustering |
|
blockclust |
blockclust |
BlockClust detects transcripts with similar processing patterns. |
2015-02-28 |
https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust |
1.1.1 |
blockclust |
1.1.1 |
Up-to-date |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
52 |
85 |
524 |
1578 |
40 |
40 |
132 |
132 |
15 |
17 |
704 |
758 |
0 |
0 |
0 |
0 |
2468 |
1360 |
142 |
107 |
https://usegalaxy.eu/published/workflow?id=2e1feecca56bb0b8, https://usegalaxy.eu/published/workflow?id=5ec0d6d108e02e1a, https://usegalaxy.eu/published/workflow?id=667d05ae290d11ea, https://usegalaxy.eu/published/workflow?id=7d343d982f1105bf, https://usegalaxy.eu/published/workflow?id=c7026cd5578c8678, https://usegalaxy.eu/published/workflow?id=f00b862b06093636, https://usegalaxy.org.au/published/workflow?id=4a7f22081ecde089, https://workflowhub.eu/workflows/1671?version=1 |
transcriptomics/small_ncrna_clustering |
|
bowtie_wrappers |
bowtie_wrapper |
Galaxy wrappers for the Bowtie short read mapping tools. |
2012-11-26 |
http://bowtie-bio.sourceforge.net/ |
1.2.0 |
bowtie |
1.3.1 |
To update |
Next Gen Mappers |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1375 |
1733 |
22683 |
29140 |
117 |
17507 |
5706 |
205094 |
383 |
443 |
20521 |
20859 |
0 |
2 |
0 |
82 |
255175 |
48910 |
19685 |
1875 |
https://usegalaxy.eu/published/workflow?id=2a123e08436a89f1, https://usegalaxy.org.au/published/workflow?id=5cf5334877cc1297, https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a, https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33, https://usegalaxy.org/published/workflow?id=07739fbbd53755f6, https://usegalaxy.org/published/workflow?id=0b3af7e9ac69a6b7, https://usegalaxy.org/published/workflow?id=11dac9cba49be089, https://usegalaxy.org/published/workflow?id=14f62361a15f8a24, https://usegalaxy.org/published/workflow?id=1b385fd45ee48614, https://usegalaxy.org/published/workflow?id=246da6fd63cbd49d, https://usegalaxy.org/published/workflow?id=29a80db9f3208c29, https://usegalaxy.org/published/workflow?id=31dea5361ec9421c, https://usegalaxy.org/published/workflow?id=344a79d4f12d2cff, https://usegalaxy.org/published/workflow?id=3d1f4bd67ce30f99, https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4, https://usegalaxy.org/published/workflow?id=486ee20613d58dcf, https://usegalaxy.org/published/workflow?id=48adcc44fe62a99c, https://usegalaxy.org/published/workflow?id=4a9b0534b1c88609, https://usegalaxy.org/published/workflow?id=4aad96570d252f95, https://usegalaxy.org/published/workflow?id=5004f1087f5e87db, https://usegalaxy.org/published/workflow?id=5aa2caa2dcae1477, https://usegalaxy.org/published/workflow?id=62401f33a369bac0, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=85c3a1fc1d3d3df8, https://usegalaxy.org/published/workflow?id=92a233e5f2405830, https://usegalaxy.org/published/workflow?id=a24092b7f00b4e2a, https://usegalaxy.org/published/workflow?id=a57db139837dd24c, https://usegalaxy.org/published/workflow?id=ab23c641cfdefe0c, https://usegalaxy.org/published/workflow?id=b0a12221ce09c001, https://usegalaxy.org/published/workflow?id=b2176abeb937f026, https://usegalaxy.org/published/workflow?id=b5c79535c499bc58, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9, https://usegalaxy.org/published/workflow?id=d2864aa3631b3bf6, https://usegalaxy.org/published/workflow?id=dcb73fce390b36b2, https://usegalaxy.org/published/workflow?id=eb20150175a6ab03, https://usegalaxy.org/published/workflow?id=f201ce61becf9a80, https://usegalaxy.org/published/workflow?id=f823b87dd06ba4ac, https://usegalaxy.org/published/workflow?id=fc09d17e0bce18f8, https://workflowhub.eu/workflows/1530?version=1 |
genome-annotation/tnseq |
|
canonical_correlation_analysis |
cca1 |
Canonical Correlation Analysis |
2014-05-19 |
|
1.0.0 |
R |
|
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
20 |
23 |
39 |
82 |
16 |
147 |
30 |
505 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
587 |
69 |
170 |
36 |
|
|
|
canu |
canu |
Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). |
2018-06-07 |
https://github.com/marbl/canu |
2.3 |
canu |
2.3 |
Up-to-date |
Assembly |
De-novo assembly |
De-novo assembly |
Genomics |
Genomics |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/canu |
https://github.com/bgruening/galaxytools/tree/master/tools/canu |
canu |
CANU |
De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1644 |
1843 |
13768 |
17494 |
0 |
0 |
0 |
0 |
454 |
485 |
3744 |
4325 |
37 |
37 |
480 |
480 |
22299 |
17992 |
2365 |
2135 |
|
|
|
categorize_elements_satisfying_criteria |
categorize_elements_satisfying_criteria |
Categorize Elements satisfying criteria. |
2013-09-25 |
|
1.0.0 |
|
|
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3 |
5 |
4 |
41 |
0 |
0 |
0 |
0 |
14 |
16 |
169 |
232 |
0 |
0 |
0 |
0 |
273 |
173 |
21 |
17 |
|
|
|
ccat |
peakcalling_ccat |
Control-based ChIP-seq Analysis Tool |
2014-01-27 |
|
0.0.2 |
ccat |
3.0 |
To update |
ChIP-seq |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
27 |
44 |
61 |
183 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
183 |
61 |
44 |
27 |
|
|
|
cd_hit_dup |
cd_hit_dup |
simple tool for removing duplicates from sequencing reads |
2015-04-28 |
|
0.0.1 |
cd-hit-auxtools |
4.8.1 |
To update |
Metagenomics, Sequence Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
501 |
770 |
7542 |
9437 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9437 |
7542 |
770 |
501 |
https://usegalaxy.org/published/workflow?id=35c2626849348f2c |
|
|
cellpose |
cellpose |
Cellpose is an anatomical segmentation algorithm |
2024-02-29 |
https://github.com/MouseLand/cellpose |
3.1.0 |
|
|
To update |
Imaging |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/cellpose |
https://github.com/bgruening/galaxytools/tree/master/tools/cellpose |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
14 |
14 |
1269 |
1269 |
0 |
0 |
0 |
0 |
3 |
3 |
216 |
216 |
0 |
0 |
0 |
0 |
1485 |
1485 |
17 |
17 |
|
|
|
cellprofiler |
cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects |
cellProfiler wrapper |
2020-03-06 |
|
|
|
|
To update |
Imaging |
Quantification, Image analysis, Parsing |
Quantification, Image analysis, Parsing |
Imaging, Microarray experiment, Genotype and phenotype |
Imaging, Microarray experiment, Genotype and phenotype |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools |
https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler |
CellProfiler |
CellProfiler |
Tool for quantifying data from biological images, particularly in high-throughput experiments. |
cellprofiler |
0 |
23 |
23 |
19 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
19 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
19 |
23 |
19 |
63 |
67 |
3870 |
4976 |
0 |
0 |
0 |
0 |
10 |
10 |
8293 |
8293 |
0 |
0 |
0 |
0 |
13269 |
12163 |
77 |
73 |
https://usegalaxy.eu/published/workflow?id=3dbee72d7c550b0c, https://workflowhub.eu/workflows/115?version=1, https://workflowhub.eu/workflows/1503?version=1, https://workflowhub.eu/workflows/1505?version=1, https://workflowhub.eu/workflows/41?version=2 |
imaging/object-tracking-using-cell-profiler, imaging/tutorial-CP |
|
cellprofiler4 |
cp_cellprofiler4 |
cellProfiler4 wrapper |
2021-09-15 |
https://github.com/CellProfiler/CellProfiler |
4.2.8 |
|
|
To update |
Imaging |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools |
https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
12 |
12 |
60 |
60 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
60 |
60 |
12 |
12 |
|
|
|
change_case |
ChangeCase |
Convert column case. |
2012-12-04 |
|
1.0.1 |
perl |
|
To update |
Text Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case |
|
|
|
|
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
1 |
0 |
1 |
0 |
1 |
1 |
1 |
2560 |
3231 |
12348 |
15871 |
2179 |
2957 |
10632 |
19461 |
290 |
318 |
1023 |
1208 |
102 |
104 |
635 |
687 |
37227 |
24638 |
6610 |
5131 |
https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.org.au/published/workflow?id=2cef9a1633e0a067, https://usegalaxy.org.au/published/workflow?id=5490661d0153962b, https://usegalaxy.org.au/published/workflow?id=71bad95f72c9f30d, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=e75a7802d2941f31, https://workflowhub.eu/workflows/1713?version=1 |
transcriptomics/ref-based |
|
chatgpt_openai_api |
chatgpt_openai_api |
Using the OpenAI GPT models to generate text based on user input. |
2024-08-12 |
https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt |
2024 |
python |
|
To update |
Machine Learning |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt |
https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
59 |
59 |
612 |
612 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
612 |
612 |
59 |
59 |
https://usegalaxy.eu/published/workflow?id=a2284469005518e1 |
|
|
chipseeker |
chipseeker |
A tool for ChIP peak annotation and visualization |
2018-05-24 |
https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html |
1.32.0 |
bioconductor-chipseeker |
1.42.0 |
To update |
ChIP-seq, Genome annotation |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker |
https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1169 |
1326 |
20836 |
25212 |
2625 |
3151 |
35077 |
40734 |
121 |
128 |
3595 |
3974 |
0 |
0 |
0 |
0 |
69920 |
59508 |
4605 |
3915 |
https://usegalaxy.eu/published/workflow?id=6bce1d419a179c50, https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf, https://usegalaxy.org/published/workflow?id=7643e66a9b4e9c11 |
|
|
chromosome_diagram |
chromosome_diagram |
Chromosome Diagrams using Biopython |
2013-09-26 |
|
0.0.3 |
biopython |
1.70 |
To update |
Graphics, Sequence Analysis, Visualization |
|
|
|
|
peterjc |
|
https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
circexplorer |
circexplorer |
A combined strategy to identify circular RNAs (circRNAs and ciRNAs) |
2016-06-06 |
https://github.com/YangLab/CIRCexplorer |
1.1.9.0 |
circexplorer |
1.1.10 |
To update |
Sequence Analysis, RNA |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer |
https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
28 |
44 |
132 |
291 |
0 |
0 |
0 |
0 |
7 |
7 |
341 |
341 |
0 |
0 |
0 |
0 |
632 |
473 |
51 |
35 |
https://usegalaxy.org.au/published/workflow?id=5aff01d0b5fabd84 |
|
|
clc_assembly_cell |
clc_assembler, clc_mapper |
Galaxy wrapper for the CLC Assembly Cell suite from CLCBio |
2013-10-28 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell |
0.0.7 |
samtools |
1.22.1 |
To update |
Assembly, Next Gen Mappers, SAM |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell |
https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
cleanlab |
cleanlab_issue_handler |
CleanLab is a package to find various types of issues in a dataset. |
2025-05-05 |
https://cleanlab.ai |
2.7.1 |
cleanlab |
|
To update |
Machine Learning |
|
|
|
|
bgruening |
https://github.com/cleanlab/cleanlab |
https://github.com/bgruening/galaxytools/tree/master/tools/cleanlab |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
|
|
|
clinod |
clinod |
NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins |
2013-05-02 |
http://www.compbio.dundee.ac.uk/www-nod/ |
0.1.0 |
clinod |
1.3 |
To update |
Sequence Analysis |
Nucleic acid sequence analysis |
Nucleic acid sequence analysis |
Sequence analysis |
Sequence analysis |
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod |
https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod |
clinod |
clinod |
The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
31 |
31 |
585 |
585 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
585 |
585 |
31 |
31 |
|
|
|
cluster |
gops_cluster_1 |
Cluster the intervals of a dataset |
2014-04-01 |
https://github.com/galaxyproject/gops |
1.0.0 |
bx-python |
0.14.0 |
To update |
Genomic Interval Operations |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
11 |
37 |
132 |
894 |
128 |
1555 |
1898 |
30742 |
16 |
20 |
1259 |
1528 |
1 |
2 |
1 |
11 |
33175 |
3290 |
1614 |
156 |
https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf, https://usegalaxy.org/published/workflow?id=6f836f4b71d399e7, https://usegalaxy.org/published/workflow?id=7cff5c4dadffaad5 |
|
|
cmsearch_deoverlap |
cmsearch_deoverlap |
removes lower scoring overlaps from cmsearch results. |
2023-08-19 |
https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl |
0.08+galaxy2 |
perl |
|
To update |
RNA |
Comparison, Alignment |
Comparison, Alignment |
Biology, Medicine |
Biology, Medicine |
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap |
cmsearch-deoverlap |
cmsearch-deoverlap |
Removes lower scoring overlaps from cmsearch results.This tool removes lower-scoring overlaps from cmsearch results. Given information about the clans and the cmsearch tbl output this tool returns a filtered cmsearch tbl output. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
6 |
6 |
3102 |
3102 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3104 |
3104 |
7 |
7 |
https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1842?version=1 |
microbiome/mgnify-amplicon |
|
cmv |
cmcv, cmv, hmmcv, hmmv |
cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. |
2017-09-22 |
https://github.com/eggzilla/cmv |
1.0.8 |
cmv |
1.0.8 |
Up-to-date |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
8 |
14 |
19 |
114 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
114 |
19 |
14 |
8 |
https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1 |
|
|
cofold |
cofold |
Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. |
2015-02-28 |
http://www.e-rna.org/cofold/ |
2.0.4.0 |
cofold |
2.0.4 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
24 |
32 |
106 |
365 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
365 |
106 |
32 |
24 |
|
|
|
column_arrange_by_header |
bg_column_arrange_by_header |
Column arrange by header name |
2015-03-02 |
|
0.2 |
|
|
To update |
Text Manipulation |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header |
https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
486 |
576 |
7809 |
8379 |
504 |
504 |
2800 |
2800 |
98 |
155 |
1659 |
2063 |
32 |
32 |
202 |
202 |
13444 |
12470 |
1267 |
1120 |
https://usegalaxy.eu/published/workflow?id=0f7acf235096b708, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e, https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=4f62794453f65cba, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=6ed1016dfdf9f928, https://usegalaxy.eu/published/workflow?id=83049910e2cd5128, https://usegalaxy.eu/published/workflow?id=8f677efac7100097, https://usegalaxy.eu/published/workflow?id=930a9757252d3ca6, https://usegalaxy.eu/published/workflow?id=9a0275211e74698a, https://usegalaxy.eu/published/workflow?id=ce1712139b4a4273, https://usegalaxy.eu/published/workflow?id=ff2fd4a4bb27d859, https://usegalaxy.org.au/published/workflow?id=20d472fc5563a640, https://usegalaxy.org.au/published/workflow?id=4f837b7f90d5ebac, https://usegalaxy.org/published/workflow?id=682b1c7e2ad9d443, https://workflowhub.eu/workflows/1678?version=1, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1 |
single-cell/bulk-deconvolution-evaluate, variant-analysis/somatic-variants |
|
combine_metaphlan2_humann2 |
combine_metaphlan_humann |
Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances |
2023-07-20 |
|
0.3.0 |
python |
|
To update |
Metagenomics |
Aggregation |
Aggregation |
Metagenomics, Molecular interactions, pathways and networks |
Metagenomics, Molecular interactions, pathways and networks |
bebatut |
https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 |
https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann |
combine_metaphlan_and_humann |
Combine Metaphlan and HUMAnN |
This tool combine MetaPhlAn outputs and HUMANnN outputs |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
112 |
112 |
1972 |
1972 |
31 |
31 |
128 |
128 |
0 |
0 |
0 |
0 |
12 |
12 |
25 |
25 |
2125 |
2125 |
155 |
155 |
https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1466?version=2 |
microbiome/metatranscriptomics |
|
compalignp |
compalignp |
Compute fractional identity between trusted alignment and test alignment |
2015-06-03 |
|
1.0 |
compalignp |
1.0 |
Up-to-date |
RNA, Sequence Analysis |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp |
|
|
|
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0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
3 |
29 |
3 |
222 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
222 |
3 |
29 |
3 |
|
|
|
compare_humann2_output |
compare_humann2_output |
Compare outputs of HUMAnN2 for several samples and extract similar and specific information |
2022-10-19 |
|
0.2.0 |
|
|
To update |
Metagenomics |
Comparison |
Comparison |
Metagenomics, Gene and protein families |
Metagenomics, Gene and protein families |
bebatut |
https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output |
https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output |
compare_humann2_outputs |
Compare HUMAnN2 outputs |
This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
23 |
32 |
248 |
332 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
332 |
248 |
32 |
23 |
|
|
|
complement |
gops_complement_1 |
Complement intervals of a dataset |
2014-04-01 |
https://github.com/galaxyproject/gops |
1.0.0 |
bx-python |
0.14.0 |
To update |
Genomic Interval Operations |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement |
|
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0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
12 |
27 |
20 |
241 |
154 |
845 |
422 |
4836 |
7 |
8 |
343 |
531 |
1 |
1 |
1 |
1 |
5609 |
786 |
881 |
174 |
|
|
|
compute_motif_frequencies_for_all_motifs |
compute_motif_frequencies_for_all_motifs |
Compute Motif Frequencies For All Motifs, motif by motif. |
2013-09-25 |
|
1.0.0 |
|
|
To update |
Sequence Analysis, Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs |
|
|
|
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0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
12 |
15 |
29 |
101 |
0 |
0 |
0 |
0 |
8 |
8 |
326 |
424 |
0 |
0 |
0 |
0 |
525 |
355 |
23 |
20 |
|
|
|
compute_motifs_frequency |
compute_motifs_frequency |
Compute Motif Frequencies in indel flanking regions. |
2013-09-25 |
|
1.0.0 |
|
|
To update |
Sequence Analysis, Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency |
|
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0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
2 |
0 |
65 |
0 |
0 |
0 |
0 |
5 |
5 |
321 |
425 |
0 |
0 |
0 |
0 |
490 |
321 |
7 |
5 |
|
|
|
compute_q_values |
compute_q_values |
Compute q-values based on multiple simultaneous tests p-values |
2014-04-01 |
|
1.0.1 |
R |
|
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values |
|
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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0 |
0 |
0 |
0 |
0 |
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3 |
0 |
35 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
35 |
0 |
3 |
0 |
|
|
|
concat |
gops_concat_1 |
Concatenate two bed files |
2014-04-01 |
https://github.com/galaxyproject/gops |
1.0.1 |
bx-python |
0.14.0 |
To update |
Genomic Interval Operations |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat |
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1 |
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0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
705 |
862 |
578868 |
579385 |
683 |
3613 |
43922 |
86389 |
108 |
125 |
19198 |
19510 |
52 |
53 |
1321 |
1331 |
686615 |
643309 |
4653 |
1548 |
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microbiome/mgnify-amplicon |
|
condense_characters |
Condense characters1 |
Condense consecutive characters. |
2012-12-04 |
|
1.0.0 |
|
|
To update |
Text Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters |
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21 |
371 |
38 |
2179 |
6 |
9 |
200 |
256 |
0 |
1 |
0 |
10 |
2445 |
238 |
381 |
27 |
|
|
|
convert_characters |
Convert characters1 |
Convert delimiters to tab. |
2012-12-04 |
|
1.0.1 |
python |
|
To update |
Text Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters |
|
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1 |
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0 |
1 |
1 |
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1 |
0 |
1 |
0 |
1 |
1 |
1 |
1355 |
1634 |
39589 |
47190 |
2351 |
9220 |
23233 |
166636 |
283 |
395 |
4508 |
6913 |
137 |
142 |
1448 |
1550 |
222289 |
68778 |
11391 |
4126 |
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assembly/vgp_genome_assembly, ecology/ref-based-rad-seq, proteomics/neoantigen-variant-annotation, proteomics/secretome-prediction |
|
convert_solid_color2nuc |
color2nuc |
Convert Color Space to Nucleotides |
2014-05-19 |
|
1.0.0 |
|
|
To update |
Fasta Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
coprarna |
coprarna |
Target prediction for prokaryotic trans-acting small RNAs |
2017-11-01 |
https://github.com/PatrickRWright/CopraRNA |
2.1.1 |
coprarna |
2.1.4 |
To update |
RNA, Sequence Analysis |
|
|
|
|
rnateam |
https://github.com/PatrickRWright/CopraRNA |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
correlation |
cor2 |
Correlation for numeric columns |
2014-07-28 |
|
1.0.0 |
rpy |
|
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
110 |
157 |
347 |
945 |
68 |
756 |
230 |
5569 |
24 |
32 |
209 |
303 |
7 |
8 |
18 |
19 |
6836 |
804 |
953 |
209 |
|
|
|
count_gff_features |
count_gff_features |
Count GFF Features |
2014-07-28 |
|
0.2 |
galaxy-ops |
1.1.0 |
To update |
Sequence Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
136 |
155 |
279 |
384 |
336 |
693 |
707 |
1484 |
65 |
91 |
503 |
660 |
11 |
11 |
20 |
20 |
2548 |
1509 |
950 |
548 |
https://workflowhub.eu/workflows/1469?version=1 |
microbiome/metaplasmidome_query |
|
count_roi_variants |
count_roi_variants |
Count sequence variants in region of interest in BAM file |
2016-02-05 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants |
0.0.6 |
samtools |
1.22.1 |
To update |
Assembly, SAM |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants |
https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
coverage |
gops_coverage_1 |
Coverage of a set of intervals on second set of intervals |
2014-04-01 |
https://github.com/galaxyproject/gops |
1.0.0 |
bx-python |
0.14.0 |
To update |
Genomic Interval Operations |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
42 |
65 |
955 |
1867 |
160 |
2124 |
2523 |
44304 |
13 |
20 |
294 |
447 |
1 |
2 |
4 |
14 |
46632 |
3776 |
2211 |
216 |
https://usegalaxy.eu/published/workflow?id=668a9f5da768fa30, https://usegalaxy.eu/published/workflow?id=99c4dce722c023d1, https://usegalaxy.org/published/workflow?id=08ca80ae36c8c576, https://usegalaxy.org/published/workflow?id=468c5a8fe7a40778, https://usegalaxy.org/published/workflow?id=9cc814d43379c2a6, https://usegalaxy.org/published/workflow?id=e6550f5289099efc |
|
|
coverage_stats |
coverage_stats |
BAM coverage statistics using samtools idxstats and depth |
2014-11-20 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats |
0.1.0 |
samtools |
1.22.1 |
To update |
Assembly, SAM |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats |
https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
cpat |
cpat |
Coding-potential assessment tool using an alignment-free logistic regression model. |
2023-02-01 |
https://github.com/liguowang/cpat |
3.0.5 |
cpat |
3.0.5 |
Up-to-date |
Transcriptomics |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/cpat |
https://github.com/bgruening/galaxytools/tree/master/tools/cpat |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
82 |
82 |
369 |
369 |
86 |
86 |
363 |
363 |
16 |
16 |
244 |
244 |
1 |
1 |
1 |
1 |
977 |
977 |
185 |
185 |
https://usegalaxy.eu/published/workflow?id=11eba1b28ec87963, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://usegalaxy.org.au/published/workflow?id=a1b97364f84022cf, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/878?version=1 |
transcriptomics/differential-isoform-expression |
|
create_tool_recommendation_model |
create_tool_recommendation_model |
Create model to recommend tools |
2019-08-20 |
https://github.com/bgruening/galaxytools |
0.0.5 |
python |
|
To update |
Machine Learning |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model |
https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model |
|
|
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|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
23 |
26 |
86 |
474 |
33 |
33 |
74 |
74 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
548 |
160 |
59 |
56 |
|
|
|
crispr_recognition_tool |
crispr_recognition_tool |
CRISPR Recognition Tool |
2015-02-28 |
|
1.2.0 |
crisper_recognition_tool |
1.2 |
To update |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/crt |
https://github.com/bgruening/galaxytools/tree/master/tools/crt |
|
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|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
236 |
263 |
14780 |
14943 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
14943 |
14780 |
263 |
236 |
https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95 |
|
|
ctd_batch |
ctdBatch_1 |
CTD analysis of chemicals, diseases, or genes |
2013-09-25 |
|
1.0.0 |
|
|
To update |
Sequence Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
39 |
53 |
152 |
224 |
0 |
161 |
0 |
447 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
671 |
152 |
214 |
39 |
https://usegalaxy.org/published/workflow?id=44b27a1296633366 |
|
|
cummerbund |
cummeRbund |
Wrapper for the Bioconductor cummeRbund library |
2015-04-24 |
https://bioconductor.org/packages/release/bioc/html/cummeRbund.html |
2.16.0 |
fonts-conda-ecosystem |
|
To update |
RNA, Visualization |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
60 |
169 |
556 |
1813 |
360 |
2056 |
2233 |
15201 |
16 |
159 |
2052 |
3885 |
0 |
0 |
0 |
0 |
20899 |
4841 |
2384 |
436 |
https://usegalaxy.eu/published/workflow?id=17e720bee3b9104f, https://usegalaxy.org.au/published/workflow?id=189c584ea4bde59a, https://usegalaxy.org.au/published/workflow?id=1ac197bae296b2bf, https://usegalaxy.org.au/published/workflow?id=427e27f87b8048a3, https://usegalaxy.org.au/published/workflow?id=581c455f74aa55a4, https://usegalaxy.org.au/published/workflow?id=80a1493fb9593bb3, https://usegalaxy.org.au/published/workflow?id=cc6de673126c56cb, https://usegalaxy.org.au/published/workflow?id=d3989c6c2c663cd3, https://usegalaxy.org/published/workflow?id=82681bd5f059e39a |
|
|
cummerbund_to_tabular |
cummerbund_to_cuffdiff |
Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. |
2014-12-22 |
|
1.0.1 |
|
|
To update |
Convert Formats, Next Gen Mappers |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular |
|
|
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0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
27 |
97 |
154 |
1208 |
75 |
486 |
362 |
2693 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3901 |
516 |
583 |
102 |
https://usegalaxy.eu/published/workflow?id=17e720bee3b9104f, https://usegalaxy.org/published/workflow?id=82681bd5f059e39a |
|
|
cut_columns |
Cut1 |
Select columns from a dataset. |
2012-12-04 |
|
1.0.2 |
|
|
To update |
Text Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns |
|
|
|
|
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
1 |
0 |
1 |
0 |
1 |
1 |
1 |
14961 |
16891 |
2072099 |
2157279 |
14168 |
33789 |
388825 |
866777 |
2962 |
3394 |
141636 |
149042 |
819 |
826 |
12927 |
13224 |
3186322 |
2615487 |
54900 |
32910 |
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https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1464?version=1, https://workflowhub.eu/workflows/1466?version=2, https://workflowhub.eu/workflows/1468?version=1, https://workflowhub.eu/workflows/1469?version=1, https://workflowhub.eu/workflows/1479?version=1, https://workflowhub.eu/workflows/1486?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/1489?version=1, https://workflowhub.eu/workflows/1490?version=1, https://workflowhub.eu/workflows/1492?version=2, https://workflowhub.eu/workflows/1496?version=1, https://workflowhub.eu/workflows/1515?version=1, https://workflowhub.eu/workflows/1518?version=1, https://workflowhub.eu/workflows/1520?version=1, https://workflowhub.eu/workflows/1524?version=1, https://workflowhub.eu/workflows/1530?version=1, https://workflowhub.eu/workflows/1533?version=1, https://workflowhub.eu/workflows/1536?version=1, https://workflowhub.eu/workflows/1537?version=1, https://workflowhub.eu/workflows/1539?version=1, https://workflowhub.eu/workflows/1543?version=1, https://workflowhub.eu/workflows/1551?version=1, https://workflowhub.eu/workflows/1552?version=1, https://workflowhub.eu/workflows/1555?version=1, https://workflowhub.eu/workflows/1560?version=1, https://workflowhub.eu/workflows/1565?version=1, https://workflowhub.eu/workflows/1567?version=1, https://workflowhub.eu/workflows/1571?version=1, https://workflowhub.eu/workflows/1575?version=1, https://workflowhub.eu/workflows/1579?version=1, https://workflowhub.eu/workflows/1594?version=1, https://workflowhub.eu/workflows/1601?version=1, https://workflowhub.eu/workflows/1624?version=1, https://workflowhub.eu/workflows/1629?version=1, https://workflowhub.eu/workflows/1632?version=1, https://workflowhub.eu/workflows/1638?version=1, https://workflowhub.eu/workflows/1650?version=1, https://workflowhub.eu/workflows/1659?version=1, https://workflowhub.eu/workflows/1665?version=1, https://workflowhub.eu/workflows/1677?version=1, https://workflowhub.eu/workflows/1679?version=1, https://workflowhub.eu/workflows/1684?version=1, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/1699?version=1, https://workflowhub.eu/workflows/1702?version=1, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1713?version=1, https://workflowhub.eu/workflows/1715?version=1, https://workflowhub.eu/workflows/1717?version=2, https://workflowhub.eu/workflows/1718?version=1, https://workflowhub.eu/workflows/1884?version=1, https://workflowhub.eu/workflows/248?version=4, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/561?version=11, https://workflowhub.eu/workflows/603?version=2, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/612?version=24, https://workflowhub.eu/workflows/622?version=11, https://workflowhub.eu/workflows/624?version=1, https://workflowhub.eu/workflows/625?version=26, https://workflowhub.eu/workflows/629?version=1, https://workflowhub.eu/workflows/633?version=22, https://workflowhub.eu/workflows/641?version=29, https://workflowhub.eu/workflows/642?version=24, https://workflowhub.eu/workflows/643?version=5, https://workflowhub.eu/workflows/645?version=13, https://workflowhub.eu/workflows/655?version=1, https://workflowhub.eu/workflows/689?version=1, https://workflowhub.eu/workflows/698?version=1, https://workflowhub.eu/workflows/751?version=17, https://workflowhub.eu/workflows/794?version=2, https://workflowhub.eu/workflows/876?version=1, https://workflowhub.eu/workflows/880?version=1 |
assembly/assembly-decontamination, assembly/ecoli_comparison, contributing/create-new-tutorial, data-science/data-manipulation-olympics, digital-humanities/open-refine-tutorial, digital-humanities/text_mining_chinese, ecology/Obitools-metabarcoding, ecology/ref-based-rad-seq, epigenetics/atac-seq, epigenetics/ewas-suite, galaxy-interface/workflow-reports, genome-annotation/bacterial-comparative-genomics-dataset-construction, genome-annotation/gene-centric, genome-annotation/tnseq, introduction/data-manipulation-olympics, introduction/galaxy-intro-101-everyone, introduction/galaxy-intro-peaks2genes, introduction/galaxy-reproduce, microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-3-verification, microbiome/clinical-mp-4-quantitation, microbiome/metaplasmidome_query, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-3-verification, proteomics/clinical-mp-4-quantitation, proteomics/maxquant-label-free, proteomics/maxquant-msstats-dda-lfq, proteomics/metaquantome-data-creation, proteomics/neoantigen-hla-binding-novel-peptides, sequence-analysis/tapscan-streptophyte-algae, single-cell/GO-enrichment, single-cell/bulk-deconvolution-evaluate, single-cell/bulk-music-2-preparescref, single-cell/scatac-standard-processing-snapatac2, single-cell/scrna-case_alevin, single-cell/scrna-case_alevin-combine-datasets, single-cell/scrna-case_basic-pipeline, single-cell/scrna-case_monocle3-trajectories, single-cell/scrna-data-ingest, single-cell/scrna-ncbi-anndata, single-cell/scrna-seurat-pbmc3k, statistics/gpu_jupyter_lab, transcriptomics/differential-isoform-expression, transcriptomics/minerva-pathways, transcriptomics/mirna-target-finder, transcriptomics/network-analysis-with-heinz, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-genes-to-pathways, transcriptomics/rna-seq-viz-with-heatmap2, variant-analysis/non-dip, variant-analysis/pox-tiled-amplicon, visualisation/circos, visualisation/circos-microbial |
|
delete_overlapping_indels |
delete_overlapping_indels |
Delete Overlapping Indels from a chromosome indels file |
2013-09-25 |
|
1.0.0 |
|
|
To update |
Sequence Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
5 |
7 |
13 |
40 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
40 |
13 |
7 |
5 |
|
|
|
dewseq |
dewseq |
DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data |
2022-10-20 |
https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers |
0.1.0+galaxy0 |
python |
|
To update |
Sequence Analysis, RNA, CLIP-seq |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
21 |
21 |
100 |
100 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
100 |
100 |
21 |
21 |
|
|
|
dgidb_annotator |
dgidb_annotate |
Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) |
2013-11-28 |
|
0.1 |
|
|
To update |
Systems Biology, Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
26 |
32 |
38 |
71 |
0 |
133 |
0 |
304 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
375 |
38 |
165 |
26 |
|
|
|
diff |
diff |
GNU diff tool that calculates the differences between two files. |
2020-03-29 |
http://www.gnu.org/software/diffutils/ |
3.10 |
diffutils |
|
To update |
Text Manipulation |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/diff |
https://github.com/bgruening/galaxytools/tree/master/tools/diff |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
133 |
133 |
657 |
657 |
37 |
37 |
71 |
71 |
2 |
2 |
115 |
115 |
0 |
0 |
0 |
0 |
843 |
843 |
172 |
172 |
https://usegalaxy.eu/published/workflow?id=0b568c9735c03360, https://usegalaxy.eu/published/workflow?id=c917db7d7ba7ea6f, https://workflowhub.eu/workflows/1623?version=1, https://workflowhub.eu/workflows/1953?version=1 |
digital-humanities/introduction_to_dh, digital-humanities/text_mining_chinese |
|
diffbind |
|
Diffbind provides functions for processing ChIP-Seq data. |
2015-02-28 |
http://bioconductor.org/packages/release/bioc/html/DiffBind.html |
|
|
|
To update |
ChIP-seq |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/diffbind |
https://github.com/bgruening/galaxytools/tree/master/tools/diffbind |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
divide_pg_snp |
dividePgSnp |
Separate pgSnp alleles into columns |
2013-09-25 |
|
1.0.0 |
|
|
To update |
Sequence Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
8 |
10 |
13 |
38 |
17 |
56 |
41 |
176 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
214 |
54 |
66 |
25 |
|
|
|
dorina |
dorina_search |
data source for RNA interactions in post-transcriptional regulation |
2015-05-20 |
|
1.0 |
|
|
To update |
RNA, Data Source |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
31 |
684 |
1639 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1639 |
684 |
31 |
3 |
|
|
|
dot2ct |
rnastructure_dot2ct |
Dot-Bracket to Connect Table (CT) |
2015-06-10 |
|
5.7.a |
rnastructure |
6.4 |
To update |
Sequence Analysis, RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
dotknot |
dotknot |
DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence |
2015-09-17 |
http://dotknot.csse.uwa.edu.au/ |
1.3.1 |
vienna_rna |
|
To update |
RNA, Proteomics |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
8 |
16 |
23 |
91 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
91 |
23 |
16 |
8 |
|
|
|
draw_stacked_barplots |
draw_stacked_barplots |
Draw Stacked Bar Plots for different categories and different criteria |
2013-09-25 |
|
1.0.0 |
R |
|
To update |
Graphics, Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
61 |
69 |
188 |
252 |
0 |
0 |
0 |
0 |
24 |
39 |
192 |
272 |
8 |
8 |
11 |
11 |
535 |
391 |
116 |
93 |
|
|
|
dwt_cor_ava_perclass |
compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom |
Compute P-values and Correlation Coefficients for Feature Occurrences |
2014-01-27 |
|
1.0.1 |
r-waveslim |
1.7.5 |
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass |
|
|
|
|
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
12 |
176 |
187 |
0 |
0 |
0 |
0 |
187 |
176 |
12 |
9 |
|
|
|
dwt_cor_avb_all |
compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom |
Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features |
2014-01-27 |
|
1.0.1 |
r-waveslim |
1.7.5 |
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all |
|
|
|
|
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
8 |
164 |
170 |
0 |
0 |
0 |
0 |
170 |
164 |
8 |
7 |
|
|
|
dwt_ivc_all |
compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom |
Compute P-values and Second Moments for Feature Occurrences |
2014-01-27 |
|
1.0.1 |
r-waveslim |
1.7.5 |
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all |
|
|
|
|
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
7 |
161 |
168 |
0 |
0 |
0 |
0 |
168 |
161 |
7 |
5 |
|
|
|
dwt_var_perclass |
compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom |
Compute P-values and Max Variances for Feature Occurrences |
2014-01-27 |
|
1.0.1 |
r-waveslim |
1.7.5 |
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass |
|
|
|
|
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
8 |
170 |
177 |
0 |
0 |
0 |
0 |
177 |
170 |
8 |
7 |
|
|
|
dwt_var_perfeature |
dwt_var1 |
Wavelet variance using Discrete Wavelet Transfoms |
2014-01-27 |
|
1.0.2 |
r-bitops |
|
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
4 |
2 |
36 |
4 |
4 |
11 |
11 |
5 |
7 |
207 |
265 |
2 |
2 |
2 |
2 |
314 |
222 |
17 |
12 |
|
|
|
edta |
edta |
The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. |
2022-10-16 |
https://github.com/oushujun/EDTA |
|
edta |
2.2.2 |
To update |
Variant Analysis |
De-novo assembly, Deisotoping, Genome annotation |
De-novo assembly, Deisotoping, Genome annotation |
Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms |
Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms |
bgruening |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta |
https://github.com/bgruening/galaxytools/tree/master/tools/edta |
edta |
The Extensive de novo TE Annotator (EDTA) |
The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
164 |
164 |
4750 |
4750 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4750 |
4750 |
164 |
164 |
|
|
|
effectivet3 |
effectiveT3 |
Find bacterial type III effectors in protein sequences |
2013-04-30 |
http://effectors.org |
0.0.21 |
effectiveT3 |
1.0.1 |
To update |
Sequence Analysis |
Sequence classification |
Sequence classification |
Sequence analysis |
Sequence analysis |
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 |
effectivet3 |
EffectiveT3 |
Prediction of putative Type-III secreted proteins. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
epicseg |
epicseg_segment |
EpiCSeg is a tool for conducting chromatin segmentation. |
2018-03-02 |
https://github.com/lamortenera/epicseg |
@VERSION_STRING@ |
epicseg |
1.0 |
To update |
Epigenetics |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/epicseg |
https://github.com/bgruening/galaxytools/tree/master/tools/epicseg |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
16 |
22 |
86 |
257 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
257 |
86 |
22 |
16 |
|
|
|
erga_ear |
make_ear |
A tool to compile assembly reports and stastics from assembly pipeline |
2024-06-07 |
https://github.com/ERGA-consortium/EARs/tree/main |
24.10.15 |
reportlab |
|
To update |
Sequence Analysis, Assembly |
|
|
|
|
bgruening |
https://github.com/ERGA-consortium/EARs/tree/main |
https://github.com/bgruening/galaxytools/tree/master/tools/ear |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
99 |
99 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
99 |
99 |
4 |
4 |
|
|
|
exparna |
exparna |
ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. |
2015-02-28 |
http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp |
1.0.1 |
exparna |
1.0.1 |
Up-to-date |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
express |
express |
Quantify the abundances of a set of target sequences from sampled subsequences |
2014-01-27 |
|
1.1.1 |
eXpress |
1.5.1 |
To update |
RNA |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/express |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/express |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
34 |
51 |
235 |
372 |
0 |
117 |
0 |
1184 |
21 |
61 |
2444 |
2995 |
0 |
0 |
0 |
0 |
4551 |
2679 |
229 |
55 |
|
|
|
fasta_compute_length |
fasta_compute_length |
Compute sequence length |
2014-05-19 |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length |
1.0.4 |
python |
|
To update |
Fasta Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1172 |
1456 |
10749 |
12600 |
1571 |
6133 |
19547 |
54934 |
189 |
236 |
5789 |
6166 |
21 |
22 |
332 |
342 |
74042 |
36417 |
7847 |
2953 |
https://usegalaxy.eu/published/workflow?id=08f41680101a1a45, https://usegalaxy.eu/published/workflow?id=0de5fcc38ef1501d, https://usegalaxy.eu/published/workflow?id=0e492839192d26e0, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=29c565eff0080e42, https://usegalaxy.eu/published/workflow?id=2d0400b5d05c6c10, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=2f053b615d9788bf, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=4f9f7065975b3f97, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=6e1fe7372e93fae0, https://usegalaxy.eu/published/workflow?id=972db4abc51bb3ab, https://usegalaxy.eu/published/workflow?id=a018307be3563f28, https://usegalaxy.eu/published/workflow?id=a31100610fba17a1, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=ada52ba09b462567, https://usegalaxy.eu/published/workflow?id=b556b0a67ad979da, https://usegalaxy.eu/published/workflow?id=b77e3b08092fa73e, https://usegalaxy.eu/published/workflow?id=c696b37d1bf68e9b, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7, https://usegalaxy.eu/published/workflow?id=e522be58f0bac656, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.org.au/published/workflow?id=5cfea39918e8632d, https://usegalaxy.org.au/published/workflow?id=6b1b0a945d367b4c, https://usegalaxy.org.au/published/workflow?id=b432a1312859edd2, https://usegalaxy.org.au/published/workflow?id=b808cd1c0090b068, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc, https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=1d923ce15c17b1fe, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=386d3b300cf05305, https://usegalaxy.org/published/workflow?id=400c1d170f073279, https://usegalaxy.org/published/workflow?id=505c826e8c99d7bf, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=89d3c800d3be6050, https://usegalaxy.org/published/workflow?id=8b7e03f09b0183d9, https://usegalaxy.org/published/workflow?id=8e1c6ad6ff623015, https://usegalaxy.org/published/workflow?id=c03ada2070e9ca8a, https://usegalaxy.org/published/workflow?id=c88fe3dc11bc4905, https://usegalaxy.org/published/workflow?id=cdf5dffbed938d49, https://usegalaxy.org/published/workflow?id=cfa9e6e722b086c8, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c, https://usegalaxy.org/published/workflow?id=fb789920b057fe8d, https://workflowhub.eu/workflows/1632?version=1, https://workflowhub.eu/workflows/1638?version=1, https://workflowhub.eu/workflows/439?version=3, https://workflowhub.eu/workflows/625?version=26, https://workflowhub.eu/workflows/880?version=1 |
assembly/ecoli_comparison, sequence-analysis/viral_primer_design, single-cell/scatac-batch-correction-snapatac2, single-cell/scatac-standard-processing-snapatac2, variant-analysis/pox-tiled-amplicon |
|
fasta_concatenate_by_species |
fasta_concatenate0 |
Concatenate FASTA alignment by species |
2014-05-19 |
|
0.0.1 |
bx-python |
0.14.0 |
To update |
Fasta Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
276 |
332 |
39190 |
42990 |
580 |
1506 |
21098 |
27311 |
97 |
129 |
1927 |
2787 |
6 |
8 |
323 |
344 |
73432 |
62538 |
1975 |
959 |
https://usegalaxy.org/published/workflow?id=1d923ce15c17b1fe, https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4 |
|
|
fasta_filter_by_id |
fasta_filter_by_id |
Filter FASTA sequences by ID (DEPRECATED) |
2017-02-02 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id |
0.0.7 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fasta Manipulation, Sequence Analysis, Text Manipulation |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id |
https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
fasta_filter_by_length |
fasta_filter_by_length |
Filter sequences by length |
2014-05-19 |
|
1.2 |
python |
|
To update |
Fasta Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1122 |
1339 |
55587 |
76393 |
1415 |
4026 |
50212 |
106640 |
289 |
358 |
3630 |
6298 |
26 |
27 |
437 |
447 |
189778 |
109866 |
5750 |
2852 |
https://usegalaxy.eu/published/workflow?id=08f41680101a1a45, https://usegalaxy.eu/published/workflow?id=0e492839192d26e0, https://usegalaxy.eu/published/workflow?id=1860e02bcb894a64, https://usegalaxy.eu/published/workflow?id=69be516a48761365, https://usegalaxy.eu/published/workflow?id=8b2f53745e720d0f, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=a018307be3563f28, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=d2f75f70c33394ee, https://usegalaxy.org.au/published/workflow?id=9c60b83feaa22415, https://usegalaxy.org.au/published/workflow?id=b59fada651043735, https://usegalaxy.org.au/published/workflow?id=b808cd1c0090b068, https://usegalaxy.org.au/published/workflow?id=fc3c83b11f527977, https://usegalaxy.org/published/workflow?id=1708fdfd1d485434, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=b097fce5358c01e5, https://usegalaxy.org/published/workflow?id=de9c2db125a5ea27, https://workflowhub.eu/workflows/1612?version=1, https://workflowhub.eu/workflows/1616?version=1, https://workflowhub.eu/workflows/1638?version=1 |
assembly/assembly-with-preprocessing, assembly/ecoli_comparison |
|
fasta_to_tabular |
fasta2tab |
FASTA-to-Tabular converter |
2014-05-19 |
|
1.1.1 |
python |
|
To update |
Fasta Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1996 |
2390 |
117300 |
135717 |
2227 |
9101 |
56007 |
198933 |
343 |
435 |
5795 |
8617 |
40 |
45 |
931 |
959 |
344226 |
180033 |
11971 |
4606 |
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microbiome/clinical-mp-2-discovery, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/clinical-mp-2-discovery, proteomics/database-handling, proteomics/maxquant-msstats-dda-lfq, proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation |
|
fastq_filter_by_id |
fastq_filter_by_id |
Filter FASTQ sequences by ID (DEPRECATED) |
2017-02-02 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id |
0.0.7 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation, Sequence Analysis, Text Manipulation |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id |
https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
fastq_info |
fastq_info |
FASTQ info allows to validate single or paired fastq files |
2021-09-12 |
https://github.com/nunofonseca/fastq_utils |
0.25.1 |
fastq_utils |
0.25.3 |
To update |
Fastq Manipulation |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info |
https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1769 |
1769 |
17127 |
17127 |
2373 |
2373 |
10656 |
10656 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
27783 |
27783 |
4142 |
4142 |
https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a |
|
|
fastq_pair_names |
fastq_pair_names |
Extract FASTQ paired read names |
2014-05-05 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names |
0.0.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Sequence Analysis |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names |
https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
fastq_paired_unpaired |
fastq_paired_unpaired |
Divide FASTQ file into paired and unpaired reads |
2013-09-26 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired |
0.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Sequence Analysis, Text Manipulation |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired |
https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
fastq_trimmer_by_quality |
fastq_quality_trimmer |
FASTQ Quality Trimmer by sliding window |
2014-01-27 |
|
1.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
984 |
1208 |
5036 |
7413 |
2977 |
11843 |
25265 |
102069 |
237 |
393 |
2092 |
3355 |
112 |
112 |
309 |
309 |
113146 |
32702 |
13556 |
4310 |
https://usegalaxy.eu/published/workflow?id=b6eb5fe7e37f680a, https://usegalaxy.org.au/published/workflow?id=0fc7c14c4d1ac8f5, https://usegalaxy.org.au/published/workflow?id=427e27f87b8048a3, https://usegalaxy.org.au/published/workflow?id=8d47811c6154d347, https://usegalaxy.org.au/published/workflow?id=9176f8ebac92d10c, https://usegalaxy.org.au/published/workflow?id=d3989c6c2c663cd3, https://usegalaxy.org/published/workflow?id=1cd08f3549cf5589, https://usegalaxy.org/published/workflow?id=1d1ee1fad4e20eeb, https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=3fbaa9ae67362495, https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95, https://usegalaxy.org/published/workflow?id=61d324b1eca6300e, https://usegalaxy.org/published/workflow?id=712d9ae42b45c4b9, https://usegalaxy.org/published/workflow?id=7253824f78a90431, https://usegalaxy.org/published/workflow?id=73d98e5f821a78b3, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=c64719e91e7346a2, https://usegalaxy.org/published/workflow?id=d69ea491b99016f4, https://usegalaxy.org/published/workflow?id=d89e626fa4f9434f, https://usegalaxy.org/published/workflow?id=e2fa6584853a0dee, https://usegalaxy.org/published/workflow?id=ea69f4fbdbb88c71 |
|
|
fastqsolexa_to_fasta_qual |
fastqsolexa_to_fasta_qual |
FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data |
2014-05-19 |
|
1.0.0 |
|
|
To update |
Convert Formats, Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
0 |
3 |
0 |
|
|
|
featurecounter |
featureCoverage1 |
Feature coverage |
2014-04-01 |
|
2.0.0 |
bx-python |
0.14.0 |
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
18 |
23 |
22243 |
22395 |
51 |
354 |
202 |
13720 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
36115 |
22445 |
377 |
69 |
https://usegalaxy.org/published/workflow?id=4b52f6a8dcfc8045, https://usegalaxy.org/published/workflow?id=66748e20a243eafe |
|
|
ffmpeg |
ffmpeg_converter |
A complete, cross-platform solution to record, convert and stream audio and video. |
2025-04-21 |
https://ffmpeg.org |
0.1.0 |
ffmpeg |
|
To update |
Convert Formats |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/ffmpeg |
https://github.com/bgruening/galaxytools/tree/master/tools/ffmpeg |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
|
|
|
filter_transcripts_via_tracking |
filter_combined_via_tracking |
Filter Combined Transcripts |
2014-01-27 |
|
0.1 |
|
|
To update |
RNA |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
9 |
11 |
22 |
25 |
17 |
243 |
47 |
643 |
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
670 |
71 |
256 |
28 |
|
|
|
find_diag_hits |
find_diag_hits |
Find diagnostic hits |
2014-01-27 |
https://bitbucket.org/natefoo/taxonomy |
1.0.0 |
taxonomy |
0.10.1 |
To update |
Metagenomics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
9 |
13 |
26 |
71 |
1 |
204 |
3 |
1787 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1858 |
29 |
217 |
10 |
|
|
|
find_subsequences |
bg_find_subsequences |
|
2015-03-19 |
|
0.3 |
biopython |
1.70 |
To update |
|
|
|
|
|
bgruening |
|
https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
64 |
87 |
884 |
1408 |
260 |
409 |
2621 |
3777 |
3 |
3 |
264 |
264 |
0 |
0 |
0 |
0 |
5449 |
3769 |
499 |
327 |
https://usegalaxy.eu/published/workflow?id=2a123e08436a89f1, https://usegalaxy.eu/published/workflow?id=b86f3775aa1f13bc, https://workflowhub.eu/workflows/1530?version=1 |
genome-annotation/tnseq |
|
flanking_features |
flanking_features_1 |
Fetch closest non-overlapping feature for every interval |
2014-04-01 |
https://github.com/galaxyproject/gops |
4.0.1 |
bx-python |
0.14.0 |
To update |
Genomic Interval Operations |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
52 |
70 |
466 |
844 |
232 |
2573 |
1669 |
33003 |
18 |
26 |
1282 |
1664 |
2 |
3 |
14 |
24 |
35535 |
3431 |
2672 |
304 |
https://usegalaxy.org/published/workflow?id=6471aa8abbb3fa40, https://usegalaxy.org/published/workflow?id=7bc71a005c6f18d0 |
|
|
flexynesis |
flexynesis, flexynesis_cbioportal_import, flexynesis_plot, flexynesis_utils |
This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. |
2024-08-12 |
https://github.com/BIMSBbioinfo/flexynesis/tree/main |
0.2.20 |
flexynesis |
1.1.1 |
To update |
Machine Learning, Statistics, Systems Biology |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis |
https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis |
|
|
|
|
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
303 |
303 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
303 |
303 |
5 |
5 |
https://workflowhub.eu/workflows/1849?version=1, https://workflowhub.eu/workflows/1852?version=1, https://workflowhub.eu/workflows/1873?version=1, https://workflowhub.eu/workflows/1874?version=1 |
statistics/flexynesis_cbio_import, statistics/flexynesis_classification, statistics/flexynesis_survival, statistics/flexynesis_unsupervised |
|
flye |
flye |
Assembly of long and error-prone reads. |
2018-09-22 |
https://github.com/fenderglass/Flye/ |
2.9.6 |
flye |
2.9.6 |
Up-to-date |
Assembly |
Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly |
Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly |
Sequence assembly, Metagenomics, Whole genome sequencing, Genomics |
Sequence assembly, Metagenomics, Whole genome sequencing |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/flye |
https://github.com/bgruening/galaxytools/tree/master/tools/flye |
Flye |
Flye |
Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
4818 |
4961 |
49679 |
51133 |
4110 |
4110 |
36053 |
36053 |
2250 |
2274 |
13882 |
14419 |
185 |
185 |
1088 |
1088 |
102693 |
100702 |
11530 |
11363 |
https://usegalaxy.eu/published/workflow?id=0ebfab0e957b7267, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=30b514cfb9cce524, https://usegalaxy.eu/published/workflow?id=34a07bf6407510ef, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc, https://usegalaxy.eu/published/workflow?id=77e5bbd317750915, https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://usegalaxy.eu/published/workflow?id=86cf02cc0868d238, https://usegalaxy.eu/published/workflow?id=8b2f53745e720d0f, https://usegalaxy.eu/published/workflow?id=968f0ac2617aa524, https://usegalaxy.eu/published/workflow?id=9ddb703e1db13504, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=b1d9e56aef03672b, https://usegalaxy.eu/published/workflow?id=b2dfa74f55a73409, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=cf8591391a17a914, https://usegalaxy.eu/published/workflow?id=d2f75f70c33394ee, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.org.au/published/workflow?id=02c74095a7128c9d, https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060, https://usegalaxy.org.au/published/workflow?id=1ad4c47cee851dda, https://usegalaxy.org.au/published/workflow?id=22bd45f60c60a338, https://usegalaxy.org.au/published/workflow?id=2cb16d321a804b1a, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=479c6b0a96ea1610, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=5b32e2f0d390a4ba, https://usegalaxy.org.au/published/workflow?id=68f5c371adbe5490, https://usegalaxy.org.au/published/workflow?id=7c343e5b55474d19, https://usegalaxy.org.au/published/workflow?id=803ef29108e36e58, https://usegalaxy.org.au/published/workflow?id=8a40059343cf4b87, https://usegalaxy.org.au/published/workflow?id=b5403e4fff2961f9, https://usegalaxy.org.au/published/workflow?id=b6bad1f167257248, https://usegalaxy.org.au/published/workflow?id=c4d23297f6fbf5f3, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=d832905fbaf2ca31, https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2, https://usegalaxy.org.au/published/workflow?id=fc664a96d8099652, https://usegalaxy.org/published/workflow?id=00596e862edb23f2, https://usegalaxy.org/published/workflow?id=0602c14704dbe1ff, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5, https://usegalaxy.org/published/workflow?id=48dafc35989f13b1, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=5626a440a5798458, https://usegalaxy.org/published/workflow?id=562bcaa9b4d2e8a4, https://usegalaxy.org/published/workflow?id=69d8863d40524120, https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1, https://usegalaxy.org/published/workflow?id=7fc8b2398b6f093f, https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8, https://usegalaxy.org/published/workflow?id=bff206b4625375bc, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://usegalaxy.org/published/workflow?id=c8d74054c1820087, https://usegalaxy.org/published/workflow?id=cce88bc57b180d09, https://usegalaxy.org/published/workflow?id=cdcf91a8ddb5dcd1, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/1062?version=1, https://workflowhub.eu/workflows/1114?version=1, https://workflowhub.eu/workflows/1495?version=1, https://workflowhub.eu/workflows/1595?version=1, https://workflowhub.eu/workflows/1613?version=1, https://workflowhub.eu/workflows/1617?version=1, https://workflowhub.eu/workflows/1621?version=1, https://workflowhub.eu/workflows/225?version=1, https://workflowhub.eu/workflows/51?version=1, https://workflowhub.eu/workflows/750?version=3, https://workflowhub.eu/workflows/788?version=1 |
assembly/chloroplast-assembly, assembly/hifi-assembly, assembly/largegenome, assembly/mrsa-nanopore, microbiome/pathogen-detection-from-nanopore-foodborne-data |
|
footprint |
footprint |
Find transcription factor footprints |
2017-04-18 |
https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ |
1.0.0 |
footprint |
1.0.1 |
To update |
Epigenetics |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/footprint |
https://github.com/bgruening/galaxytools/tree/master/tools/footprint |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
4 |
5 |
56 |
57 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
57 |
56 |
5 |
4 |
|
|
|
format_cd_hit_output |
format_cd_hit_output |
Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file |
2022-10-19 |
|
1.0.0+galaxy1 |
|
|
To update |
Fasta Manipulation |
|
|
|
|
bebatut |
https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ |
https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
68 |
78 |
228 |
287 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
287 |
228 |
78 |
68 |
|
|
|
format_metaphlan2_output |
format_metaphlan2_output |
Format MetaPhlAn2 output to extract abundance at different taxonomic levels |
2022-10-19 |
|
0.2.0 |
|
|
To update |
Metagenomics |
Formatting |
Formatting |
Taxonomy, Metagenomics |
Taxonomy, Metagenomics |
bebatut |
https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ |
https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output |
format_metaphlan2_output |
Format metaphlan2 output |
This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
555 |
731 |
6485 |
7678 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7678 |
6485 |
731 |
555 |
https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b |
|
|
generate_pc_lda_matrix |
generate_matrix_for_pca_and_lda1 |
Generate a Matrix for using PC and LDA |
2014-07-28 |
|
1.0.0 |
|
|
To update |
Sequence Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
30 |
36 |
94 |
151 |
95 |
274 |
434 |
1071 |
14 |
17 |
186 |
244 |
2 |
2 |
2 |
2 |
1468 |
716 |
329 |
141 |
|
|
|
get_flanks |
get_flanks1 |
Get flanks returns flanking region/s for every gene |
2014-04-01 |
https://github.com/galaxyproject/gops |
1.0.0 |
bx-python |
0.14.0 |
To update |
Genomic Interval Operations |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1635 |
2463 |
4589 |
326514 |
2009 |
6814 |
8393 |
243076 |
102 |
156 |
742 |
1198 |
10 |
11 |
14 |
24 |
570812 |
13738 |
9444 |
3756 |
https://usegalaxy.eu/published/workflow?id=d2ef6d4a2189c0a6, https://usegalaxy.eu/published/workflow?id=f30c8054f064ac9f, https://usegalaxy.org.au/published/workflow?id=19e3488987d58d73, https://usegalaxy.org/published/workflow?id=013bf76cb3a8bd66, https://usegalaxy.org/published/workflow?id=4f02edb5c9bb84ab, https://usegalaxy.org/published/workflow?id=888bfce1c214ab64, https://usegalaxy.org/published/workflow?id=8a3e457a9453c313, https://usegalaxy.org/published/workflow?id=94de815260acc3a8, https://usegalaxy.org/published/workflow?id=c2b299627d2baf48, https://usegalaxy.org/published/workflow?id=f25a3da4b00eddbb, https://workflowhub.eu/workflows/1478?version=1 |
introduction/galaxy-intro-peaks2genes |
|
get_orfs_or_cdss |
get_orfs_or_cdss |
Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) |
2013-09-26 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss |
0.2.3 |
biopython |
1.70 |
To update |
Sequence Analysis |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss |
https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
268 |
268 |
1372 |
1372 |
0 |
0 |
0 |
0 |
312 |
312 |
2219 |
2219 |
8 |
10 |
65 |
72 |
3663 |
3656 |
590 |
588 |
https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a, https://usegalaxy.eu/published/workflow?id=a1518a029132ee3d, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6, https://usegalaxy.org.au/published/workflow?id=0f71c97671bb401f, https://usegalaxy.org.au/published/workflow?id=cb6f49d4ebfa0891 |
|
|
getindelrates_3way |
indelRates_3way |
Estimate Indel Rates for 3-way alignments |
2014-04-01 |
|
1.0.0 |
bx-python |
0.14.0 |
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
88 |
30 |
296 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
296 |
30 |
88 |
16 |
|
|
|
getindels_2way |
getIndels_2way |
Fetch Indels from pairwise alignments |
2014-04-01 |
|
1.0.0 |
numpy |
|
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
21 |
61 |
27 |
237 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
237 |
27 |
61 |
21 |
|
|
|
gfastats |
gfastats |
Tool for generating sequence statistics and simultaneous genome assembly file manipulation. |
2022-03-08 |
https://github.com/vgl-hub/gfastats |
1.3.11 |
gfastats |
1.3.11 |
Up-to-date |
Sequence Analysis |
Data handling |
Data handling |
Computational biology |
Computational biology |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/gfastats |
https://github.com/bgruening/galaxytools/tree/master/tools/gfastats |
gfastats |
gfastats |
gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1105 |
1105 |
19582 |
19582 |
735 |
735 |
15352 |
15352 |
183 |
183 |
4128 |
4128 |
5 |
5 |
453 |
453 |
39515 |
39515 |
2028 |
2028 |
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https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1162?version=2, https://workflowhub.eu/workflows/1163?version=2, https://workflowhub.eu/workflows/1164?version=2, https://workflowhub.eu/workflows/1327?version=6, https://workflowhub.eu/workflows/1594?version=1, https://workflowhub.eu/workflows/1641?version=1, https://workflowhub.eu/workflows/605?version=1, https://workflowhub.eu/workflows/606?version=2, https://workflowhub.eu/workflows/608?version=1, https://workflowhub.eu/workflows/612?version=24, https://workflowhub.eu/workflows/625?version=26, https://workflowhub.eu/workflows/633?version=22, https://workflowhub.eu/workflows/641?version=29, https://workflowhub.eu/workflows/642?version=24, https://workflowhub.eu/workflows/643?version=5, https://workflowhub.eu/workflows/645?version=13, https://workflowhub.eu/workflows/701?version=1, https://workflowhub.eu/workflows/702?version=1, https://workflowhub.eu/workflows/751?version=17, https://workflowhub.eu/workflows/788?version=1, https://workflowhub.eu/workflows/789?version=1 |
assembly/ERGA-post-assembly-QC, assembly/assembly-decontamination, assembly/vgp_genome_assembly |
|
gi2taxonomy |
Fetch Taxonomic Ranks |
Fetch taxonomic representation |
2014-01-27 |
https://bitbucket.org/natefoo/taxonomy |
1.1.1 |
taxonomy |
0.10.1 |
To update |
Metagenomics |
Database search, ID mapping |
Database search, ID mapping |
Taxonomy |
Taxonomy |
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy |
gi2taxonomy |
gi2taxonomy |
The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI). |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
68 |
116 |
244 |
713 |
17 |
1798 |
113 |
14058 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
6 |
14777 |
357 |
1915 |
85 |
https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c |
|
|
glimmer_hmm |
|
GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) |
2015-02-28 |
https://ccb.jhu.edu/software/glimmerhmm/ |
|
|
|
To update |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm |
https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gmaj |
gmaj_1 |
GMAJ Multiple Alignment Viewer |
2014-01-27 |
|
2.0.1 |
|
|
To update |
Visualization |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
7 |
7 |
12 |
12 |
22 |
230 |
67 |
985 |
5 |
8 |
8 |
11 |
1 |
1 |
1 |
1 |
1009 |
88 |
246 |
35 |
|
|
|
gotohscan |
rbc_gotohscan |
Find subsequences in db |
2015-07-02 |
|
1.3.0 |
gotohscan |
2.0 |
To update |
Sequence Analysis |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan |
https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
5 |
8 |
6 |
73 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
73 |
6 |
8 |
5 |
|
|
|
graph_converter |
graph_converter |
Convert between different graph formats |
2015-02-28 |
|
0.1.0 |
|
|
To update |
Convert Formats |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter |
https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
graphclust |
graphclust |
GraphClust can be used for structural clustering of RNA sequences. |
2015-02-28 |
http://www.bioinf.uni-freiburg.de/Software/GraphClust/ |
0.1 |
GraphClust |
|
To update |
RNA |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/graphclust |
https://github.com/bgruening/galaxytools/tree/master/tools/graphclust |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
0 |
1 |
0 |
|
|
|
graphclust_aggregate_alignments |
graphclust_aggregate_alignments |
Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster. |
2018-10-24 |
|
0.6.0 |
graphclust-wrappers |
0.6.0 |
Up-to-date |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
13 |
17 |
17 |
120 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
120 |
17 |
17 |
13 |
|
|
|
graphclust_align_cluster |
graphclust_align_cluster |
Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. |
2018-10-22 |
|
0.1 |
graphclust-wrappers |
0.6.0 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
27 |
31 |
91 |
3113 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3113 |
91 |
31 |
27 |
|
|
|
graphclust_cmfinder |
cmFinder |
Determines consensus motives for sequences. |
2016-12-15 |
|
0.4 |
graphclust-wrappers |
0.6.0 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
44 |
68 |
24130 |
57259 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
57259 |
24130 |
68 |
44 |
https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7 |
|
|
graphclust_fasta_to_gspan |
gspan |
Second step of GraphClust |
2016-12-15 |
|
0.4 |
graphclust-wrappers |
0.6.0 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
19 |
28 |
66 |
164 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
164 |
66 |
28 |
19 |
|
|
|
graphclust_mlocarna |
locarna_best_subtree |
MLocARNA computes a multiple sequence-structure alignment of RNA sequences. |
2016-12-15 |
|
0.4 |
graphclust-wrappers |
0.6.0 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
43 |
68 |
24174 |
57392 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
57392 |
24174 |
68 |
43 |
https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7 |
|
|
graphclust_motif_finder_plot |
motifFinderPlot |
Plotting results for GraphClust |
2017-02-22 |
|
0.4 |
seaborn |
|
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
7 |
10 |
13 |
71 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
71 |
13 |
10 |
7 |
|
|
|
graphclust_nspdk |
NSPDK_candidateClust, nspdk_sparse |
Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets. |
2016-12-15 |
|
9.2.3.1 |
graphclust-wrappers |
0.6.0 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
47 |
75 |
2223 |
63256 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
63256 |
2223 |
75 |
47 |
https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7 |
|
|
graphclust_postprocessing |
glob_report |
Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. |
2016-12-15 |
|
0.5 |
graphclust-wrappers |
0.6.0 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
48 |
73 |
725 |
2236 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2236 |
725 |
73 |
48 |
https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7 |
|
|
graphclust_postprocessing_no_align |
graphclust_glob_report_no_align |
Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously. |
2018-10-25 |
|
0.5 |
graphclust-wrappers |
0.6.0 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
3 |
0 |
108 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
108 |
0 |
3 |
0 |
|
|
|
graphclust_prepocessing_for_mlocarna |
preMloc |
This tool prepares files for locarna step. |
2016-12-15 |
|
0.4 |
graphclust-wrappers |
0.6.0 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
48 |
74 |
798 |
2247 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2247 |
798 |
74 |
48 |
https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7 |
|
|
graphclust_preprocessing |
preproc |
Preprocessing input for GraphClust |
2016-12-15 |
|
0.5 |
graphclust-wrappers |
0.6.0 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
56 |
84 |
733 |
2026 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2026 |
733 |
84 |
56 |
https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7 |
|
|
graphicsmagick |
graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage |
Contains tools based on GraphicsMagick |
2016-12-26 |
http://www.graphicsmagick.org |
1.3.45 |
graphicsmagick |
1.3.26 |
To update |
Imaging |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick |
https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick |
|
|
|
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
75 |
88 |
2336 |
3749 |
10 |
10 |
94 |
94 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3843 |
2430 |
98 |
85 |
https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=0b2304aa2083bd1a, https://usegalaxy.eu/published/workflow?id=0c6dd9e75d9a2130, https://usegalaxy.eu/published/workflow?id=2571f7d13686efb2, https://usegalaxy.eu/published/workflow?id=4f0f3b911b4e4921, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc, https://usegalaxy.eu/published/workflow?id=6afc245029ce5008, https://usegalaxy.eu/published/workflow?id=751e3e2c338949c0, https://usegalaxy.eu/published/workflow?id=7f8ff64c5ea03a9b, https://usegalaxy.eu/published/workflow?id=b4bfcbf8acee9cc3, https://workflowhub.eu/workflows/1432?version=1, https://workflowhub.eu/workflows/1745?version=2, https://workflowhub.eu/workflows/1840?version=1, https://workflowhub.eu/workflows/1848?version=1, https://workflowhub.eu/workflows/807?version=1 |
climate/pangeo, ecology/x-array-map-plot, galaxy-interface/workflow-posters, imaging/electrophoresis-gel-bands-image-analysis, imaging/yolo-segmentation-training |
|
graphmap |
graphmap_align, graphmap_overlap |
Mapper for long, error-prone reads. |
2018-09-27 |
https://github.com/isovic/graphmap/ |
0.5.2 |
graphmap |
0.6.4 |
To update |
Assembly |
Sequence trimming, EST assembly, Read mapping |
Sequence trimming, EST assembly, Read mapping |
Gene transcripts, RNA-Seq, RNA splicing |
Gene transcripts, RNA-Seq, RNA splicing |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/graphmap |
https://github.com/bgruening/galaxytools/tree/master/tools/graphmap |
graphmap |
graphmap |
Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads |
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
325 |
372 |
6375 |
7914 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
8 |
8 |
7922 |
6383 |
377 |
330 |
|
|
|
graphprot |
graphprot_predict_profile |
GraphProt models binding preferences of RNA-binding proteins. |
2018-05-24 |
https://github.com/dmaticzka/GraphProt |
1.1.7+galaxy2 |
graphprot |
1.1.7 |
To update |
Sequence Analysis, RNA, CLIP-seq |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
20 |
24 |
181 |
504 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
504 |
181 |
24 |
20 |
https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf |
|
|
hclust2 |
hclust2 |
Plots heatmaps |
2018-07-22 |
https://bitbucket.org/nsegata/hclust2/ |
0.99 |
hclust2 |
1.0.0 |
To update |
Data Visualization |
|
|
|
|
rnateam |
https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 |
https://github.com/bgruening/galaxytools/tree/master/tools/hclust2 |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
hgv_fundo |
hgv_funDo |
FunDO human genes associated with disease terms |
2013-09-25 |
|
1.0.0 |
|
|
To update |
Sequence Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
19 |
397 |
55 |
1794 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1794 |
55 |
397 |
19 |
|
|
|
hgv_hilbertvis |
hgv_hilbertvis |
HVIS visualization of genomic data with the Hilbert curve |
2013-09-25 |
https://www.ebi.ac.uk/huber-srv/hilbert/ |
1.0.0 |
R |
|
To update |
Graphics, Visualization |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
12 |
60 |
110 |
265 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
265 |
110 |
60 |
12 |
|
|
|
hictk |
hictk |
Convert cooler to juicebox_hic |
2024-02-03 |
https://github.com/paulsengroup/hictk |
2.0.2 |
hictk |
2.1.4 |
To update |
Convert Formats, Epigenetics |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/hictk |
https://github.com/bgruening/galaxytools/tree/master/tools/hictk |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
28 |
28 |
160 |
160 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
160 |
160 |
28 |
28 |
|
|
|
hicup |
hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater |
The HiCUP-Pipeline from the Bioinformatics Babraham Institute. |
2017-03-09 |
https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html |
0.9.2 |
|
|
To update |
Epigenetics |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/hicup |
https://github.com/bgruening/galaxytools/tree/master/tools/hicup |
|
|
|
|
0 |
0 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
6 |
39 |
47 |
782 |
1243 |
38 |
38 |
766 |
766 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2009 |
1548 |
85 |
77 |
https://usegalaxy.eu/published/workflow?id=57b96a59cca0e8df, https://usegalaxy.eu/published/workflow?id=7d49f41cd294e15b, https://usegalaxy.eu/published/workflow?id=83fea2e4508bc3ed, https://usegalaxy.eu/published/workflow?id=cbe9e09ed3e91e2e, https://usegalaxy.org/published/workflow?id=2ffae50d0916b641, https://usegalaxy.org/published/workflow?id=43cea919ebf9d978, https://usegalaxy.org/published/workflow?id=748c1a9d85eb61e2, https://usegalaxy.org/published/workflow?id=ba4815ec62edab04 |
|
|
hisat |
hisat |
HISAT is a fast and sensitive spliced alignment program. |
2015-05-13 |
http://ccb.jhu.edu/software/hisat/index.shtml |
1.0.3 |
hisat |
|
To update |
Assembly |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
0 |
228 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
228 |
0 |
12 |
0 |
|
|
|
histogram |
histogram_rpy |
Histogram of a numeric column |
2014-07-28 |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram |
1.0.5 |
rpy2 |
2.7.8 |
To update |
Graphics, Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
971 |
1233 |
4048 |
5378 |
1552 |
7484 |
6094 |
49673 |
218 |
372 |
712 |
1126 |
188 |
190 |
482 |
590 |
56767 |
11336 |
9279 |
2929 |
https://usegalaxy.eu/published/workflow?id=9e0d784860d6cc91, https://usegalaxy.eu/published/workflow?id=a2b386eef5645acd, https://usegalaxy.org.au/published/workflow?id=43a951ec514498f6, https://usegalaxy.org.au/published/workflow?id=781457327e644c7e, https://usegalaxy.org.au/published/workflow?id=da79aa2dfd6b34bc, https://usegalaxy.org/published/workflow?id=07739fbbd53755f6, https://usegalaxy.org/published/workflow?id=13a550ed56b56502, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc, https://usegalaxy.org/published/workflow?id=25adc55d2a26e34b, https://usegalaxy.org/published/workflow?id=9cc814d43379c2a6, https://usegalaxy.org/published/workflow?id=d2864aa3631b3bf6, https://usegalaxy.org/published/workflow?id=f823b87dd06ba4ac, https://workflowhub.eu/workflows/1448?version=1, https://workflowhub.eu/workflows/1449?version=1, https://workflowhub.eu/workflows/1458?version=1, https://workflowhub.eu/workflows/1462?version=1, https://workflowhub.eu/workflows/1469?version=1 |
microbiome/metaplasmidome_query, proteomics/DIA_Analysis_MSstats, proteomics/maxquant-label-free, proteomics/protein-quant-sil |
|
homer |
|
Software for motif discovery and next generation sequencing analysis. |
2015-02-28 |
http://homer.salk.edu/homer/ |
|
|
|
To update |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/homer |
https://github.com/bgruening/galaxytools/tree/master/tools/homer |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
htseq_clip |
htseq_clip |
htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets |
2022-10-11 |
https://github.com/EMBL-Hentze-group/htseq-clip |
0.1.0+galaxy0 |
htseq-clip |
2.19.0b0 |
To update |
Sequence Analysis, RNA, CLIP-seq |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
27 |
27 |
146 |
146 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
146 |
146 |
27 |
27 |
|
|
|
illumina_methylation_analyser |
illumina_methylation_analyser |
Methylation analyzer for Illumina 450k DNA emthylation microarrays |
2015-02-28 |
https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser |
0.1 |
Rscript |
|
To update |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser |
https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
imagej2 |
imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary |
ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. |
2015-05-05 |
http://fiji.sc |
20240614 |
|
|
To update |
Imaging |
Image analysis, Image annotation, Visualisation |
Image analysis, Image annotation, Visualisation |
Imaging |
Imaging |
imgteam |
https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 |
https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 |
imagej |
ImageJ2 |
It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. |
imagej2 |
0 |
0 |
27 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
27 |
27 |
12 |
13 |
515 |
1918 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1918 |
515 |
13 |
12 |
https://workflowhub.eu/workflows/1259?version=1 |
|
|
imagemagick |
imagemagick_image_compare, imagemagick_image_convert, imagemagick_image_montage |
Contains tools based on ImageMagick |
2025-08-29 |
https://imagemagick.org/ |
7.1.2-2 |
imagemagick |
|
To update |
Imaging |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagemagick |
https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagemagick |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
https://usegalaxy.org/published/workflow?id=c03ada2070e9ca8a, https://workflowhub.eu/workflows/625?version=26 |
|
|
indels_3way |
indels_3way |
Fetch Indels from 3-way alignments |
2013-09-25 |
|
1.0.3 |
|
|
To update |
Sequence Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1 |
0 |
22 |
2 |
21 |
3 |
292 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
314 |
3 |
22 |
2 |
|
|
|
infernal |
infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat |
Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. |
2015-02-28 |
http://infernal.janelia.org/ |
1.1.5 |
infernal |
1.1.5 |
Up-to-date |
RNA |
Nucleic acid feature detection |
Nucleic acid feature detection |
Sequence sites, features and motifs, Structural genomics |
Sequence sites, features and motifs, Structural genomics |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/infernal |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal |
infernal |
Infernal |
Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. |
|
0 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
103 |
149 |
57566 |
128051 |
2 |
2 |
8 |
8 |
10 |
10 |
1244 |
1548 |
0 |
0 |
0 |
0 |
129607 |
58818 |
161 |
115 |
https://usegalaxy.eu/published/workflow?id=2e1feecca56bb0b8, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=5ec0d6d108e02e1a, https://usegalaxy.eu/published/workflow?id=7d343d982f1105bf, https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1, https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1842?version=1 |
microbiome/mgnify-amplicon |
|
inforna |
|
INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. |
2015-02-28 |
http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp |
|
|
|
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
instagraal |
instagraal |
Large genome reassembly based on Hi-C data |
2022-11-10 |
https://github.com/koszullab/instaGRAAL |
0.1.6 |
|
|
To update |
Assembly |
Genome assembly, Mapping assembly, Genetic mapping, Scaffolding |
Genome assembly, Mapping assembly, Genetic mapping, Scaffolding |
Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites |
Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/instagraal |
https://github.com/bgruening/galaxytools/tree/master/tools/instagraal |
instagraal |
instaGRAAL |
Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13) |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
16 |
16 |
160 |
160 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
160 |
160 |
16 |
16 |
|
|
|
intarna |
intarna |
Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. |
2017-02-09 |
https://github.com/BackofenLab/IntaRNA |
3.4.1 |
intarna |
3.4.1 |
Up-to-date |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
44 |
55 |
223683 |
228312 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
228312 |
223683 |
55 |
44 |
|
|
|
intersect |
gops_intersect_1 |
Intersect the intervals of two datasets |
2014-04-01 |
https://github.com/galaxyproject/gops |
1.0.0 |
bx-python |
0.14.0 |
To update |
Genomic Interval Operations |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2552 |
3495 |
19923 |
352369 |
4361 |
14841 |
49357 |
791098 |
578 |
687 |
6876 |
8443 |
110 |
112 |
744 |
764 |
1152674 |
76900 |
19135 |
7601 |
https://usegalaxy.eu/published/workflow?id=013cc98f55b01d5d, https://usegalaxy.eu/published/workflow?id=0edf0e9a778cb732, https://usegalaxy.eu/published/workflow?id=124f884ee53685e8, https://usegalaxy.eu/published/workflow?id=13a7b30df801ea47, https://usegalaxy.eu/published/workflow?id=24ef0d03f58d4fc5, https://usegalaxy.eu/published/workflow?id=4309cbf427fa1f78, https://usegalaxy.eu/published/workflow?id=4516fe237a7112cc, https://usegalaxy.eu/published/workflow?id=68f7300f922f548d, https://usegalaxy.eu/published/workflow?id=69eed719f9b5b99d, https://usegalaxy.eu/published/workflow?id=6a48604ef9ceb8b8, https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=937fa7f2f83bb735, https://usegalaxy.eu/published/workflow?id=941bc727b61c09ab, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.eu/published/workflow?id=ad636a8e1763580a, https://usegalaxy.eu/published/workflow?id=af7926dfd0f3501c, https://usegalaxy.eu/published/workflow?id=c4cefff5b812aae9, https://usegalaxy.eu/published/workflow?id=d2ef6d4a2189c0a6, https://usegalaxy.eu/published/workflow?id=f30c8054f064ac9f, https://usegalaxy.org.au/published/workflow?id=19e3488987d58d73, https://usegalaxy.org.au/published/workflow?id=5668c42a05ca6be4, https://usegalaxy.org.au/published/workflow?id=a9e52a40b63d26fc, https://usegalaxy.org.au/published/workflow?id=b0b8b8f79b467cf6, https://usegalaxy.org.au/published/workflow?id=f27f6ed478d7a258, https://usegalaxy.org/published/workflow?id=013bf76cb3a8bd66, https://usegalaxy.org/published/workflow?id=165af757a6b84be9, https://usegalaxy.org/published/workflow?id=27e1a8c651d9a298, https://usegalaxy.org/published/workflow?id=30507545aa971637, https://usegalaxy.org/published/workflow?id=37383240151a472a, https://usegalaxy.org/published/workflow?id=4375f00f8a285088, https://usegalaxy.org/published/workflow?id=44b27a1296633366, https://usegalaxy.org/published/workflow?id=4f02edb5c9bb84ab, https://usegalaxy.org/published/workflow?id=56530f4d41413832, https://usegalaxy.org/published/workflow?id=60b080dc16141121, https://usegalaxy.org/published/workflow?id=7942748c29d718f8, https://usegalaxy.org/published/workflow?id=888bfce1c214ab64, https://usegalaxy.org/published/workflow?id=8e5efd04399c6838, https://usegalaxy.org/published/workflow?id=8e9882d890ee5ec7, https://usegalaxy.org/published/workflow?id=9005ecd577bd9bfa, https://usegalaxy.org/published/workflow?id=9238f7208033d0d6, https://usegalaxy.org/published/workflow?id=b0f85c802c1ea7f8, https://usegalaxy.org/published/workflow?id=b1cd3f793187d667, https://usegalaxy.org/published/workflow?id=baf01109a1bf8d0d, https://usegalaxy.org/published/workflow?id=c2b299627d2baf48, https://usegalaxy.org/published/workflow?id=dd949127e22f9f1f, https://usegalaxy.org/published/workflow?id=e3c1736cca484dda, https://usegalaxy.org/published/workflow?id=e4f6b68301aafd38, https://usegalaxy.org/published/workflow?id=e81a10ac8b20c801, https://usegalaxy.org/published/workflow?id=ebac500f62f4a469, https://usegalaxy.org/published/workflow?id=f365c53b5024d7f1, https://usegalaxy.org/published/workflow?id=f637ea9a753cfbe8, https://workflowhub.eu/workflows/1475?version=1, https://workflowhub.eu/workflows/1478?version=1, https://workflowhub.eu/workflows/1518?version=1, https://workflowhub.eu/workflows/1544?version=1 |
genome-annotation/gene-centric, introduction/galaxy-intro-peaks2genes, introduction/galaxy-intro-strands |
|
iprscan5 |
|
Interproscan queries the interpro database and provides annotations. |
2015-02-28 |
http://www.ebi.ac.uk/Tools/pfa/iprscan5/ |
|
|
|
To update |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 |
https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
itsx |
itsx |
ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. |
2022-05-02 |
https://microbiology.se/software/itsx/ |
1.1.3 |
itsx |
1.1.3 |
Up-to-date |
Metagenomics |
Sequence feature detection |
Sequence feature detection |
Functional, regulatory and non-coding RNA, Microbiology |
Functional, regulatory and non-coding RNA, Microbiology |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/itsx |
https://github.com/bgruening/galaxytools/tree/master/tools/itsx |
ITSx |
ITSx |
TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
140 |
140 |
2878 |
2878 |
0 |
0 |
0 |
0 |
18 |
18 |
198 |
198 |
0 |
0 |
0 |
0 |
3076 |
3076 |
158 |
158 |
https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67 |
|
|
jbrowse2 |
jbrowse2 |
JBrowse2 Genome Browser integrated as a Galaxy Tool |
2024-06-04 |
https://jbrowse.org |
2.17.0 |
jbrowse2 |
3.6.5 |
To update |
Sequence Analysis |
Genome visualisation, Structure visualisation, Pathway visualisation |
Genome visualisation, Structure visualisation, Pathway visualisation |
Mapping, Structural variation, Genomics, Gene structure, Sequence assembly |
Mapping, Structural variation, Genomics, Gene structure, Sequence assembly |
fubar |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 |
https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2 |
jbrowse_2 |
JBrowse 2 |
Modular genome browser with views of synteny and structural variation. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
626 |
626 |
3765 |
3765 |
349 |
349 |
1248 |
1248 |
95 |
95 |
603 |
603 |
0 |
0 |
0 |
0 |
5616 |
5616 |
1070 |
1070 |
https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2cd5670f075704ab, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=84414f3441946702, https://usegalaxy.eu/published/workflow?id=972db4abc51bb3ab, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org/published/workflow?id=386d3b300cf05305, https://usegalaxy.org/published/workflow?id=505c826e8c99d7bf, https://usegalaxy.org/published/workflow?id=89d3c800d3be6050 |
epigenetics/formation_of_super-structures_on_xi |
|
join |
gops_join_1 |
Join the intervals of two datasets side-by-side |
2014-04-01 |
https://github.com/galaxyproject/gops |
1.0.0 |
bx-python |
0.14.0 |
To update |
Genomic Interval Operations |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1323 |
2559 |
14041 |
332406 |
6315 |
39946 |
37461 |
517154 |
149 |
303 |
942 |
1764 |
34 |
35 |
216 |
226 |
851550 |
52660 |
42843 |
7821 |
https://usegalaxy.eu/published/workflow?id=04b838103aed1929, https://usegalaxy.eu/published/workflow?id=29346872085adf1f, https://usegalaxy.eu/published/workflow?id=2f7149d02db43b7b, https://usegalaxy.eu/published/workflow?id=3e91f8417a66d02c, https://usegalaxy.eu/published/workflow?id=4a33a8348ac03f00, https://usegalaxy.eu/published/workflow?id=51cce3b98da3e822, https://usegalaxy.eu/published/workflow?id=579a56c129883cf3, https://usegalaxy.eu/published/workflow?id=61dcc0998fa4d309, https://usegalaxy.eu/published/workflow?id=6ea9c7e45df94bf8, https://usegalaxy.eu/published/workflow?id=7878623b7e959284, https://usegalaxy.eu/published/workflow?id=7bcac5c6594e866c, https://usegalaxy.eu/published/workflow?id=7fbde7faec75c781, https://usegalaxy.eu/published/workflow?id=81abf01f79f358fe, https://usegalaxy.eu/published/workflow?id=8c44228d11782e61, https://usegalaxy.eu/published/workflow?id=9d888cef61f5072f, https://usegalaxy.eu/published/workflow?id=a6a36943accc9b7d, 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https://usegalaxy.org/published/workflow?id=d3811603bbd4a940, https://usegalaxy.org/published/workflow?id=d5cba8a5ba6880fd, https://usegalaxy.org/published/workflow?id=d7c03007ef8a618e, https://usegalaxy.org/published/workflow?id=d7ea4bdc208ae5e8, https://usegalaxy.org/published/workflow?id=d87b4e14e8e1d39e, https://usegalaxy.org/published/workflow?id=db7989d9479c80aa, https://usegalaxy.org/published/workflow?id=e004b6e4717296cb, https://usegalaxy.org/published/workflow?id=e586940a7c93ef73, https://usegalaxy.org/published/workflow?id=e67ce2ce587a6f39, https://usegalaxy.org/published/workflow?id=e9e8ac517480c291, https://usegalaxy.org/published/workflow?id=eb77b976984afa9c, https://usegalaxy.org/published/workflow?id=ebe6ac57f3c17dc4, https://usegalaxy.org/published/workflow?id=eca0449a7460480c, https://usegalaxy.org/published/workflow?id=f03bf569d526e51a, https://usegalaxy.org/published/workflow?id=f966a8498497ee13, https://usegalaxy.org/published/workflow?id=fcc39f74d5cddf12 |
|
|
join_files_on_column_fuzzy |
join_files_on_column_fuzzy |
Join two files on a common column, allowing a certain difference. |
2017-11-26 |
|
1.0.1 |
python |
|
To update |
Text Manipulation |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy |
https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
354 |
498 |
1870 |
2985 |
0 |
0 |
0 |
0 |
56 |
66 |
1383 |
1538 |
7 |
7 |
17 |
17 |
4540 |
3270 |
571 |
417 |
https://usegalaxy.eu/published/workflow?id=a5ca8b9807ed3f73, https://usegalaxy.eu/published/workflow?id=e573c6b697524e3a, https://usegalaxy.org.au/published/workflow?id=3678781bf7619a89, https://workflowhub.eu/workflows/1587?version=1 |
metabolomics/msi-finding-nglycans |
|
kernel_canonical_correlation_analysis |
kcca1 |
Kernel Canonical Correlation Analysis |
2014-05-19 |
|
1.0.0 |
rpy |
|
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
4 |
5 |
5 |
71 |
36 |
84 |
152 |
364 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
435 |
157 |
89 |
40 |
|
|
|
kernel_principal_component_analysis |
kpca1 |
Kernel Principal Component Analysis |
2014-05-19 |
|
1.0.0 |
rpy |
|
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
24 |
33 |
99 |
160 |
84 |
259 |
225 |
728 |
0 |
0 |
0 |
0 |
4 |
4 |
7 |
7 |
895 |
331 |
296 |
112 |
|
|
|
kinwalker |
|
Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. |
2015-02-28 |
http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ |
|
|
|
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
kraken2tax |
Kraken2Tax |
Convert Kraken output to Galaxy taxonomy data. |
2015-08-05 |
https://bitbucket.org/natefoo/taxonomy |
1.2+galaxy0 |
gawk |
|
To update |
Metagenomics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1365 |
1376 |
33158 |
33186 |
1892 |
2555 |
18299 |
28718 |
564 |
576 |
19721 |
19871 |
0 |
0 |
0 |
0 |
81775 |
71178 |
4507 |
3821 |
https://usegalaxy.eu/published/workflow?id=0bafeb17c21ebc9c, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=a459c311f461adce, https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999, https://usegalaxy.eu/published/workflow?id=bd4e3cdc7f29049b, https://usegalaxy.eu/published/workflow?id=ca80039c4933aa0a, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b, https://usegalaxy.eu/published/workflow?id=ee0005a5487653ba, https://usegalaxy.org/published/workflow?id=a63927dd19759714, https://usegalaxy.org/published/workflow?id=b68ec42db8953569, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/101?version=1, https://workflowhub.eu/workflows/124?version=1 |
|
|
labels |
bg_labels |
remaps and annotates alignments |
2015-02-28 |
https://github.com/bgruening/galaxytools/tree/master/tools/labels |
1.0.5.0 |
labels |
|
To update |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/labels |
https://github.com/bgruening/galaxytools/tree/master/tools/labels |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
lastz_paired_reads |
lastz_paired_reads_wrapper |
Galaxy wrapper for the Lastz alignment tool on paired reads |
2012-11-26 |
|
1.1.1 |
lastz |
1.04.52 |
To update |
Next Gen Mappers |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2 |
4 |
2 |
9 |
0 |
0 |
0 |
0 |
3 |
5 |
5 |
10 |
0 |
0 |
0 |
0 |
19 |
7 |
9 |
5 |
|
|
|
lca_wrapper |
lca1 |
Find lowest diagnostic rank |
2014-01-27 |
https://bitbucket.org/natefoo/taxonomy |
1.0.1 |
taxonomy |
0.10.1 |
To update |
Metagenomics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3 |
20 |
11 |
137 |
14 |
1112 |
112 |
6136 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6273 |
123 |
1132 |
17 |
https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c |
|
|
lda_analysis |
lda_analy1 |
Perform Linear Discriminant Analysis |
2014-07-28 |
|
1.0.1 |
R |
|
To update |
Graphics, Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
46 |
57 |
125 |
178 |
95 |
336 |
780 |
1639 |
0 |
3 |
0 |
4 |
5 |
5 |
19 |
19 |
1840 |
924 |
401 |
146 |
|
|
|
lighter |
lighter |
Lighter is a kmer-based error correction method for whole genome sequencing data |
2016-06-04 |
https://github.com/mourisl/Lighter |
1.0 |
lighter |
1.1.3 |
To update |
Sequence Analysis, Fasta Manipulation |
k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection |
k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection |
Sequencing, Whole genome sequencing, DNA, Genomics |
Whole genome sequencing, DNA, Genomics |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/lighter |
https://github.com/bgruening/galaxytools/tree/master/tools/lighter |
lighter |
Lighter |
Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
31 |
37 |
106 |
196 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
196 |
106 |
37 |
31 |
|
|
|
linear_regression |
LinearRegression1 |
Perform Linear Regression |
2014-04-01 |
|
1.0.1 |
R |
|
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
31 |
282 |
102 |
1146 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1146 |
102 |
282 |
31 |
https://usegalaxy.org/published/workflow?id=857db984ff571191 |
|
|
llm_hub |
llm_hub |
LiteLLM - Call all LLM APIs using the OpenAI format. |
2025-08-20 |
https://github.com/bgruening/galaxytools/tree/master/tools/llm_hub |
1.101.0 |
python |
|
To update |
Machine Learning |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/llm_hub |
https://github.com/bgruening/galaxytools/tree/master/tools/llm_hub |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
37 |
37 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
37 |
37 |
8 |
8 |
|
|
|
locarna |
locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile |
LocARNA - A suite for multiple alignment and folding of RNAs |
2015-02-28 |
http://www.bioinf.uni-freiburg.de/Software/LocARNA/ |
2.0.1 |
locarna |
2.0.1 |
Up-to-date |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
33 |
50 |
318 |
370 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
370 |
318 |
50 |
33 |
https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73 |
|
|
logistic_regression_vif |
LogisticRegression |
Perform Logistic Regression with vif |
2014-04-01 |
|
1.0.1 |
numpy |
|
To update |
Sequence Analysis, Variant Analysis, Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
48 |
23 |
173 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
173 |
23 |
48 |
10 |
|
|
|
maf_cpg_filter |
cpgFilter |
Mask CpG/non-CpG sites from MAF file |
2014-04-01 |
|
1.0.0 |
bx-python |
0.14.0 |
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
28 |
9 |
356 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
356 |
9 |
28 |
5 |
|
|
|
mafft |
rbc_mafft_add, rbc_mafft |
Multiple alignment program for amino acid or nucleotide sequences |
2015-06-16 |
https://mafft.cbrc.jp/alignment/software/ |
7.526 |
mafft |
7.525 |
To update |
RNA |
Multiple sequence alignment |
Multiple sequence alignment |
Sequence analysis |
Sequence analysis |
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/mafft |
https://github.com/bgruening/galaxytools/tree/master/tools/mafft |
MAFFT |
MAFFT |
MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
2844 |
3060 |
164403 |
217226 |
4659 |
6641 |
99571 |
145229 |
1279 |
1462 |
23332 |
25716 |
158 |
160 |
5367 |
5382 |
393553 |
292673 |
11323 |
8940 |
https://usegalaxy.eu/published/workflow?id=402b14906a03b2ef, https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=9155ed0e7a6a7b60, https://usegalaxy.eu/published/workflow?id=941400d10c346b2c, https://usegalaxy.eu/published/workflow?id=a06b1ed5cd25922f, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.eu/published/workflow?id=d102a20c31d4673c, https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd, https://usegalaxy.eu/published/workflow?id=e97b938ca4723827, https://usegalaxy.eu/published/workflow?id=ec50dd6d56f50db1, https://usegalaxy.fr/published/workflow?id=297b71156b297a73, https://usegalaxy.fr/published/workflow?id=5ec6d378e60f7ccc, https://usegalaxy.fr/published/workflow?id=63b49f322ec366b5, https://usegalaxy.fr/published/workflow?id=7ebb54181b404733, https://usegalaxy.fr/published/workflow?id=894143d81af8dff0, https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4, https://usegalaxy.fr/published/workflow?id=b3974acb70608e38, https://usegalaxy.fr/published/workflow?id=c7be6e229a045fad, https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee, https://usegalaxy.fr/published/workflow?id=e134e9637adfc5b6, https://usegalaxy.org.au/published/workflow?id=3242ec69dec6e13f, https://usegalaxy.org.au/published/workflow?id=42137e36791652bc, https://usegalaxy.org.au/published/workflow?id=a01c3004bcef9dd3, https://usegalaxy.org.au/published/workflow?id=d62b6717202f42c9, https://usegalaxy.org.au/published/workflow?id=f21446cc44da50ce, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=23212ae74fc2d2b5, https://usegalaxy.org/published/workflow?id=2d1ca299c1b058f6, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=75c2cf36253194c2, https://usegalaxy.org/published/workflow?id=8d8e8927d63803ef, https://usegalaxy.org/published/workflow?id=956987e628530c79, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://usegalaxy.org/published/workflow?id=9c4038fa15af6995, https://usegalaxy.org/published/workflow?id=b0f85c802c1ea7f8, https://usegalaxy.org/published/workflow?id=be54e57345ce7ca5, https://usegalaxy.org/published/workflow?id=f737593a1db217c8, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/1518?version=1, https://workflowhub.eu/workflows/1559?version=1, https://workflowhub.eu/workflows/1627?version=1, https://workflowhub.eu/workflows/1650?version=1, https://workflowhub.eu/workflows/1839?version=1 |
evolution/abc_intro_phylo, genome-annotation/gene-centric, sequence-analysis/tapscan-streptophyte-algae, sequence-analysis/viral_primer_design, variant-analysis/aiv-analysis, variant-analysis/pox-tiled-amplicon |
|
mapping_to_ucsc |
mapToUCSC |
Format mapping data as UCSC custom track |
2014-05-19 |
|
1.0.0 |
|
|
To update |
Visualization, Convert Formats, Next Gen Mappers |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
markitdown |
markitdown |
Convert documents to Markdown using markitdown |
2025-04-21 |
https://github.com/microsoft/markitdown |
0.1.1 |
|
|
To update |
Convert Formats |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/markitdown |
https://github.com/bgruening/galaxytools/tree/master/tools/markitdown |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
51 |
51 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
51 |
51 |
8 |
8 |
|
|
|
mavedb_importer |
mavedb_importer |
data source for MaveDB |
2023-12-13 |
|
0.9 |
|
|
To update |
Data Source |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ |
https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
2 |
2 |
|
|
|
mea |
mea |
Maximum expected accuracy prediction |
2015-07-29 |
http://www.bioinf.uni-leipzig.de/Software/mea |
0.6.4.1 |
mea |
0.6.4 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
3 |
5 |
9 |
86 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
86 |
9 |
5 |
3 |
|
|
|
megablast_xml_parser |
megablast_xml_parser |
Parse blast XML output |
2014-05-19 |
|
1.0.1 |
python |
|
To update |
Next Gen Mappers, Convert Formats |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
98 |
152 |
1457 |
1614 |
88 |
477 |
258 |
2907 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4521 |
1715 |
629 |
186 |
https://usegalaxy.eu/published/workflow?id=33312e5643279e8a |
|
|
merge |
gops_merge_1 |
Merge the overlapping intervals of a dataset |
2014-04-01 |
https://github.com/galaxyproject/gops |
1.0.0 |
bx-python |
0.14.0 |
To update |
Genomic Interval Operations |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
432 |
482 |
567865 |
568928 |
561 |
4421 |
45860 |
108947 |
93 |
139 |
19554 |
20122 |
9 |
10 |
1171 |
1181 |
699178 |
634450 |
5052 |
1095 |
https://usegalaxy.eu/published/workflow?id=06544e74f583fd05, https://usegalaxy.eu/published/workflow?id=3aaea772745ca295, https://usegalaxy.eu/published/workflow?id=522500fac247be6f, https://usegalaxy.eu/published/workflow?id=5ded4002e684a02c, https://usegalaxy.eu/published/workflow?id=6c91fe92ef069d64, https://usegalaxy.eu/published/workflow?id=7b7d6a5c6c65d74b, https://usegalaxy.eu/published/workflow?id=b8fc492025ad6ff0, https://usegalaxy.eu/published/workflow?id=c832ecfa83bcda14, https://usegalaxy.eu/published/workflow?id=d52ff93f4ffdd981, https://usegalaxy.fr/published/workflow?id=0df61a88d64de252, https://usegalaxy.fr/published/workflow?id=a3e9062133fdf7c2, https://usegalaxy.fr/published/workflow?id=bf8ffe72b7ce4570, https://usegalaxy.org.au/published/workflow?id=2955ea7be1cdda29, https://usegalaxy.org.au/published/workflow?id=2b71eb1dc2aa28a1, https://usegalaxy.org.au/published/workflow?id=4b681937a01df465, https://usegalaxy.org.au/published/workflow?id=5cd7f1824db7a960, https://usegalaxy.org.au/published/workflow?id=61a21c9928182ae4, https://usegalaxy.org.au/published/workflow?id=6795e545b0cafded, https://usegalaxy.org.au/published/workflow?id=851552cc3e830253, https://usegalaxy.org.au/published/workflow?id=a77ce877e786d44a, https://usegalaxy.org.au/published/workflow?id=e154a9b605ea0886, https://usegalaxy.org.au/published/workflow?id=ebd1ee73906fdea0, https://usegalaxy.org.au/published/workflow?id=f65b54fcffaa11e5, https://usegalaxy.org/published/workflow?id=0392de36b6f55a8f, https://usegalaxy.org/published/workflow?id=31cc891be77cbc6f, https://usegalaxy.org/published/workflow?id=44b27a1296633366, https://usegalaxy.org/published/workflow?id=4ffdb2cf21759d26, https://usegalaxy.org/published/workflow?id=507c817755b2410d, https://usegalaxy.org/published/workflow?id=5834e562fa403732, https://usegalaxy.org/published/workflow?id=65f3a5772ae05a7a, https://usegalaxy.org/published/workflow?id=6ba03802169c0063, https://usegalaxy.org/published/workflow?id=7b20a62d69d53efc, https://usegalaxy.org/published/workflow?id=d136d24e4c96962a, https://usegalaxy.org/published/workflow?id=f25a3da4b00eddbb, https://usegalaxy.org/published/workflow?id=f365c53b5024d7f1, https://workflowhub.eu/workflows/138?version=9, https://workflowhub.eu/workflows/356?version=1 |
|
|
merge_cols |
mergeCols1 |
Merge columns together. |
2012-12-04 |
|
1.0.3 |
python |
|
To update |
Text Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols |
|
|
|
|
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
1 |
0 |
1 |
0 |
1 |
1 |
1 |
2264 |
2636 |
27989 |
40501 |
841 |
3343 |
19933 |
135060 |
101 |
167 |
1612 |
2136 |
115 |
116 |
616 |
626 |
178323 |
50150 |
6262 |
3321 |
https://usegalaxy.eu/published/workflow?id=0e492839192d26e0, https://usegalaxy.eu/published/workflow?id=14714876dda7186d, https://usegalaxy.eu/published/workflow?id=57cfe5062c8e01bf, https://usegalaxy.eu/published/workflow?id=5e09d5e991009cda, https://usegalaxy.eu/published/workflow?id=c5de0b794849e1b1, https://usegalaxy.eu/published/workflow?id=c94a1d028357c81e, https://usegalaxy.eu/published/workflow?id=d0ae255151450dad, https://usegalaxy.eu/published/workflow?id=d33ab07e4cf44f8c, https://usegalaxy.eu/published/workflow?id=f7a7c72489d6b3d4, https://usegalaxy.org.au/published/workflow?id=b808cd1c0090b068, https://usegalaxy.org.au/published/workflow?id=bdb498b1f0e8944f, https://usegalaxy.org/published/workflow?id=138311394c077827, https://usegalaxy.org/published/workflow?id=1d923ce15c17b1fe, https://usegalaxy.org/published/workflow?id=2d64e09025ae8ed4, https://usegalaxy.org/published/workflow?id=44b27a1296633366, https://usegalaxy.org/published/workflow?id=5bc973dd30f22525, https://usegalaxy.org/published/workflow?id=66748e20a243eafe, https://usegalaxy.org/published/workflow?id=68a9f03d99676bdc, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=8b1eedebcb94ba93, https://usegalaxy.org/published/workflow?id=941ced9f12eecd3c, https://usegalaxy.org/published/workflow?id=9864961cc6132562, https://usegalaxy.org/published/workflow?id=b8742810ac30429d, https://usegalaxy.org/published/workflow?id=c17fa637bcdec86e, https://usegalaxy.org/published/workflow?id=c3ea8fa3bb202dc6, https://usegalaxy.org/published/workflow?id=cd1badac800122c2, https://usegalaxy.org/published/workflow?id=e3e646407e3f921d, https://usegalaxy.org/published/workflow?id=e75a7802d2941f31, https://workflowhub.eu/workflows/1208?version=1, https://workflowhub.eu/workflows/1638?version=1, https://workflowhub.eu/workflows/1680?version=1, https://workflowhub.eu/workflows/1696?version=1, https://workflowhub.eu/workflows/1703?version=1, https://workflowhub.eu/workflows/1704?version=1 |
assembly/ecoli_comparison, ecology/Ecoregionalization_tutorial, ecology/PAMPA-toolsuite-tutorial, ecology/regionalGAM, transcriptomics/rna-seq-counts-to-genes |
|
methtools |
methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling |
tools for methylation analysis |
2015-02-28 |
https://github.com/bgruening/galaxytools/tree/master/tools/methtools |
0.1.1 |
methtools |
|
To update |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/methtools |
https://github.com/bgruening/galaxytools/tree/master/tools/methtools |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
31 |
124 |
423 |
5461 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5461 |
423 |
124 |
31 |
|
|
|
methylkit |
methylkit |
A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. |
2016-12-20 |
http://bioconductor.org/packages/release/bioc/html/methylKit.html |
0.99.2 |
bioconductor-methylkit |
1.32.0 |
To update |
Epigenetics |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/methylkit |
https://github.com/bgruening/galaxytools/tree/master/tools/methylkit |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
10 |
10 |
10 |
10 |
3 |
3 |
|
|
|
metilene |
metilene |
Differential DNA methylation calling |
2015-12-14 |
|
0.2.6.1 |
metilene |
0.2.8 |
To update |
RNA, Statistics |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/metilene |
https://github.com/bgruening/galaxytools/tree/master/tools/metilene |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
285 |
505 |
3013 |
5261 |
148 |
148 |
786 |
786 |
57 |
57 |
450 |
452 |
1 |
1 |
1 |
1 |
6500 |
4250 |
711 |
491 |
https://usegalaxy.eu/published/workflow?id=489926f9299594fe, https://usegalaxy.eu/published/workflow?id=bffeb3cd0c708441, https://usegalaxy.eu/published/workflow?id=c46345ba876d5bfe, https://usegalaxy.org.au/published/workflow?id=91c8daa5f2bcf7c0, https://usegalaxy.org/published/workflow?id=e20e1371e50bdcee, https://workflowhub.eu/workflows/1566?version=1 |
epigenetics/methylation-seq |
|
mgnify_seqprep |
mgnify_seqprep |
A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. |
2024-05-14 |
https://github.com/jstjohn/SeqPrep |
1.2 |
|
|
To update |
Fastq Manipulation, Sequence Analysis |
Nucleic acid design |
Nucleic acid design |
Genomics, Sequence assembly, Sequencing, Probes and primers |
Genomics, Sequence assembly, Sequencing, Probes and primers |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep |
https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep |
seqprep |
SeqPrep |
Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
1348 |
1348 |
109 |
109 |
444 |
444 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1792 |
1792 |
115 |
115 |
https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1854?version=1 |
microbiome/mgnify-amplicon |
|
miclip |
mi_clip |
Identification of binding sites in CLIP-Seq data. |
2015-02-28 |
https://cran.r-project.org/src/contrib/Archive/MiClip/ |
1.2.0 |
Rscript |
|
To update |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/miclip |
https://github.com/bgruening/galaxytools/tree/master/tools/miclip |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
microsatellite_birthdeath |
microsatellite_birthdeath |
Identify microsatellite births and deaths |
2013-09-25 |
|
1.0.0 |
|
|
To update |
Sequence Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
microsats_alignment_level |
microsats_align1 |
Extract Orthologous Microsatellites from pair-wise alignments |
2014-04-01 |
|
1.0.0 |
sputnik |
|
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
50 |
147 |
98 |
987 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
987 |
98 |
147 |
50 |
|
|
|
microsats_mutability |
microsats_mutability1 |
Estimate microsatellite mutability by specified attributes |
2014-04-01 |
|
1.1.0 |
bx-python |
0.14.0 |
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
24 |
91 |
36 |
318 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
318 |
36 |
91 |
24 |
|
|
|
minced |
minced |
MinCED - Mining CRISPRs in Environmental Datasets |
2015-02-28 |
http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README |
0.2.0 |
minced |
0.4.2 |
To update |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/minced |
https://github.com/bgruening/galaxytools/tree/master/tools/minced |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
152 |
169 |
8010 |
8360 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8360 |
8010 |
169 |
152 |
|
|
|
mine |
maximal_information_based_nonparametric_exploration |
Maximal Information-based Nonparametric Exploration |
2014-07-28 |
|
0.0.1 |
MINE |
|
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
7 |
9 |
7 |
12 |
7 |
22 |
20 |
68 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
80 |
27 |
31 |
14 |
|
|
|
minipolish |
minipolish |
Polishing miniasm assemblies |
2022-10-19 |
https://github.com/rrwick/Minipolish |
0.2.0 |
minipolish |
0.2.0 |
Up-to-date |
Sequence Analysis |
Localised reassembly, Read depth analysis |
Localised reassembly, Read depth analysis |
Sequence assembly, Sequencing |
Sequence assembly, Sequencing |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/minipolish |
https://github.com/bgruening/galaxytools/tree/master/tools/minipolish |
minipolish |
minipolish |
A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
43 |
43 |
278 |
278 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
278 |
278 |
43 |
43 |
|
|
|
mitohifi |
mitohifi |
Assembly mitogenomes from Pacbio HiFi read. |
2021-05-29 |
https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 |
3.2.3 |
|
|
To update |
Assembly |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi |
https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
265 |
265 |
1632 |
1632 |
177 |
177 |
1198 |
1198 |
45 |
45 |
983 |
983 |
0 |
0 |
0 |
0 |
3813 |
3813 |
487 |
487 |
https://usegalaxy.eu/published/workflow?id=2062c7e1c50b05f3, https://usegalaxy.eu/published/workflow?id=32a0c4bbe6f9add9, https://usegalaxy.eu/published/workflow?id=c0c8228673b7191f, https://usegalaxy.eu/published/workflow?id=e71ae1076d5f0584, https://usegalaxy.org.au/published/workflow?id=2f49a0a03d99c57a, https://usegalaxy.org.au/published/workflow?id=614898119cf0dabf, https://usegalaxy.org.au/published/workflow?id=8004dce1906ec057, https://usegalaxy.org.au/published/workflow?id=fc74419b109527b2, https://usegalaxy.org/published/workflow?id=40be58638e230ab5, https://usegalaxy.org/published/workflow?id=5f621330d6339655, https://usegalaxy.org/published/workflow?id=67b9046dc5dbc009, https://usegalaxy.org/published/workflow?id=982a3eb2b4c4f5ae, https://workflowhub.eu/workflows/1648?version=1, https://workflowhub.eu/workflows/738?version=4 |
assembly/mitochondrion-assembly |
|
molecule_to_gspan |
bg_mol2gspan |
converter |
2015-02-28 |
https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan |
0.2 |
openbabel |
2.3.90dev7d621d9 |
To update |
Convert Formats |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan |
https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
motus |
mereg_mOTUs_tables, motus_profiler |
Tool for profiling the abundance of microbial taxa. |
2024-09-06 |
https://github.com/motu-tool/mOTUs |
3.1.0 |
motus |
3.1.0 |
Up-to-date |
Metagenomics |
Taxonomic classification |
Taxonomic classification |
Metagenomics |
Metagenomics |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs |
https://github.com/bgruening/galaxytools/tree/master/tools/motus |
mOTUs |
Metagenomic operational taxonomic units (mOTUs) |
Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall. |
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
40 |
40 |
377 |
377 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
377 |
377 |
40 |
40 |
|
|
|
mqc |
mqc |
Ribosome profiling mapping quality control tool |
2017-08-11 |
https://github.com/Biobix/mQC |
1.9 |
mqc |
1.10 |
To update |
Sequence Analysis |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
8 |
11 |
45 |
81 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
81 |
45 |
11 |
8 |
|
|
|
multispecies_orthologous_microsats |
multispecies_orthologous_microsats |
Extract orthologous microsatellites |
2013-09-25 |
|
1.0.0 |
bx-sputnik |
|
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
mummer |
mummerplot_wrapper |
Draw dotplots using mummer, mucmer, or promer with mummerplot |
2014-05-22 |
http://mummer.sourceforge.net/ |
0.0.8 |
ghostscript |
9.18 |
To update |
Graphics, Sequence Analysis, Visualization |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer |
https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
265 |
299 |
1105 |
1224 |
308 |
308 |
1031 |
1031 |
15 |
49 |
48 |
202 |
1 |
1 |
3 |
3 |
2460 |
2187 |
657 |
589 |
|
|
|
music |
music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution |
Multi-subject Single Cell deconvolution (MuSiC) |
2021-09-12 |
https://github.com/xuranw/MuSiC |
0.1.1 |
music-deconvolution |
0.1.1 |
Up-to-date |
Transcriptomics, Single Cell |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution |
https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution |
music_deconvolution |
MuSiC Deconvolution |
MuSiC utilizes cell-type specific gene expression from single-cell RNA sequencing (RNA-seq) data to characterize cell type compositions from bulk RNA-seq data in complex tissues. By appropriate weighting of genes showing cross-subject and cross-cell consistency, MuSiC enables the transfer of cell type-specific gene expression information from one dataset to another. |
|
0 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
117 |
117 |
4406 |
4406 |
57 |
57 |
652 |
652 |
11 |
11 |
2332 |
2332 |
0 |
0 |
0 |
0 |
7390 |
7390 |
185 |
185 |
https://usegalaxy.eu/published/workflow?id=030e978022e19375, https://usegalaxy.eu/published/workflow?id=2ae4a83327615155, https://usegalaxy.eu/published/workflow?id=39dd6365ff076dc4, https://usegalaxy.eu/published/workflow?id=cb978151b1686b71, https://usegalaxy.eu/published/workflow?id=d1ab8eabcbe0a004, https://workflowhub.eu/workflows/1498?version=1, https://workflowhub.eu/workflows/1542?version=1, https://workflowhub.eu/workflows/1548?version=1, https://workflowhub.eu/workflows/1553?version=1, https://workflowhub.eu/workflows/1557?version=1, https://workflowhub.eu/workflows/1575?version=1 |
single-cell/bulk-deconvolution-evaluate, single-cell/bulk-music, single-cell/bulk-music-2-preparescref, single-cell/bulk-music-3-preparebulk, single-cell/bulk-music-4-compare |
|
mutate_snp_codon |
mutate_snp_codon_1 |
Mutate Codons with SNPs |
2013-09-25 |
|
1.0.0 |
|
|
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
4 |
5 |
8 |
49 |
16 |
122 |
27 |
424 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
473 |
35 |
127 |
20 |
https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4 |
|
|
nanopolish |
nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants |
Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. |
2018-05-28 |
https://github.com/jts/nanopolish |
0.14.0 |
nanopolish |
0.14.0 |
Up-to-date |
|
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish |
https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish |
|
|
|
|
0 |
4 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
4 |
88 |
108 |
8229 |
9899 |
0 |
0 |
0 |
0 |
16 |
17 |
2510 |
3015 |
4 |
4 |
75 |
75 |
12989 |
10814 |
129 |
108 |
https://usegalaxy.eu/published/workflow?id=1cc3b4f1b50ba427, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d, https://usegalaxy.eu/published/workflow?id=816815a93cc68244, https://usegalaxy.eu/published/workflow?id=b2dfa74f55a73409, https://workflowhub.eu/workflows/50?version=1, https://workflowhub.eu/workflows/51?version=1 |
|
|
nastiseq |
nastiseq |
A method to identify cis-NATs using ssRNA-seq |
2017-02-21 |
https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ |
1.0 |
r-nastiseq |
1.0 |
Up-to-date |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2 |
2 |
42 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
42 |
2 |
2 |
1 |
|
|
|
netboxr |
netboxr |
netboxr enables automated discovery of biological process modules by network analysis |
2022-08-24 |
|
1.6.0 |
bioconductor-netboxr |
1.9.0 |
To update |
Systems Biology |
|
|
|
|
bgruening |
|
https://github.com/bgruening/galaxytools/tree/master/tools/netboxr |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
11 |
11 |
28 |
28 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
28 |
28 |
11 |
11 |
|
|
|
nextdenovo |
nextdenovo |
String graph-based de novo assembler for long reads |
2023-02-09 |
https://github.com/Nextomics/NextDenovo |
2.5.0 |
nextdenovo |
2.5.2 |
To update |
Assembly |
De-novo assembly, Genome assembly |
De-novo assembly, Genome assembly |
Sequencing, Sequence assembly |
Sequencing, Sequence assembly |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo |
https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo |
nextdenovo |
NextDenovo |
NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
252 |
252 |
703 |
703 |
111 |
111 |
265 |
265 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
968 |
968 |
363 |
363 |
https://workflowhub.eu/workflows/789?version=1 |
|
|
nlstradamus |
nlstradamus |
Find nuclear localization signals (NLSs) in protein sequences |
2013-04-17 |
http://www.moseslab.csb.utoronto.ca/NLStradamus |
0.0.11 |
NLStradamus |
1.8 |
To update |
Fasta Manipulation, Sequence Analysis |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus |
https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
nucleosome_prediction |
Nucleosome |
Prediction of Nucleosomes Positions on the Genome |
2016-09-27 |
https://genie.weizmann.ac.il/software/nucleo_exe.html |
3.0 |
nucleosome_prediction |
3.0 |
Up-to-date |
Sequence Analysis |
Prediction and recognition, Nucleosome position prediction, Sequence analysis |
Prediction and recognition, Nucleosome position prediction, Sequence analysis |
Structural genomics, Nucleic acid sites, features and motifs |
Structural genomics, Nucleic acid sites, features and motifs |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction |
https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction |
nucleosome_prediction |
nucleosome_prediction |
Prediction of Nucleosomes Positions on the Genome |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
12 |
27 |
20 |
866 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
866 |
20 |
27 |
12 |
|
|
|
numeric_clustering |
numeric_clustering |
Clustering tool for numberic values |
2015-12-19 |
http://scikit-learn.org/stable/index.html |
0.9 |
anaconda |
|
To update |
Statistics |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering |
https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
11 |
1 |
486 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
4 |
4 |
490 |
5 |
14 |
4 |
|
|
|
openms |
AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter |
OpenMS in version 2.1. |
2015-02-28 |
|
2.1.0 |
openms |
3.4.1 |
To update |
Proteomics |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/openms |
https://github.com/bgruening/galaxytools/tree/master/tools/openms |
|
|
|
|
0 |
34 |
135 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
19 |
135 |
134 |
583 |
698 |
30109 |
114383 |
10 |
10 |
417 |
417 |
33 |
34 |
1321 |
1325 |
0 |
0 |
0 |
0 |
116125 |
31847 |
742 |
626 |
https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=68edbb8eec38ad00, https://usegalaxy.eu/published/workflow?id=7463b26aab6a965d, https://usegalaxy.eu/published/workflow?id=86d50bbaaa3936dc, https://usegalaxy.eu/published/workflow?id=afb138fc03ca61a8, https://usegalaxy.eu/published/workflow?id=d55df785d4c71876, https://usegalaxy.eu/published/workflow?id=da10c475c83c5469, https://usegalaxy.eu/published/workflow?id=e9e41c23261d4ac5, https://usegalaxy.eu/published/workflow?id=eaf4d8f8fb3e683d, https://usegalaxy.org.au/published/workflow?id=03efeb2948494130, https://usegalaxy.org.au/published/workflow?id=236e0f306916149b, https://usegalaxy.org.au/published/workflow?id=33922db405a97cbb, https://usegalaxy.org.au/published/workflow?id=59c9a6efaf57ce35, https://usegalaxy.org.au/published/workflow?id=65a659982f955743, https://usegalaxy.org.au/published/workflow?id=7cddb345877f08bf, https://usegalaxy.org.au/published/workflow?id=88fa3e250db2d70e, https://usegalaxy.org.au/published/workflow?id=c2f449e69d06ccf5, https://usegalaxy.org.au/published/workflow?id=da79aa2dfd6b34bc, https://usegalaxy.org/published/workflow?id=0775ff66d1bc04b5, https://usegalaxy.org/published/workflow?id=9865fee6c68fc201, https://usegalaxy.org/published/workflow?id=f9048d9678e21f36, https://workflowhub.eu/workflows/1394?version=1, https://workflowhub.eu/workflows/1399?version=1, https://workflowhub.eu/workflows/1421?version=1, https://workflowhub.eu/workflows/1424?version=1, https://workflowhub.eu/workflows/1434?version=1, https://workflowhub.eu/workflows/1438?version=1, https://workflowhub.eu/workflows/1446?version=1, https://workflowhub.eu/workflows/1449?version=1, https://workflowhub.eu/workflows/1452?version=1, https://workflowhub.eu/workflows/1463?version=1, https://workflowhub.eu/workflows/613?version=2 |
proteomics/DIA_Analysis_OSW, proteomics/DIA_lib_OSW, proteomics/database-handling, proteomics/ntails, proteomics/protein-id-oms, proteomics/protein-id-sg-ps, proteomics/protein-quant-sil |
|
pandas_rolling_window |
pandas_rolling_window |
Rolling window calculations |
2019-05-20 |
https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html |
0.1 |
numpy |
|
To update |
Statistics |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window |
https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
12 |
14 |
115 |
288 |
25 |
25 |
68 |
68 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
356 |
183 |
39 |
37 |
|
|
|
paralyzer |
paralyzer |
A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. |
2016-12-02 |
https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ |
1.5 |
paralyzer |
1.5 |
Up-to-date |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
19 |
29 |
256 |
358 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
358 |
256 |
29 |
19 |
https://usegalaxy.eu/published/workflow?id=a108b575b16e6cb9 |
|
|
partialr_square |
partialRsq |
Compute partial R square |
2014-04-01 |
|
1.0.0 |
R |
|
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
44 |
15 |
144 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
144 |
15 |
44 |
8 |
|
|
|
peakachu |
peakachu |
PEAKachu is a peak-caller for CLIP- and RIP-Seq data |
2018-01-30 |
|
0.2.0+galaxy1 |
peakachu |
0.2.0 |
To update |
Sequence Analysis, RNA |
|
|
|
|
rnateam |
https://github.com/tbischler/PEAKachu |
https://github.com/bgruening/galaxytools/tree/master/tools/peakachu |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
176 |
217 |
2688 |
3707 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3707 |
2688 |
217 |
176 |
https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c, https://workflowhub.eu/workflows/1706?version=1 |
transcriptomics/clipseq |
|
pearson_correlation |
Pearson_and_apos_Correlation1 |
Pearson and apos Correlation between any two numeric columns |
2014-07-28 |
|
1.0.0 |
|
|
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
2 |
0 |
0 |
0 |
0 |
2 |
0 |
2 |
0 |
|
|
|
pfamscan |
pfamscan |
Search a FASTA sequence against a library of Pfam HMM. |
2023-02-02 |
http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ |
1.6 |
pfam_scan |
1.6 |
Up-to-date |
Sequence Analysis |
Protein sequence analysis |
Protein sequence analysis |
Sequence analysis |
Sequence analysis |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan |
https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan |
pfamscan |
PfamScan |
This tool is used to search a FASTA sequence against a library of Pfam HMM. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
146 |
146 |
7522 |
7522 |
143 |
143 |
881 |
881 |
33 |
33 |
545 |
545 |
1 |
1 |
1 |
1 |
8949 |
8949 |
323 |
323 |
https://usegalaxy.eu/published/workflow?id=11eba1b28ec87963, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://workflowhub.eu/workflows/1688?version=1 |
transcriptomics/differential-isoform-expression |
|
pgsnp2gd_snp |
pgSnp2gd_snp |
Convert from pgSnp to gd_snp |
2014-07-28 |
|
1.0.0 |
|
|
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
pgtools |
pg_dump, pg_import, pg_query |
tool suite for dealing with Postgresql databases from Galaxy's history |
2017-09-28 |
https://www.postgresql.org |
|
postgresql |
|
To update |
Data Export, Data Source |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tools/pgtools |
https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
pharmcat |
pharmcat |
Pharmacogenomics Clinical Annotation Tool |
2022-01-28 |
https://pharmcat.org/ |
|
|
|
To update |
Variant Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat |
https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
41 |
41 |
163 |
163 |
108 |
108 |
331 |
331 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
494 |
494 |
149 |
149 |
|
|
|
pileometh |
pileometh |
A tool for processing bisulfite sequencing alignments |
2017-02-14 |
https://github.com/dpryan79/MethylDackel |
0.5.2 |
methyldackel |
0.6.1 |
To update |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel |
https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
662 |
1068 |
18187 |
25413 |
475 |
475 |
12892 |
12892 |
124 |
124 |
3414 |
3430 |
1 |
1 |
3 |
3 |
41738 |
34496 |
1668 |
1262 |
https://usegalaxy.eu/published/workflow?id=489926f9299594fe, https://usegalaxy.eu/published/workflow?id=bffeb3cd0c708441, https://usegalaxy.eu/published/workflow?id=c46345ba876d5bfe, https://usegalaxy.org.au/published/workflow?id=91c8daa5f2bcf7c0, https://usegalaxy.org/published/workflow?id=e20e1371e50bdcee, https://usegalaxy.org/published/workflow?id=eb4f7dbca0114270, https://workflowhub.eu/workflows/1566?version=1 |
epigenetics/methylation-seq |
|
pileup_interval |
pileup_interval |
Pileup-to-Interval condenses pileup format into ranges of bases |
2015-03-06 |
|
1.0.3 |
bx-python |
0.14.0 |
To update |
SAM |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
51 |
68 |
145 |
687 |
183 |
1591 |
1254 |
7973 |
19 |
31 |
685 |
966 |
1 |
1 |
2 |
2 |
9628 |
2086 |
1691 |
254 |
https://usegalaxy.org/published/workflow?id=0b3af7e9ac69a6b7 |
|
|
pileup_parser |
pileup_parser |
Filter pileup on coverage and SNPs |
2013-08-26 |
https://github.com/galaxyproject/tools-devteam/ |
1.0.2 |
perl |
|
To update |
SAM |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
473 |
547 |
3396 |
4352 |
1121 |
4651 |
7364 |
53190 |
143 |
332 |
1908 |
2971 |
4 |
4 |
196 |
196 |
60709 |
12864 |
5534 |
1741 |
https://usegalaxy.eu/published/workflow?id=36a4646959829018, https://usegalaxy.eu/published/workflow?id=99022559adf01c4a, https://usegalaxy.org.au/published/workflow?id=83c20d8e5fd97313, https://usegalaxy.org/published/workflow?id=0b3af7e9ac69a6b7, https://usegalaxy.org/published/workflow?id=11dac9cba49be089, https://usegalaxy.org/published/workflow?id=26d2c2d51d6a7158, https://usegalaxy.org/published/workflow?id=31dea5361ec9421c, https://usegalaxy.org/published/workflow?id=34ed5c1ceeed43c1, https://usegalaxy.org/published/workflow?id=4339d5625c15ae78, https://usegalaxy.org/published/workflow?id=558c28293ec2d239, https://usegalaxy.org/published/workflow?id=578f46106f72c971, https://usegalaxy.org/published/workflow?id=6c68099053763993, https://usegalaxy.org/published/workflow?id=7c3faadda8f89749, https://usegalaxy.org/published/workflow?id=80fa8f0fe6330b88, https://usegalaxy.org/published/workflow?id=c7aca0f5bb660907, https://usegalaxy.org/published/workflow?id=e8b1d1e5e889c986 |
|
|
pipmir |
pipmir |
A method to identify novel plant miRNA. |
2016-11-25 |
https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ |
0.1.0 |
pipmir |
1.1 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
43 |
54 |
296 |
385 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
385 |
296 |
54 |
43 |
|
|
|
piranha |
piranha |
Piranha is a peak-caller for CLIP- and RIP-Seq data |
2015-07-02 |
|
1.2.1.0 |
piranha |
1.2.1 |
To update |
Sequence Analysis, RNA |
|
|
|
|
rnateam |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha |
https://github.com/bgruening/galaxytools/tree/master/tools/piranha |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
90 |
128 |
1127 |
2135 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2135 |
1127 |
128 |
90 |
https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf |
|
|
platypus |
bg_platypus |
efficient and accurate variant-detection in high-throughput sequencing data |
2015-02-28 |
http://www.well.ox.ac.uk/platypus |
0.0.11 |
platypus |
|
To update |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/platypus |
https://github.com/bgruening/galaxytools/tree/master/tools/platypus |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
plot_from_lda |
plot_for_lda_output1 |
Draw ROC plot on "Perform LDA" output |
2014-07-28 |
|
1.0.1 |
R |
|
To update |
Graphics, Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
14 |
26 |
23 |
78 |
40 |
355 |
91 |
919 |
7 |
10 |
98 |
155 |
3 |
3 |
3 |
3 |
1155 |
215 |
394 |
64 |
|
|
|
plotly_ml_performance_plots |
plotly_ml_performance_plots |
performance plots for machine learning problems |
2018-10-11 |
http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics |
0.4 |
galaxy-ml |
0.10.0 |
To update |
Visualization |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots |
https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
212 |
271 |
1209 |
1809 |
183 |
197 |
1178 |
1393 |
26 |
29 |
770 |
906 |
0 |
0 |
0 |
0 |
4108 |
3157 |
497 |
421 |
https://usegalaxy.eu/published/workflow?id=1d55d5d20c581b16, https://usegalaxy.eu/published/workflow?id=77fa6e5a8fa3f911, https://usegalaxy.eu/published/workflow?id=fdbf1a1a584a429c, https://usegalaxy.org.au/published/workflow?id=517f947adc81a16a, https://usegalaxy.org.au/published/workflow?id=bfd7ed2abc95b53d, https://usegalaxy.org/published/workflow?id=0cf9868ebc9ec1dc, https://usegalaxy.org/published/workflow?id=728ce1ce56c4d3da, https://workflowhub.eu/workflows/1588?version=1, https://workflowhub.eu/workflows/1592?version=1 |
statistics/classification_machinelearning, statistics/classification_regression |
|
plotly_parallel_coordinates_plot |
plotly_parallel_coordinates_plot |
parallel coordinates plot produced with plotly |
2018-09-23 |
https://plot.ly/python/parallel-coordinates-plot/ |
0.2 |
python |
|
To update |
Visualization |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot |
https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
76 |
125 |
155 |
670 |
99 |
129 |
539 |
690 |
25 |
29 |
671 |
745 |
0 |
0 |
0 |
0 |
2105 |
1365 |
283 |
200 |
https://usegalaxy.eu/published/workflow?id=83fe480cdbb70099, https://usegalaxy.eu/published/workflow?id=c15303fcc0b53df6, https://usegalaxy.org.au/published/workflow?id=92b5a29a956a3afc, https://workflowhub.eu/workflows/1722?version=1 |
statistics/age-prediction-with-ml |
|
plotly_regression_performance_plots |
plotly_regression_performance_plots |
performance plots for regression problems |
2018-10-30 |
http://scikit-learn.org/stable/supervised_learning.html#supervised-learning |
0.1 |
python |
|
To update |
Visualization |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots |
https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
203 |
301 |
625 |
1074 |
134 |
145 |
555 |
606 |
30 |
32 |
239 |
273 |
0 |
0 |
0 |
0 |
1953 |
1419 |
478 |
367 |
https://usegalaxy.eu/published/workflow?id=138d4893a1d6228e, https://usegalaxy.eu/published/workflow?id=4b383d13ff512687, https://usegalaxy.eu/published/workflow?id=a669986e1a5cee31, https://usegalaxy.eu/published/workflow?id=a824fb7e65a1a939, https://usegalaxy.org.au/published/workflow?id=350433eefb835f19, https://usegalaxy.org.au/published/workflow?id=65a8ac91d6ded9a2, https://usegalaxy.org.au/published/workflow?id=697945d5f9edbf39, https://usegalaxy.org.au/published/workflow?id=cebab4f1a2405a89, https://usegalaxy.org/published/workflow?id=1c579fc1fe256993, https://workflowhub.eu/workflows/1583?version=1, https://workflowhub.eu/workflows/1596?version=1, https://workflowhub.eu/workflows/1633?version=1, https://workflowhub.eu/workflows/1721?version=1 |
statistics/FNN, statistics/age-prediction-with-ml, statistics/classification_regression, statistics/regression_machinelearning |
|
poisson2test |
poisson2test |
Poisson two-sample test |
2014-01-27 |
https://bitbucket.org/natefoo/taxonomy |
1.0.0 |
taxonomy |
0.10.1 |
To update |
Statistics, Metagenomics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
14 |
18 |
36 |
122 |
1 |
140 |
4 |
562 |
6 |
8 |
328 |
437 |
0 |
0 |
0 |
0 |
1121 |
368 |
166 |
21 |
|
|
|
predictnls |
predictnls |
Python reimplementation of predictNLS for Galaxy |
2013-09-23 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls |
0.0.10 |
|
|
To update |
Sequence Analysis |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls |
https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
principal_component_analysis |
pca1 |
Principal Component Analysis |
2014-05-19 |
|
1.0.2 |
rpy |
|
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
194 |
270 |
9535 |
10108 |
519 |
1543 |
2512 |
8331 |
0 |
0 |
0 |
0 |
16 |
16 |
44 |
44 |
18483 |
12091 |
1829 |
729 |
https://usegalaxy.org/published/workflow?id=13a550ed56b56502, https://usegalaxy.org/published/workflow?id=7ca9c5203520ca7e, https://usegalaxy.org/published/workflow?id=e10859cc568da07c |
|
|
protease_prediction |
eden_protease_prediction |
This tool can learn the cleavage specificity of a given class of proteases. |
2016-03-13 |
https://github.com/fabriziocosta/eden |
0.9 |
eden |
2.0 |
To update |
Sequence Analysis, Proteomics |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction |
https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
18 |
26 |
37 |
168 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
168 |
37 |
26 |
18 |
|
|
|
protein_properties |
bg_protein_properties |
Calculation of various properties from given protein sequences |
2015-06-07 |
|
0.2.0 |
biopython |
1.70 |
To update |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties |
https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
99 |
123 |
497 |
720 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
720 |
497 |
123 |
99 |
|
|
|
proteomics_improviser |
proteomics_improviser |
Visualisation of PepXML files |
2015-02-28 |
http://www.improviser.uni-freiburg.de/ |
1.1.0.1 |
|
|
To update |
Proteomics |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser |
https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
pubchem_rest_tool |
pubchem_rest_tool |
This tool fetches data from pubchem via the PubChem REST API. |
2015-02-28 |
https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html |
0.1.0 |
|
|
To update |
Data Source |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool |
https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
qiime2_dbotu_q2 |
qiime2_dbotu_q2 |
q2-dbotu is a Qiime 2 plugin for performing OTU clustering |
2025-03-20 |
https://github.com/cduvallet/q2-dbotu/tree/master |
2022.11.1+galaxy0 |
|
|
To update |
Metagenomics |
Demultiplexing, Visualisation, Taxonomic classification |
Demultiplexing, Visualisation, Taxonomic classification |
Microbial ecology, Metatranscriptomics, Metagenomics |
Microbial ecology, Metatranscriptomics, Metagenomics |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/qiime2_dbotu_q2/ |
https://github.com/bgruening/galaxytools/tree/master/tools/qiime2_dbotu_q2 |
qiime2 |
QIIME 2 |
QIIME 2 is an AI-ready microbiome multi-omics data science platform that is trusted, free, open source, extensible, and community developed and supported bioinformatics. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
13 |
13 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
13 |
13 |
7 |
7 |
|
|
|
quality_filter |
qualityFilter |
Filter nucleotides based on quality scores |
2014-04-01 |
|
1.0.1 |
bx-python |
0.14.0 |
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
32 |
62 |
56 |
724 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
724 |
56 |
62 |
32 |
|
|
|
racon |
racon |
Consensus module for raw de novo DNA assembly of long uncorrected reads. |
2018-06-11 |
https://github.com/isovic/racon |
1.5.0 |
racon |
1.5.0 |
Up-to-date |
Sequence Analysis |
Genome assembly, Mapping assembly |
Genome assembly, Mapping assembly |
Whole genome sequencing, Sequence assembly |
Whole genome sequencing, Sequence assembly |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/racon |
https://github.com/bgruening/galaxytools/tree/master/tools/racon |
Racon |
Racon |
Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1046 |
1151 |
32503 |
37525 |
683 |
683 |
23074 |
23074 |
263 |
268 |
9144 |
9214 |
31 |
31 |
320 |
320 |
70133 |
65041 |
2133 |
2023 |
https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=8b2f53745e720d0f, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a4f50449afde4a05, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=0c421197e022f323, https://usegalaxy.org.au/published/workflow?id=1ff6aabb7e3954ac, https://usegalaxy.org.au/published/workflow?id=45e9910f46a210d8, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=bcdc5ce2ea8700fc, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/1599?version=1, https://workflowhub.eu/workflows/1604?version=1, https://workflowhub.eu/workflows/227?version=1, https://workflowhub.eu/workflows/228?version=1, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/51?version=1, https://workflowhub.eu/workflows/563?version=1 |
assembly/largegenome, microbiome/plasmid-metagenomics-nanopore |
|
rbpbench |
rbpbench |
Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs |
2023-12-03 |
https://github.com/michauhl/RBPBench |
0.8.1 |
rbpbench |
1.0.6 |
To update |
Sequence Analysis, RNA, CLIP-seq |
|
|
RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis |
RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis |
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench |
rbpbench |
RBPBench |
Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
135 |
135 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
135 |
135 |
12 |
12 |
|
|
|
rcas |
rcas |
RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments |
2017-04-13 |
https://github.com/BIMSBbioinfo/RCAS |
1.5.4 |
bioconductor-rcas |
1.32.0 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
89 |
110 |
718 |
1316 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1316 |
718 |
110 |
89 |
https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c, https://workflowhub.eu/workflows/1706?version=1 |
transcriptomics/clipseq |
|
rcve |
rcve1 |
Compute RCVE |
2014-04-01 |
|
1.0.0 |
R |
|
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
46 |
8 |
193 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
193 |
8 |
46 |
5 |
|
|
|
reago |
reago |
Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. |
2015-12-09 |
https://github.com/chengyuan/reago-1.1 |
1.1 |
reago |
1.1 |
Up-to-date |
Metagenomics, RNA |
Sequence assembly |
Sequence assembly |
Sequence assembly, RNA, Metagenomics, Microbiology |
Sequence assembly, RNA, Metagenomics, Microbiology |
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago |
reago |
REAGO |
This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
18 |
18 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
18 |
18 |
7 |
7 |
|
|
|
remove_beginning |
Remove beginning1 |
Remove lines from the beginning of a file. |
2012-12-04 |
|
1.0.0 |
|
|
To update |
Text Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning |
|
|
|
|
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
1 |
0 |
1 |
0 |
1 |
1 |
1 |
4474 |
5036 |
261403 |
289906 |
4475 |
9406 |
45067 |
126317 |
1866 |
2086 |
15994 |
17542 |
295 |
297 |
1881 |
1952 |
435717 |
324345 |
16825 |
11110 |
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https://workflowhub.eu/workflows/1884?version=1, https://workflowhub.eu/workflows/1953?version=1, https://workflowhub.eu/workflows/659?version=1, https://workflowhub.eu/workflows/660?version=1, https://workflowhub.eu/workflows/876?version=1 |
data-science/data-manipulation-olympics, digital-humanities/introduction_to_dh, digital-humanities/open-refine-tutorial, ecology/biodiversity-data-exploration, ecology/regionalGAM, epigenetics/ewas-suite, galaxy-interface/workflow-reports, genome-annotation/bacterial-comparative-genomics-dataset-construction, genome-annotation/secondary-metabolite-discovery, introduction/data-manipulation-olympics, introduction/galaxy-intro-101-everyone, introduction/galaxy-reproduce, microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-3-verification, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-3-verification, proteomics/metaquantome-data-creation, proteomics/neoantigen-fragpipe-discovery, proteomics/neoantigen-hla-binding-novel-peptides, sequence-analysis/tapscan-streptophyte-algae, single-cell/bulk-deconvolution-evaluate, statistics/classification_machinelearning, statistics/regression_machinelearning, transcriptomics/differential-isoform-expression, visualisation/circos |
|
remurna |
remurna |
remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation |
2016-11-24 |
https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna |
1.0.0 |
remurna |
1.0 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
8 |
10 |
38 |
71 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
71 |
38 |
10 |
8 |
|
|
|
repeat_masker |
repeatmasker_wrapper |
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. |
2015-02-28 |
http://www.repeatmasker.org/ |
0.1.2 |
RepeatMasker |
4.2.1 |
To update |
Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker |
https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1428 |
1448 |
10157 |
10293 |
1181 |
1219 |
9955 |
10202 |
413 |
413 |
4594 |
4594 |
91 |
91 |
610 |
610 |
25699 |
25316 |
3171 |
3113 |
https://usegalaxy.eu/published/workflow?id=09c534f738426a6d, https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=4a71a1e08a4a8e61, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.eu/published/workflow?id=f9279495683a8ac3, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=a71349ba0bff403a, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org.au/published/workflow?id=ffb1117077f68a9f, https://usegalaxy.org/published/workflow?id=effc17e170263ae6, https://usegalaxy.org/published/workflow?id=f2f633d2b02b6050, https://usegalaxy.org/published/workflow?id=fb8b997f516288e1, https://workflowhub.eu/workflows/1538?version=2, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1, https://workflowhub.eu/workflows/575?version=1, https://workflowhub.eu/workflows/753?version=1, https://workflowhub.eu/workflows/875?version=3 |
ecology/phylogeny-data-prep, genome-annotation/repeatmasker |
|
replace_column_by_key_value_file |
replace_column_with_key_value_file |
A tool to replace all column entries of a file given by values of a key-value file. |
2017-02-24 |
|
0.2 |
|
|
To update |
Text Manipulation |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn |
https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
511 |
584 |
578207 |
578456 |
301 |
444 |
42494 |
44816 |
118 |
118 |
2392 |
2400 |
12 |
12 |
2149 |
2149 |
627821 |
625242 |
1158 |
942 |
https://usegalaxy.eu/published/workflow?id=036990ecf300a99f, https://usegalaxy.eu/published/workflow?id=05bd1d9c61df5d16, https://usegalaxy.eu/published/workflow?id=0c94260298199d8b, https://usegalaxy.eu/published/workflow?id=20592f292c205954, https://usegalaxy.eu/published/workflow?id=27fca972f1d1a312, https://usegalaxy.eu/published/workflow?id=2d509fad86eb97fb, https://usegalaxy.eu/published/workflow?id=37b04b02ec08e84f, https://usegalaxy.eu/published/workflow?id=4ddf2ec5c460d622, https://usegalaxy.eu/published/workflow?id=6e0330de5d80e619, https://usegalaxy.eu/published/workflow?id=70ec8b1719e25982, https://usegalaxy.eu/published/workflow?id=88f5cef7e4146520, https://usegalaxy.eu/published/workflow?id=9eb29cc96d8d75c2, https://usegalaxy.eu/published/workflow?id=e4e969e9943cdaa5, https://usegalaxy.eu/published/workflow?id=eb03839cc36048f5, https://usegalaxy.fr/published/workflow?id=798c8ff19825ab2c, https://usegalaxy.fr/published/workflow?id=b168a179d1b456cb, https://usegalaxy.org.au/published/workflow?id=1764bb1f506212e8, https://usegalaxy.org.au/published/workflow?id=1782d699b0166725, https://usegalaxy.org.au/published/workflow?id=5a975438c8752269, https://usegalaxy.org.au/published/workflow?id=7a0b3968968c5994, https://usegalaxy.org.au/published/workflow?id=7cc2b5010c56f117, https://usegalaxy.org.au/published/workflow?id=800d28ec61b15244, https://usegalaxy.org.au/published/workflow?id=8e2b94c6fbf44368, https://usegalaxy.org.au/published/workflow?id=91c8daa5f2bcf7c0, https://usegalaxy.org.au/published/workflow?id=989eb73372135796, https://usegalaxy.org.au/published/workflow?id=b601f48ecec15bf4, https://usegalaxy.org.au/published/workflow?id=b920b02a23f94d11, https://usegalaxy.org.au/published/workflow?id=d0d6743450e5060d, https://usegalaxy.org.au/published/workflow?id=fbc732db2a2821b0, https://usegalaxy.org/published/workflow?id=07e761b2501971c6, https://usegalaxy.org/published/workflow?id=2967ef82911f2cca, https://usegalaxy.org/published/workflow?id=2b09f3c9465ee054, https://usegalaxy.org/published/workflow?id=2dceaa255cc8cf83, https://usegalaxy.org/published/workflow?id=6c2bb2209aad5e44, https://usegalaxy.org/published/workflow?id=7af656b8ea5e7e2e, https://usegalaxy.org/published/workflow?id=8a01c78688beae1d, https://usegalaxy.org/published/workflow?id=dcbc71347300822d, https://usegalaxy.org/published/workflow?id=f58c90061c31bd48, https://usegalaxy.org/published/workflow?id=ff3ade25b35f4893, https://workflowhub.eu/workflows/1077?version=1, https://workflowhub.eu/workflows/109?version=9, https://workflowhub.eu/workflows/1551?version=1, https://workflowhub.eu/workflows/1566?version=1 |
epigenetics/methylation-seq, single-cell/scatac-standard-processing-snapatac2 |
|
ribotaper |
ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling |
A method for defining traslated ORFs using Ribosome Profiling data. |
2016-06-07 |
https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ |
1.3.1a |
ribotaper |
1.3.1 |
To update |
RNA |
Gene expression profiling |
Gene expression profiling |
Functional genomics |
Functional genomics |
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper |
ribotaper |
RiboTaper |
New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. |
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
33 |
38 |
595 |
798 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
798 |
595 |
38 |
33 |
|
|
|
rmap |
rmap_wrapper |
RMAP for Solexa Short Reads Alignment |
2014-05-19 |
|
1.0.0 |
rmap |
2.1 |
To update |
Next Gen Mappers |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
rmapq |
rmapq_wrapper |
RMAPQ for Solexa Short Reads Alignment with Quality Scores |
2014-05-19 |
|
1.0.0 |
rmap |
2.1 |
To update |
Next Gen Mappers |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
rnabob |
rbc_rnabob |
Fast pattern searching for RNA structural motifs |
2015-02-28 |
http://eddylab.org/software.html |
2.2.1.0 |
rnabob |
2.2.1 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
10 |
14 |
55 |
206 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
206 |
55 |
14 |
10 |
|
|
|
rnacode |
rbc_rnacode |
Analyze the protein coding potential in MSA |
2015-06-16 |
|
0.3.2 |
rnacode |
0.3 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
12 |
35 |
31 |
1363 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1363 |
31 |
35 |
12 |
https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1 |
|
|
rnacommender |
rbc_rnacommender |
RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. |
2016-05-31 |
https://github.com/gianlucacorrado/RNAcommender |
0.1.1 |
sam |
3.5 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
17 |
23 |
31 |
1083 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1083 |
31 |
23 |
17 |
|
|
|
rnaformer |
infer_rnaformer |
RNAformer: RNA secondary structure prediction |
2024-07-11 |
https://github.com/automl/RNAformer |
1.2.0 |
rnaformer |
|
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
24 |
24 |
112 |
112 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
112 |
112 |
24 |
24 |
|
|
|
rnalien |
RNAlien |
RNAlien unsupervized RNA family model construction |
2017-03-07 |
http://rna.tbi.univie.ac.at/rnalien/ |
1.3.6 |
rnalien |
1.8.0 |
To update |
RNA, Sequence Analysis |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
8 |
14 |
22 |
34 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
34 |
22 |
14 |
8 |
https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1 |
|
|
rnashapes |
RNAshapes |
Compute secondary structures of RNA |
2015-02-28 |
|
3.3.0 |
@EXECUTABLE@ |
|
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
43 |
60 |
212 |
284 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
284 |
212 |
60 |
43 |
|
|
|
rnasnp |
rnasnp |
RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs |
2016-11-24 |
http://rth.dk/resources/rnasnp/ |
1.2.0 |
rnasnp |
1.2 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
16 |
24 |
46 |
100 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
100 |
46 |
24 |
16 |
|
|
|
rnaz |
rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window |
RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. |
2015-02-28 |
https://www.tbi.univie.ac.at/~wash/RNAz/ |
2.1.1 |
rnaz |
2.1.1 |
Up-to-date |
RNA |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz |
|
|
|
|
0 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
37 |
81 |
251 |
43350 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
43350 |
251 |
81 |
37 |
https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1 |
|
|
rrna |
meta_rna |
Identification of ribosomal RNA genes in metagenomic fragments. |
2015-02-28 |
http://weizhong-lab.ucsd.edu/meta_rna/ |
0.1 |
hmmsearch3.0 |
|
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rRNA |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
run_jupyter_job |
run_jupyter_job |
Run jupyter notebook script in Galaxy |
2021-12-11 |
|
0.0.1 |
|
|
To update |
Machine Learning |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job |
https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
33 |
33 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
33 |
33 |
3 |
3 |
|
|
|
sailfish |
sailfish |
Sailfish is a tool for transcript quantification from RNA-seq data |
2015-02-28 |
http://www.cs.cmu.edu/~ckingsf/software/sailfish/ |
0.10.1.1 |
bzip2 |
|
To update |
Sequence Analysis, RNA |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/sailfish |
https://github.com/bgruening/galaxytools/tree/master/tools/sailfish |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
161 |
230 |
3461 |
4740 |
487 |
1218 |
7744 |
15838 |
142 |
205 |
2781 |
3621 |
2 |
2 |
57 |
57 |
24256 |
14043 |
1655 |
792 |
https://usegalaxy.org/published/workflow?id=53834a5fb46ca0f6, https://usegalaxy.org/published/workflow?id=6dada297572d77bd |
|
|
salmon |
alevin, salmon, salmonquantmerge |
Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. |
2016-03-21 |
https://github.com/COMBINE-lab/salmon |
1.10.1 |
salmon |
1.10.3 |
To update |
Sequence Analysis, RNA, Transcriptomics, Single Cell |
Sequence composition calculation, RNA-Seq quantification, Gene expression analysis |
Sequence composition calculation, RNA-Seq quantification, Gene expression analysis |
RNA-Seq, Gene expression, Transcriptomics |
RNA-Seq, Transcriptomics |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/salmon |
https://github.com/bgruening/galaxytools/tree/master/tools/salmon |
salmon |
Salmon |
A tool for transcript expression quantification from RNA-seq data |
|
0 |
3 |
3 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
1 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
2199 |
2418 |
82278 |
93457 |
3368 |
5386 |
96508 |
145803 |
536 |
668 |
14784 |
19109 |
141 |
142 |
1347 |
1350 |
259719 |
194917 |
8614 |
6244 |
https://usegalaxy.eu/published/workflow?id=0d6bed63a2e4c3d6, https://usegalaxy.eu/published/workflow?id=1590085d315aa80e, https://usegalaxy.eu/published/workflow?id=1d2e17a4f71f2455, https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=1ffc058273ab357e, https://usegalaxy.eu/published/workflow?id=21dd4bd16579fc12, https://usegalaxy.eu/published/workflow?id=2a73d658446747de, https://usegalaxy.eu/published/workflow?id=2d2d0c2231babc50, https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=350d7e6976e15d30, https://usegalaxy.eu/published/workflow?id=48fe9c4de045d414, https://usegalaxy.eu/published/workflow?id=65aed668233d5f73, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=83ae28e23099a3f6, https://usegalaxy.eu/published/workflow?id=8bc1c3b9e665ea37, https://usegalaxy.eu/published/workflow?id=9a9bbd8046da7b19, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=dd8b55e7768843b1, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f28459c5b16549b7, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.org.au/published/workflow?id=13a2c5bd07705985, https://usegalaxy.org.au/published/workflow?id=3f45685df9b9e792, https://usegalaxy.org.au/published/workflow?id=954318db8c8d9219, https://usegalaxy.org.au/published/workflow?id=b0614274c66efa95, https://usegalaxy.org/published/workflow?id=07fdeadce7a6d5cb, https://usegalaxy.org/published/workflow?id=08bdcecd1cb0bda3, https://usegalaxy.org/published/workflow?id=092be3cf6e40282c, https://usegalaxy.org/published/workflow?id=0930f955bdac93e8, https://usegalaxy.org/published/workflow?id=173ecc0c88090d0e, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=228ae7f537a60226, https://usegalaxy.org/published/workflow?id=427fce51fd9508eb, https://usegalaxy.org/published/workflow?id=43c39bc86399188f, https://usegalaxy.org/published/workflow?id=5203bc68df3cf819, https://usegalaxy.org/published/workflow?id=6d0a3f36d2736087, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=82681bd5f059e39a, https://usegalaxy.org/published/workflow?id=93650de42fb8c015, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d, https://usegalaxy.org/published/workflow?id=a89def2c2462674a, https://usegalaxy.org/published/workflow?id=aac2ae0419f7d515, https://usegalaxy.org/published/workflow?id=b094b6e1e7d48416, https://usegalaxy.org/published/workflow?id=b1b75a9323d25085, https://usegalaxy.org/published/workflow?id=c2c6779a8b1821e0, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8, https://usegalaxy.org/published/workflow?id=dec0cf06fa059e65, https://workflowhub.eu/workflows/1533?version=1, https://workflowhub.eu/workflows/1537?version=1, https://workflowhub.eu/workflows/1676?version=1, https://workflowhub.eu/workflows/1717?version=2 |
single-cell/scrna-case_alevin, transcriptomics/mirna-target-finder, transcriptomics/srna |
|
sam2interval |
sam2interval |
Convert SAM to interval. |
2013-08-26 |
|
1.0.2 |
python |
|
To update |
SAM |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
51 |
67 |
1241 |
1493 |
137 |
1759 |
2387 |
19317 |
8 |
17 |
576 |
740 |
4 |
4 |
5 |
5 |
21555 |
4209 |
1847 |
200 |
https://usegalaxy.org/published/workflow?id=0115daec07bb1da6, https://usegalaxy.org/published/workflow?id=4b52f6a8dcfc8045, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=c6a3b066c3072e4a |
|
|
sam_bitwise_flag_filter |
sam_bw_filter |
Filter SAM on bitwise flag values |
2013-08-26 |
|
1.0.1 |
python |
|
To update |
SAM |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter |
|
|
|
|
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2 |
26 |
4 |
278 |
207 |
6356 |
1665 |
76071 |
16 |
32 |
232 |
403 |
2 |
2 |
24 |
24 |
76776 |
1925 |
6416 |
227 |
https://usegalaxy.eu/published/workflow?id=4412f7223a557b48, https://usegalaxy.org/published/workflow?id=0017c434354b6f6a, https://usegalaxy.org/published/workflow?id=055eb85c8ecf0ca3, https://usegalaxy.org/published/workflow?id=07739fbbd53755f6, https://usegalaxy.org/published/workflow?id=165c8a58baffe64c, https://usegalaxy.org/published/workflow?id=1b385fd45ee48614, https://usegalaxy.org/published/workflow?id=1e2e064c33b9c521, https://usegalaxy.org/published/workflow?id=26d2c2d51d6a7158, https://usegalaxy.org/published/workflow?id=2b3970d9b28810a1, https://usegalaxy.org/published/workflow?id=34ed5c1ceeed43c1, https://usegalaxy.org/published/workflow?id=3696bd8abe0f7746, https://usegalaxy.org/published/workflow?id=378159d1ad2e98f9, https://usegalaxy.org/published/workflow?id=38f5ab09779a6495, https://usegalaxy.org/published/workflow?id=4a5730954d776cb2, https://usegalaxy.org/published/workflow?id=4a9b0534b1c88609, https://usegalaxy.org/published/workflow?id=555e68f5c807ff73, https://usegalaxy.org/published/workflow?id=578f46106f72c971, https://usegalaxy.org/published/workflow?id=6172b57f4c49e364, https://usegalaxy.org/published/workflow?id=6f436066dffbc37d, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=83fbcdf3e29c41d0, https://usegalaxy.org/published/workflow?id=84aa86200ff74b4a, https://usegalaxy.org/published/workflow?id=92a233e5f2405830, https://usegalaxy.org/published/workflow?id=99e754eaabd7f362, https://usegalaxy.org/published/workflow?id=a23bf4cd3bc97f2a, https://usegalaxy.org/published/workflow?id=a57db139837dd24c, https://usegalaxy.org/published/workflow?id=b2176abeb937f026, https://usegalaxy.org/published/workflow?id=b4bb2c7d8c7b5139, https://usegalaxy.org/published/workflow?id=b4dda054d2cf15b7, https://usegalaxy.org/published/workflow?id=b72edafe11293d93, https://usegalaxy.org/published/workflow?id=c4a1246974f279c5, https://usegalaxy.org/published/workflow?id=c6a3b066c3072e4a, https://usegalaxy.org/published/workflow?id=c7aca0f5bb660907, https://usegalaxy.org/published/workflow?id=ca5ca2f38c1719e1, https://usegalaxy.org/published/workflow?id=e35ac40c58953f74, https://usegalaxy.org/published/workflow?id=e8b1d1e5e889c986, https://usegalaxy.org/published/workflow?id=ea817818a6de77e0, https://usegalaxy.org/published/workflow?id=eb20150175a6ab03, https://usegalaxy.org/published/workflow?id=f3983646b6df24bf |
|
|
sambamba |
sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort |
Sambamba: process your BAM data faster! |
2016-06-23 |
https://github.com/biod/sambamba |
1.0.1 |
sambamba |
1.0.1 |
Up-to-date |
SAM |
|
|
|
|
bgruening |
https://github.com/biod/sambamba |
https://github.com/bgruening/galaxytools/tree/master/tools/sambamba |
|
|
|
|
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
229 |
229 |
6620 |
6620 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6620 |
6620 |
229 |
229 |
https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1164?version=2 |
|
|
sample_seqs |
sample_seqs |
Sub-sample sequences files (e.g. to reduce coverage) |
2014-02-18 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs |
0.2.6 |
biopython |
1.70 |
To update |
Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs |
https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
376 |
457 |
3760 |
4585 |
274 |
274 |
2029 |
2029 |
54 |
54 |
2601 |
2601 |
9 |
9 |
113 |
113 |
9328 |
8503 |
794 |
713 |
|
transcriptomics/mirna-target-finder |
|
samtools_depad |
samtools_depad |
Re-align a SAM/BAM file with a padded reference (using samtools depad) |
2014-04-14 |
http://www.htslib.org/ |
0.0.5 |
samtools |
1.22.1 |
To update |
Assembly, SAM, Sequence Analysis |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad |
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
samtools_depth |
samtools_depth |
Coverage depth via samtools |
2014-11-19 |
http://www.htslib.org/ |
0.0.3 |
samtools |
1.22.1 |
To update |
Assembly, Sequence Analysis, SAM |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth |
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1071 |
1130 |
8403 |
9175 |
1771 |
1964 |
11692 |
12814 |
99 |
99 |
761 |
761 |
77 |
77 |
151 |
151 |
22901 |
21007 |
3270 |
3018 |
https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=60e0b2a28a900178, https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8, https://usegalaxy.eu/published/workflow?id=64abcddeb516a712, https://usegalaxy.eu/published/workflow?id=6aa2891bd2b41f32, https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f, https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.org.au/published/workflow?id=0e11619979c2830c, https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad, https://usegalaxy.org.au/published/workflow?id=38f57cffaeb0e39f, https://usegalaxy.org.au/published/workflow?id=76a0a3af8de11622, https://usegalaxy.org.au/published/workflow?id=857e482acfcb2dba, https://usegalaxy.org/published/workflow?id=06d6dcd2655592af, https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6, https://usegalaxy.org/published/workflow?id=3e703abaeb870f6f, https://usegalaxy.org/published/workflow?id=3f2d1003ff959c7c, https://usegalaxy.org/published/workflow?id=6d778eeb176d563c, https://usegalaxy.org/published/workflow?id=71f8a4090877f171, https://usegalaxy.org/published/workflow?id=8daa91d54040ba95, https://usegalaxy.org/published/workflow?id=b561d3d9645a2726, https://usegalaxy.org/published/workflow?id=c4af6c5f5dfaae82, https://usegalaxy.org/published/workflow?id=cb810cdaa4915f4b, https://usegalaxy.org/published/workflow?id=f3ed710e251833a7, https://workflowhub.eu/workflows/1063?version=5, https://workflowhub.eu/workflows/1479?version=1, https://workflowhub.eu/workflows/1738?version=1, https://workflowhub.eu/workflows/1739?version=1, https://workflowhub.eu/workflows/1740?version=1, https://workflowhub.eu/workflows/1741?version=1 |
microbiome/pathogen-detection-from-nanopore-foodborne-data |
|
samtools_idxstats |
samtools_idxstats |
BAM mapping statistics (using samtools idxstats) |
2013-11-11 |
http://www.htslib.org/ |
0.0.6 |
samtools |
1.22.1 |
To update |
Assembly, Next Gen Mappers, SAM |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats |
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
5115 |
5963 |
62930 |
71062 |
8050 |
12101 |
84370 |
129360 |
1344 |
1722 |
18420 |
20536 |
473 |
475 |
2848 |
2865 |
223823 |
168568 |
20261 |
14982 |
https://usegalaxy.eu/published/workflow?id=1089e5c66dbcc1a3, https://usegalaxy.eu/published/workflow?id=111527fe542846af, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=25aa944237d7fb82, https://usegalaxy.eu/published/workflow?id=2f51a82838722bec, https://usegalaxy.eu/published/workflow?id=30e7dc81e323cbdb, https://usegalaxy.eu/published/workflow?id=36a4646959829018, https://usegalaxy.eu/published/workflow?id=3b8ef7905c902b27, https://usegalaxy.eu/published/workflow?id=45f63151bf4f1a49, https://usegalaxy.eu/published/workflow?id=48f63ef14a12f306, https://usegalaxy.eu/published/workflow?id=4daa0c33d6d50379, https://usegalaxy.eu/published/workflow?id=54b91dd86f463391, https://usegalaxy.eu/published/workflow?id=70e93addf6d1b08e, https://usegalaxy.eu/published/workflow?id=7e0ba4c14803448e, https://usegalaxy.eu/published/workflow?id=8132c3b710fd6d48, https://usegalaxy.eu/published/workflow?id=93a7047396080fda, 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https://workflowhub.eu/workflows/1620?version=1, https://workflowhub.eu/workflows/1692?version=1, https://workflowhub.eu/workflows/1695?version=1, https://workflowhub.eu/workflows/1715?version=1, https://workflowhub.eu/workflows/399?version=19 |
epigenetics/atac-seq, epigenetics/estrogen-receptor-binding-site-identification, epigenetics/formation_of_super-structures_on_xi, epigenetics/tal1-binding-site-identification, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts |
|
scatterplot |
scatterplot_rpy |
Scatterplot of two numeric columns |
2014-07-28 |
|
1.0.3 |
numpy |
|
To update |
Graphics, Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
193 |
302 |
1045 |
1916 |
189 |
1969 |
634 |
9419 |
0 |
18 |
0 |
49 |
20 |
20 |
55 |
55 |
11439 |
1734 |
2309 |
402 |
https://usegalaxy.eu/published/workflow?id=17ad465d9515cd25, https://usegalaxy.org/published/workflow?id=857db984ff571191 |
|
|
sed_wrapper |
sed_stream_editor |
Manipulate your data with the sed command line tool. |
2015-02-28 |
https://github.com/bgruening/galaxytools/tree/master/tools/sed |
0.0.1 |
sed |
|
To update |
Text Manipulation |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/sed |
https://github.com/bgruening/galaxytools/tree/master/tools/sed |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
53 |
43 |
2284 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2284 |
43 |
53 |
6 |
https://usegalaxy.eu/published/workflow?id=04dbf1e548db74fd, https://usegalaxy.eu/published/workflow?id=c94a1d028357c81e, https://usegalaxy.eu/published/workflow?id=f7a7c72489d6b3d4 |
|
|
segemehl |
segemehl |
segemehl - short read mapping with gaps |
2015-02-28 |
http://www.bioinf.uni-leipzig.de/Software/segemehl/ |
0.2.0.4 |
segemehl |
0.3.4 |
To update |
Next Gen Mappers |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/segemehl |
https://github.com/bgruening/galaxytools/tree/master/tools/segemehl |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
91 |
121 |
614 |
1352 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1352 |
614 |
121 |
91 |
|
|
|
selectsequencesfrommsa |
selectsequencesfrommsa |
SelectSequences - selects representative entries from a multiple sequence alignment in clustal format |
2017-03-11 |
https://github.com/eggzilla/SelectSequences |
1.0.5 |
selectsequencesfrommsa |
1.0.5 |
Up-to-date |
RNA, Sequence Analysis |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
38 |
51 |
161 |
473 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
473 |
161 |
51 |
38 |
https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=8f2d958cee428ca1 |
|
|
seq_composition |
seq_composition |
Sequence composition |
2014-08-12 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition |
0.0.5 |
biopython |
1.70 |
To update |
Sequence Analysis |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
176 |
237 |
1521 |
1668 |
253 |
253 |
816 |
816 |
0 |
0 |
0 |
0 |
4 |
4 |
47 |
47 |
2531 |
2384 |
494 |
433 |
https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=9275d0c90a8713d6 |
|
|
seq_filter_by_id |
seq_filter_by_id |
Filter sequences by ID |
2013-09-26 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id |
0.2.9 |
biopython |
1.70 |
To update |
Fasta Manipulation, Sequence Analysis, Text Manipulation |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
988 |
1128 |
34926 |
38056 |
849 |
851 |
31298 |
41463 |
183 |
183 |
3656 |
3656 |
31 |
31 |
1103 |
1103 |
84278 |
70983 |
2193 |
2051 |
https://usegalaxy.eu/published/workflow?id=1f88311a8e365c17, https://usegalaxy.eu/published/workflow?id=3280dc48d768b46a, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=4a39d38fde81e35d, https://usegalaxy.eu/published/workflow?id=513389e1a8c6bba9, https://usegalaxy.eu/published/workflow?id=57d3109f32defa3b, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=889f2782ad82bd69, https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d, https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264, https://usegalaxy.eu/published/workflow?id=d7aa4c258e2edc95, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.org.au/published/workflow?id=470eb26144325590, https://usegalaxy.org.au/published/workflow?id=a1b97364f84022cf, https://usegalaxy.org/published/workflow?id=3c7349268d74c576, https://workflowhub.eu/workflows/1507?version=1, https://workflowhub.eu/workflows/1702?version=1, https://workflowhub.eu/workflows/655?version=1, https://workflowhub.eu/workflows/878?version=1 |
ecology/Obitools-metabarcoding, single-cell/scrna-umis |
|
seq_filter_by_mapping |
seq_filter_by_mapping |
Filter sequencing reads using SAM/BAM mapping files |
2014-11-04 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping |
0.0.8 |
biopython |
1.70 |
To update |
Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
190 |
242 |
4624 |
5314 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5314 |
4624 |
242 |
190 |
https://usegalaxy.eu/published/workflow?id=9668976304efea5c |
|
|
seq_length |
seq_length |
Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) |
2018-05-08 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length |
0.0.5 |
biopython |
1.70 |
To update |
Fasta Manipulation, Fastq Manipulation, Sequence Analysis |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
seq_primer_clip |
seq_primer_clip |
Trim off 5' or 3' primers |
2013-09-26 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip |
0.0.18 |
galaxy_sequence_utils |
1.2.0 |
To update |
Assembly, Fasta Manipulation, Text Manipulation |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
seq_rename |
seq_rename |
Rename sequences with ID mapping from a tabular file |
2013-09-26 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename |
0.0.10 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fasta Manipulation, Sequence Analysis, Text Manipulation |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
seq_select_by_id |
seq_select_by_id |
Select sequences by ID |
2013-09-26 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id |
0.0.15 |
biopython |
1.70 |
To update |
Fasta Manipulation, Sequence Analysis, Text Manipulation |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id |
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id |
|
|
|
|
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
259 |
303 |
1772 |
3868 |
10 |
12 |
435 |
499 |
4367 |
2207 |
315 |
269 |
|
|
|
short_reads_figure_high_quality_length |
hist_high_quality_score |
Histogram of high quality score reads |
2014-05-19 |
|
1.0.0 |
rpy |
|
To update |
Sequence Analysis, Graphics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
short_reads_figure_score |
quality_score_distribution |
Build base quality distribution |
2014-05-19 |
|
1.0.2 |
fontconfig |
|
To update |
Sequence Analysis, Graphics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
23 |
30 |
71 |
163 |
5 |
711 |
67 |
3360 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3523 |
138 |
741 |
28 |
|
|
|
short_reads_trim_seq |
trim_reads |
Select high quality segments |
2014-05-19 |
|
1.0.0 |
|
|
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
39 |
60 |
85 |
220 |
59 |
1608 |
210 |
6669 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6889 |
295 |
1668 |
98 |
https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7294f75ad01ca7ed, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c |
|
|
show_beginning |
Show beginning1 |
Select lines from the beginning of a file. |
2012-12-04 |
|
1.0.0 |
|
|
To update |
Text Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning |
|
|
|
|
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
1 |
1 |
1 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
1 |
0 |
1 |
0 |
1 |
1 |
1 |
2470 |
3456 |
175984 |
186535 |
4485 |
20035 |
20107 |
91558 |
499 |
632 |
3332 |
4032 |
155 |
156 |
562 |
666 |
282791 |
199985 |
24279 |
7609 |
https://usegalaxy.eu/published/workflow?id=035f85c1615e0b7b, https://usegalaxy.eu/published/workflow?id=04b838103aed1929, https://usegalaxy.eu/published/workflow?id=1ac5745645634825, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=272e9106e50c9fe6, https://usegalaxy.eu/published/workflow?id=29346872085adf1f, https://usegalaxy.eu/published/workflow?id=2f7149d02db43b7b, https://usegalaxy.eu/published/workflow?id=3e91f8417a66d02c, https://usegalaxy.eu/published/workflow?id=3f61bd49caa49440, https://usegalaxy.eu/published/workflow?id=4a33a8348ac03f00, https://usegalaxy.eu/published/workflow?id=579a56c129883cf3, https://usegalaxy.eu/published/workflow?id=5b686090a45f803f, https://usegalaxy.eu/published/workflow?id=5cef0f268d6ff4e0, https://usegalaxy.eu/published/workflow?id=5e4135eeb4972709, https://usegalaxy.eu/published/workflow?id=6173008772bdba09, https://usegalaxy.eu/published/workflow?id=61dcc0998fa4d309, https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=6588229d0365657f, https://usegalaxy.eu/published/workflow?id=7bcac5c6594e866c, https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539, https://usegalaxy.eu/published/workflow?id=7fbde7faec75c781, https://usegalaxy.eu/published/workflow?id=81abf01f79f358fe, https://usegalaxy.eu/published/workflow?id=8c44228d11782e61, https://usegalaxy.eu/published/workflow?id=8faf828e269ca54c, https://usegalaxy.eu/published/workflow?id=99c7ec2841af3a20, https://usegalaxy.eu/published/workflow?id=9d888cef61f5072f, https://usegalaxy.eu/published/workflow?id=9dc6c073f9994265, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=a6a3c1fb4a8fe6bf, https://usegalaxy.eu/published/workflow?id=a7f2835a74bdf10c, https://usegalaxy.eu/published/workflow?id=b351b297ac7d923f, https://usegalaxy.eu/published/workflow?id=b711696909ee2b59, https://usegalaxy.eu/published/workflow?id=b89ce83b1121c95a, https://usegalaxy.eu/published/workflow?id=bf655ab3dc6fd76a, https://usegalaxy.eu/published/workflow?id=c750484145c9903b, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=ca6d971fc3a0f417, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.eu/published/workflow?id=cdf677a621166238, https://usegalaxy.eu/published/workflow?id=d20fbb95f15386f5, https://usegalaxy.eu/published/workflow?id=d3a8741131485af2, https://usegalaxy.eu/published/workflow?id=d3dfe7ba11508c72, https://usegalaxy.eu/published/workflow?id=e7e26967cf6cb8d8, https://usegalaxy.eu/published/workflow?id=fb233e418d015649, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.eu/published/workflow?id=fd97c08fdaa6a5eb, https://usegalaxy.org.au/published/workflow?id=252baad4e5ade6bc, https://usegalaxy.org.au/published/workflow?id=9f112e39bd3bd746, https://usegalaxy.org.au/published/workflow?id=bf999071343171b7, https://usegalaxy.org.au/published/workflow?id=c4a303c1571d202e, https://usegalaxy.org.au/published/workflow?id=eda00feabdd21711, https://usegalaxy.org/published/workflow?id=0ab1922bc4ea12b2, https://usegalaxy.org/published/workflow?id=100340be53c2851c, https://usegalaxy.org/published/workflow?id=100d0edb39f83ce7, https://usegalaxy.org/published/workflow?id=1207eb597775b8a0, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=1e350f8ab5978571, https://usegalaxy.org/published/workflow?id=25897c7a15f29c32, https://usegalaxy.org/published/workflow?id=292b9d1975c349f3, https://usegalaxy.org/published/workflow?id=2cfbf7d01161992c, https://usegalaxy.org/published/workflow?id=2d50f038984f2389, https://usegalaxy.org/published/workflow?id=35ec8aeeaa59f6ae, https://usegalaxy.org/published/workflow?id=36a05fd818575788, https://usegalaxy.org/published/workflow?id=414fa13b613b33d8, https://usegalaxy.org/published/workflow?id=47e190ec408a71b1, https://usegalaxy.org/published/workflow?id=4ca3b9bb720e9233, https://usegalaxy.org/published/workflow?id=4e0ce0ab562f3912, https://usegalaxy.org/published/workflow?id=56530f4d41413832, https://usegalaxy.org/published/workflow?id=5ad1bcc7e3edd504, https://usegalaxy.org/published/workflow?id=67080f040e855990, https://usegalaxy.org/published/workflow?id=6d971192efa75c8a, https://usegalaxy.org/published/workflow?id=75c2cf36253194c2, https://usegalaxy.org/published/workflow?id=79454a1e3fe171de, https://usegalaxy.org/published/workflow?id=7ca9c5203520ca7e, https://usegalaxy.org/published/workflow?id=7cae620eea6326af, https://usegalaxy.org/published/workflow?id=81c357e76c08ec02, https://usegalaxy.org/published/workflow?id=889aa91c6d3f5654, https://usegalaxy.org/published/workflow?id=88ac2698fa170993, https://usegalaxy.org/published/workflow?id=8bfd40faf59c9857, https://usegalaxy.org/published/workflow?id=92d0308b5190c4be, https://usegalaxy.org/published/workflow?id=95db417c58c586fa, https://usegalaxy.org/published/workflow?id=96b3cad73980c9d0, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://usegalaxy.org/published/workflow?id=a1a1c29486d7dd05, https://usegalaxy.org/published/workflow?id=a4a2fa50bb0f095c, https://usegalaxy.org/published/workflow?id=a97f55f0d098b07e, https://usegalaxy.org/published/workflow?id=ab0ffa36361293da, https://usegalaxy.org/published/workflow?id=ab50fc9309706fbc, https://usegalaxy.org/published/workflow?id=b11171cc4ccd84c7, https://usegalaxy.org/published/workflow?id=b62535ba597d3323, https://usegalaxy.org/published/workflow?id=bc461addefad698a, https://usegalaxy.org/published/workflow?id=be4e3c22eef28b7c, https://usegalaxy.org/published/workflow?id=bf1af666d4ea21e4, https://usegalaxy.org/published/workflow?id=c060cfc7463ab118, https://usegalaxy.org/published/workflow?id=c60eca6b739a2f11, https://usegalaxy.org/published/workflow?id=c64719e91e7346a2, https://usegalaxy.org/published/workflow?id=c81ae10f59b3f600, https://usegalaxy.org/published/workflow?id=c8e9cb724c60144c, https://usegalaxy.org/published/workflow?id=cb029d0205155150, https://usegalaxy.org/published/workflow?id=cf21a13f09fcc070, https://usegalaxy.org/published/workflow?id=d5cba8a5ba6880fd, https://usegalaxy.org/published/workflow?id=d7c03007ef8a618e, https://usegalaxy.org/published/workflow?id=d7ea4bdc208ae5e8, https://usegalaxy.org/published/workflow?id=d87b4e14e8e1d39e, https://usegalaxy.org/published/workflow?id=e004b6e4717296cb, https://usegalaxy.org/published/workflow?id=e10859cc568da07c, https://usegalaxy.org/published/workflow?id=e3e646407e3f921d, https://usegalaxy.org/published/workflow?id=e483f5a30a683925, https://usegalaxy.org/published/workflow?id=e586940a7c93ef73, https://usegalaxy.org/published/workflow?id=e67ce2ce587a6f39, https://usegalaxy.org/published/workflow?id=e9e8ac517480c291, https://usegalaxy.org/published/workflow?id=eca0449a7460480c, https://usegalaxy.org/published/workflow?id=ecb279a9114140ab, https://usegalaxy.org/published/workflow?id=f03bf569d526e51a, https://usegalaxy.org/published/workflow?id=f202add6857fabbe, https://usegalaxy.org/published/workflow?id=f806893fbe065406, https://usegalaxy.org/published/workflow?id=f966a8498497ee13, https://usegalaxy.org/published/workflow?id=fa89d2d0edabe803, https://usegalaxy.org/published/workflow?id=fbf75fbb72b488bd, https://usegalaxy.org/published/workflow?id=fcce98489c8ca7a3, https://usegalaxy.org/published/workflow?id=ffd718437128bce2, https://workflowhub.eu/workflows/1078?version=1, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/1392?version=1, https://workflowhub.eu/workflows/1486?version=1, https://workflowhub.eu/workflows/1561?version=1, https://workflowhub.eu/workflows/1601?version=1, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1745?version=2 |
data-science/data-manipulation-olympics, galaxy-interface/workflow-editor, introduction/data-manipulation-olympics, single-cell/scatac-batch-correction-snapatac2, statistics/flexynesis_classification, transcriptomics/rna-seq-analysis-clustering-viz, variant-analysis/aiv-analysis |
|
show_tail |
Show tail1 |
Select lines from the end of a file. |
2012-12-04 |
|
1.0.0 |
|
|
To update |
Text Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail |
|
|
|
|
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
1 |
1 |
1 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
1 |
0 |
1 |
0 |
1 |
1 |
1 |
403 |
680 |
1739 |
3020 |
687 |
2020 |
10501 |
25260 |
86 |
112 |
1390 |
1544 |
17 |
18 |
67 |
87 |
29911 |
13697 |
2830 |
1193 |
https://usegalaxy.eu/published/workflow?id=035f85c1615e0b7b, https://usegalaxy.org.au/published/workflow?id=a335b9c9103b57ad, https://usegalaxy.org/published/workflow?id=427fce51fd9508eb, https://usegalaxy.org/published/workflow?id=7ca9c5203520ca7e, https://usegalaxy.org/published/workflow?id=c03ada2070e9ca8a, https://usegalaxy.org/published/workflow?id=e10859cc568da07c, https://usegalaxy.org/published/workflow?id=f806893fbe065406, https://workflowhub.eu/workflows/625?version=26 |
|
|
sicer |
peakcalling_sicer |
Statistical approach for the Identification of ChIP-Enriched Regions |
2014-01-27 |
https://home.gwu.edu/~wpeng/Software.htm |
1.1 |
SICER |
1.1 |
Up-to-date |
ChIP-seq |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
25 |
45 |
136 |
394 |
120 |
1019 |
626 |
9100 |
5 |
7 |
640 |
865 |
3 |
3 |
5 |
5 |
10364 |
1407 |
1074 |
153 |
|
|
|
sklearn |
sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split |
Machine Learning tool suite from Scikit-learn |
2016-05-02 |
http://scikit-learn.org |
1.0.11.0 |
|
|
To update |
Machine Learning, Statistics |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/sklearn |
https://github.com/bgruening/galaxytools/tree/master/tools/sklearn |
|
|
|
|
0 |
14 |
31 |
16 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
29 |
31 |
27 |
281 |
374 |
30752 |
125704 |
345 |
370 |
16128 |
23522 |
38 |
41 |
21876 |
24161 |
5 |
5 |
40 |
40 |
173427 |
68796 |
790 |
669 |
https://usegalaxy.eu/published/workflow?id=011596d04aa140c1, https://usegalaxy.eu/published/workflow?id=0bfb81f2a0202b25, https://usegalaxy.eu/published/workflow?id=130bdb021a3083fb, https://usegalaxy.eu/published/workflow?id=1377a23db45877ae, https://usegalaxy.eu/published/workflow?id=138d4893a1d6228e, https://usegalaxy.eu/published/workflow?id=1526d3918b201c72, https://usegalaxy.eu/published/workflow?id=16a0725cb2063ac1, https://usegalaxy.eu/published/workflow?id=179488ec6d44852c, https://usegalaxy.eu/published/workflow?id=17e99647745eb150, https://usegalaxy.eu/published/workflow?id=19bb27eea9bcdb6f, https://usegalaxy.eu/published/workflow?id=1a38ea9798597219, https://usegalaxy.eu/published/workflow?id=1b8399d5b9fc89a6, https://usegalaxy.eu/published/workflow?id=1d55d5d20c581b16, https://usegalaxy.eu/published/workflow?id=2484b03b39b8ab98, https://usegalaxy.eu/published/workflow?id=262268f6ab4d1f6c, https://usegalaxy.eu/published/workflow?id=2ab7ae9ca0e51392, https://usegalaxy.eu/published/workflow?id=2ac5db57491b97b1, https://usegalaxy.eu/published/workflow?id=33114cbae59a89a1, https://usegalaxy.eu/published/workflow?id=34861c3c63048d6b, https://usegalaxy.eu/published/workflow?id=3aeeb7a017143bb4, https://usegalaxy.eu/published/workflow?id=3ffe3b2007167657, https://usegalaxy.eu/published/workflow?id=4384aa586c0e1300, https://usegalaxy.eu/published/workflow?id=443c014a103626bd, https://usegalaxy.eu/published/workflow?id=463a22701cf2410d, https://usegalaxy.eu/published/workflow?id=4b383d13ff512687, https://usegalaxy.eu/published/workflow?id=518469bc5efb8728, https://usegalaxy.eu/published/workflow?id=5225633f2e94fc7e, https://usegalaxy.eu/published/workflow?id=540d4c57cfe2a40f, https://usegalaxy.eu/published/workflow?id=57564e3962edb0d5, https://usegalaxy.eu/published/workflow?id=5900578d64e01001, https://usegalaxy.eu/published/workflow?id=5e1f033efa5f7d7d, https://usegalaxy.eu/published/workflow?id=6081f684d8d72e91, https://usegalaxy.eu/published/workflow?id=6842576edd59b01a, https://usegalaxy.eu/published/workflow?id=6c29cb7393b64a98, https://usegalaxy.eu/published/workflow?id=6ce19741d208f0db, https://usegalaxy.eu/published/workflow?id=6df97546214afbe6, https://usegalaxy.eu/published/workflow?id=6f66e4b653082fa5, https://usegalaxy.eu/published/workflow?id=71a7113386b2cdc1, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=77fa6e5a8fa3f911, https://usegalaxy.eu/published/workflow?id=788d5aff5b560438, https://usegalaxy.eu/published/workflow?id=7c10b78c4367ed61, https://usegalaxy.eu/published/workflow?id=7d22e5259212aaf8, https://usegalaxy.eu/published/workflow?id=7d7bfc7420479470, https://usegalaxy.eu/published/workflow?id=7e90fa21a018c0bb, https://usegalaxy.eu/published/workflow?id=8192e947a14d9cb5, https://usegalaxy.eu/published/workflow?id=81f24fe866a8a12c, https://usegalaxy.eu/published/workflow?id=81f62d8f35462c9a, https://usegalaxy.eu/published/workflow?id=83002fdc85a7911e, https://usegalaxy.eu/published/workflow?id=83fe480cdbb70099, https://usegalaxy.eu/published/workflow?id=848389c45cebe34f, https://usegalaxy.eu/published/workflow?id=8b5e642274f91390, https://usegalaxy.eu/published/workflow?id=8fc7eb7733071aba, https://usegalaxy.eu/published/workflow?id=925c89b318763574, https://usegalaxy.eu/published/workflow?id=9791e8aae12d6e63, https://usegalaxy.eu/published/workflow?id=9e497c5c9e64d9b3, https://usegalaxy.eu/published/workflow?id=a08f980909ddcff2, https://usegalaxy.eu/published/workflow?id=a3c966d53c4ba7de, https://usegalaxy.eu/published/workflow?id=a669986e1a5cee31, https://usegalaxy.eu/published/workflow?id=a824fb7e65a1a939, https://usegalaxy.eu/published/workflow?id=ab28a6da3e34094a, https://usegalaxy.eu/published/workflow?id=abd283a751a19aa5, https://usegalaxy.eu/published/workflow?id=ae380023cd06f640, https://usegalaxy.eu/published/workflow?id=b47e8dde39c6d8b7, https://usegalaxy.eu/published/workflow?id=b4bf9e3309d53af3, https://usegalaxy.eu/published/workflow?id=bb64be0ff8a5e92e, https://usegalaxy.eu/published/workflow?id=bc720034237e5b2e, https://usegalaxy.eu/published/workflow?id=c15303fcc0b53df6, https://usegalaxy.eu/published/workflow?id=c68cd416d24af9f2, https://usegalaxy.eu/published/workflow?id=c76b69a5560142de, https://usegalaxy.eu/published/workflow?id=cb3d961914ede12e, https://usegalaxy.eu/published/workflow?id=ccda8222900499a7, https://usegalaxy.eu/published/workflow?id=cda516957bcfcd9c, https://usegalaxy.eu/published/workflow?id=d63c382e98be752b, https://usegalaxy.eu/published/workflow?id=d6eb0562d0036940, https://usegalaxy.eu/published/workflow?id=db344f239d0901bd, https://usegalaxy.eu/published/workflow?id=df3732dcb6c1bcb7, https://usegalaxy.eu/published/workflow?id=e2560dd1b4aca511, https://usegalaxy.eu/published/workflow?id=e5b58ab054d7d11b, https://usegalaxy.eu/published/workflow?id=e6432be54d625d1c, https://usegalaxy.eu/published/workflow?id=e64680b4aa5541d6, https://usegalaxy.eu/published/workflow?id=e795e7f59b4de5e6, https://usegalaxy.eu/published/workflow?id=eefefcfe80e6eee0, https://usegalaxy.eu/published/workflow?id=f4a55ef0d4c2cd97, https://usegalaxy.eu/published/workflow?id=f698bed6a0867f5f, https://usegalaxy.eu/published/workflow?id=fa83e26e05418370, https://usegalaxy.eu/published/workflow?id=fa9d6ca3fe1266c4, https://usegalaxy.eu/published/workflow?id=fdbf1a1a584a429c, https://usegalaxy.org.au/published/workflow?id=350433eefb835f19, https://usegalaxy.org.au/published/workflow?id=517f947adc81a16a, https://usegalaxy.org.au/published/workflow?id=65a8ac91d6ded9a2, https://usegalaxy.org.au/published/workflow?id=697945d5f9edbf39, https://usegalaxy.org.au/published/workflow?id=92b5a29a956a3afc, https://usegalaxy.org.au/published/workflow?id=b0ee0c0a6a37f5ef, https://usegalaxy.org.au/published/workflow?id=bfd7ed2abc95b53d, https://usegalaxy.org.au/published/workflow?id=cebab4f1a2405a89, https://usegalaxy.org.au/published/workflow?id=d858cfd9303bb99a, https://usegalaxy.org/published/workflow?id=0cf9868ebc9ec1dc, https://usegalaxy.org/published/workflow?id=1c579fc1fe256993, https://usegalaxy.org/published/workflow?id=728ce1ce56c4d3da, https://usegalaxy.org/published/workflow?id=8bab8e2b5d47f2f0, https://usegalaxy.org/published/workflow?id=fcfcc7ca9ab07bce, https://workflowhub.eu/workflows/1583?version=1, https://workflowhub.eu/workflows/1588?version=1, https://workflowhub.eu/workflows/1592?version=1, https://workflowhub.eu/workflows/1596?version=1, https://workflowhub.eu/workflows/1609?version=1, https://workflowhub.eu/workflows/1618?version=1, https://workflowhub.eu/workflows/1633?version=1, https://workflowhub.eu/workflows/1637?version=1, https://workflowhub.eu/workflows/1643?version=1, https://workflowhub.eu/workflows/1720?version=1, https://workflowhub.eu/workflows/1721?version=1, https://workflowhub.eu/workflows/1722?version=1, https://workflowhub.eu/workflows/1724?version=1, https://workflowhub.eu/workflows/659?version=1 |
statistics/CNN, statistics/FNN, statistics/RNN, statistics/age-prediction-with-ml, statistics/classification_machinelearning, statistics/classification_regression, statistics/clustering_machinelearning, statistics/fruit_360, statistics/intro_deep_learning, statistics/machinelearning, statistics/regression_machinelearning |
|
snpfreq |
hgv_snpFreq |
snpFreq significant SNPs in case-control data |
2014-07-28 |
|
1.0.1 |
R |
|
To update |
Variant Analysis, Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
11 |
14 |
21 |
50 |
68 |
199 |
278 |
700 |
11 |
23 |
218 |
303 |
0 |
0 |
0 |
0 |
1053 |
517 |
236 |
90 |
|
|
|
sortmerna |
bg_sortmerna |
SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. |
2015-02-28 |
http://bioinfo.lifl.fr/RNA/sortmerna/ |
4.3.6 |
sortmerna |
4.3.7 |
To update |
RNA |
Sequence similarity search, Sequence comparison, Sequence alignment analysis |
Sequence similarity search, Sequence alignment analysis |
Metatranscriptomics, Metagenomics |
Metatranscriptomics, Metagenomics |
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna |
sortmerna |
SortMeRNA |
Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1135 |
1352 |
23920 |
26406 |
581 |
581 |
6479 |
6479 |
219 |
225 |
3668 |
3882 |
116 |
116 |
648 |
651 |
37418 |
34715 |
2274 |
2051 |
https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=72e3e5fdc766e24a, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=e423c80058601e78, https://usegalaxy.eu/published/workflow?id=f6e8a63283262518, https://usegalaxy.eu/published/workflow?id=fd90652d475ed739, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.fr/published/workflow?id=e6991d64e851b09e, https://usegalaxy.org.au/published/workflow?id=408a31694e9c85e6, https://workflowhub.eu/workflows/1444?version=2, https://workflowhub.eu/workflows/1466?version=2 |
microbiome/metatranscriptomics, microbiome/metatranscriptomics-short |
|
split_file_on_column |
tp_split_on_column |
Split a file on a specific column. |
2015-02-28 |
|
0.6 |
gawk |
|
To update |
Text Manipulation |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column |
https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
532 |
630 |
7098 |
7607 |
421 |
421 |
2961 |
2961 |
16 |
16 |
308 |
308 |
26 |
26 |
37 |
37 |
10913 |
10404 |
1093 |
995 |
https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1749616cec69fb00, https://usegalaxy.eu/published/workflow?id=1f3f6757de60d3cf, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=39dd6365ff076dc4, https://usegalaxy.eu/published/workflow?id=5f053303601cc630, https://usegalaxy.eu/published/workflow?id=739214a6dfa194e1, https://usegalaxy.eu/published/workflow?id=7c80cd57b2de54d4, https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=933ab5e7fe13a8e0, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=e87e726b57f1a875, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.org.au/published/workflow?id=7a0b3968968c5994, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=2967ef82911f2cca, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=b0f85c802c1ea7f8, https://usegalaxy.org/published/workflow?id=fbf75fbb72b488bd, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1486?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/1515?version=1, https://workflowhub.eu/workflows/1517?version=1, https://workflowhub.eu/workflows/1518?version=1, https://workflowhub.eu/workflows/1601?version=1 |
data-science/data-manipulation-olympics, genome-annotation/gene-centric, imaging/parameter-tuning, introduction/data-manipulation-olympics, microbiome/pathogen-detection-from-nanopore-foodborne-data, single-cell/GO-enrichment |
|
split_file_to_collection |
split_file_to_collection |
Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. |
2018-07-10 |
https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection |
0.5.2 |
python |
|
To update |
Text Manipulation |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection |
https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1200 |
1299 |
19621 |
21660 |
812 |
863 |
10037 |
10694 |
185 |
191 |
5507 |
5871 |
35 |
36 |
712 |
770 |
38995 |
35877 |
2389 |
2232 |
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computational-chemistry/covid19-docking, computational-chemistry/zauberkugel, metabolomics/qcxms-predictions, microbiome/pathogen-detection-from-nanopore-foodborne-data, sequence-analysis/viral_primer_design |
|
split_paired_reads |
split_paired_reads |
Split paired end reads |
2013-09-25 |
|
1.0.0 |
|
|
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
13 |
18 |
66 |
97 |
384 |
0 |
0 |
0 |
0 |
397 |
97 |
69 |
18 |
|
|
|
splitfasta |
rbc_splitfasta |
Split a multi-sequence fasta file into files containing single sequences |
2015-10-16 |
https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta |
0.5.0 |
biopython |
1.70 |
To update |
Text Manipulation |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta |
https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
395 |
424 |
4645 |
4836 |
742 |
742 |
5239 |
5239 |
1 |
1 |
8 |
8 |
0 |
0 |
0 |
0 |
10083 |
9892 |
1167 |
1138 |
https://usegalaxy.eu/published/workflow?id=1f88311a8e365c17, https://usegalaxy.eu/published/workflow?id=a8c8da047f418380, https://usegalaxy.eu/published/workflow?id=d9fa202d2ff28108, https://usegalaxy.org/published/workflow?id=929b7a83015fdcda, https://usegalaxy.org/published/workflow?id=94da3d448bb8a137, https://usegalaxy.org/published/workflow?id=d73c60e406aff265 |
|
|
sshmm |
sshmm |
ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data |
2018-07-05 |
https://github.molgen.mpg.de/heller/ssHMM |
1.0.7 |
sshmm |
1.0.7 |
Up-to-date |
Sequence Analysis, RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
15 |
20 |
156 |
228 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
228 |
156 |
20 |
15 |
|
|
|
stats_perf_tool |
stats_perf_tool |
suitable for boolean classification problems |
2015-02-28 |
http://osmot.cs.cornell.edu/kddcup/software.html |
5.11.0 |
perf |
|
To update |
|
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/perf |
https://github.com/bgruening/galaxytools/tree/master/tools/perf |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
stress_ng |
stress_ng |
stress test a computer system in various selectable ways |
2021-03-04 |
|
0.12.04 |
stress-ng |
|
To update |
Web Services |
|
|
|
|
bgruening-util |
https://github.com/ColinIanKing/stress-ng |
https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
67 |
67 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
67 |
67 |
5 |
5 |
|
|
|
structure_to_gspan |
structure_to_gspan |
Convert RNA structure to GSPAN graphs |
2017-05-18 |
|
0.4 |
graphclust-wrappers |
0.6.0 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN |
https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
48 |
73 |
659 |
3154 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3154 |
659 |
73 |
48 |
https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7 |
|
|
substitution_rates |
subRate1 |
Estimate substitution rates for non-coding regions |
2014-04-01 |
|
1.0.0 |
|
|
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
747 |
12 |
3901 |
3 |
4 |
61 |
114 |
0 |
0 |
0 |
0 |
4015 |
73 |
751 |
7 |
|
|
|
substitutions |
substitutions1 |
Fetch substitutions from pairwise alignments |
2014-04-01 |
|
1.0.1 |
bx-python |
0.14.0 |
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
84 |
41 |
901 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
901 |
41 |
84 |
10 |
|
|
|
subtract |
gops_subtract_1 |
Subtract the intervals of two datasets |
2014-04-01 |
https://github.com/galaxyproject/gops |
1.0.0 |
bx-python |
0.14.0 |
To update |
Genomic Interval Operations |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
418 |
512 |
568334 |
569352 |
1292 |
7771 |
48668 |
186026 |
130 |
191 |
20401 |
21159 |
8 |
9 |
1165 |
1175 |
777712 |
638568 |
8483 |
1848 |
https://usegalaxy.eu/published/workflow?id=06544e74f583fd05, https://usegalaxy.eu/published/workflow?id=3aaea772745ca295, https://usegalaxy.eu/published/workflow?id=522500fac247be6f, https://usegalaxy.eu/published/workflow?id=5ded4002e684a02c, https://usegalaxy.eu/published/workflow?id=5ec0d6d108e02e1a, https://usegalaxy.eu/published/workflow?id=6c91fe92ef069d64, https://usegalaxy.eu/published/workflow?id=7b7d6a5c6c65d74b, https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf, https://usegalaxy.eu/published/workflow?id=b8fc492025ad6ff0, https://usegalaxy.eu/published/workflow?id=c832ecfa83bcda14, https://usegalaxy.eu/published/workflow?id=d52ff93f4ffdd981, https://usegalaxy.fr/published/workflow?id=0df61a88d64de252, https://usegalaxy.fr/published/workflow?id=a3e9062133fdf7c2, https://usegalaxy.fr/published/workflow?id=bf8ffe72b7ce4570, https://usegalaxy.org.au/published/workflow?id=2955ea7be1cdda29, https://usegalaxy.org.au/published/workflow?id=2b71eb1dc2aa28a1, https://usegalaxy.org.au/published/workflow?id=4b681937a01df465, https://usegalaxy.org.au/published/workflow?id=5cd7f1824db7a960, https://usegalaxy.org.au/published/workflow?id=61a21c9928182ae4, https://usegalaxy.org.au/published/workflow?id=6795e545b0cafded, https://usegalaxy.org.au/published/workflow?id=851552cc3e830253, https://usegalaxy.org.au/published/workflow?id=a77ce877e786d44a, https://usegalaxy.org.au/published/workflow?id=e154a9b605ea0886, https://usegalaxy.org.au/published/workflow?id=ebd1ee73906fdea0, https://usegalaxy.org.au/published/workflow?id=f65b54fcffaa11e5, https://usegalaxy.org/published/workflow?id=0392de36b6f55a8f, https://usegalaxy.org/published/workflow?id=31cc891be77cbc6f, https://usegalaxy.org/published/workflow?id=4ffdb2cf21759d26, https://usegalaxy.org/published/workflow?id=507c817755b2410d, https://usegalaxy.org/published/workflow?id=5834e562fa403732, https://usegalaxy.org/published/workflow?id=65f3a5772ae05a7a, https://usegalaxy.org/published/workflow?id=66748e20a243eafe, https://usegalaxy.org/published/workflow?id=6ba03802169c0063, https://usegalaxy.org/published/workflow?id=7b20a62d69d53efc, https://usegalaxy.org/published/workflow?id=7bc71a005c6f18d0, https://usegalaxy.org/published/workflow?id=b1cd3f793187d667, https://usegalaxy.org/published/workflow?id=d136d24e4c96962a, https://usegalaxy.org/published/workflow?id=f365c53b5024d7f1, https://workflowhub.eu/workflows/138?version=9, https://workflowhub.eu/workflows/356?version=1 |
|
|
subtract_query |
subtract_query1 |
Subtract Whole Dataset from another dataset |
2014-04-01 |
https://github.com/galaxyproject/gops |
0.1 |
bx-python |
0.14.0 |
To update |
Genomic Interval Operations |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
126 |
162 |
1385 |
1863 |
544 |
3501 |
2449 |
40799 |
20 |
39 |
786 |
1156 |
18 |
20 |
148 |
172 |
43990 |
4768 |
3722 |
708 |
https://usegalaxy.eu/published/workflow?id=82ef590b5821805d, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.org/published/workflow?id=0115daec07bb1da6, https://usegalaxy.org/published/workflow?id=a3de4b3f7b910059, https://usegalaxy.org/published/workflow?id=b2176abeb937f026 |
|
|
sylph |
sylph_profile, sylph_query |
sylph - fast and precise species-level metagenomic profiling with ANIs |
2024-10-08 |
https://github.com/bluenote-1577/sylph |
0.8.1 |
sylph |
0.8.1 |
Up-to-date |
Metagenomics |
Taxonomic classification |
Taxonomic classification |
Metagenomics |
Metagenomics |
bgruening |
https://github.com/bgruening/galaxytools/main/tools/sylph |
https://github.com/bgruening/galaxytools/tree/master/tools/sylph |
sylph |
sylph |
fast and precise species-level metagenomic profiling with ANIs |
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
9 |
257 |
257 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
1 |
1 |
12 |
12 |
270 |
270 |
11 |
11 |
https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7 |
|
|
t2ps |
Draw_phylogram |
Draw phylogeny |
2014-01-27 |
https://bitbucket.org/natefoo/taxonomy |
1.0.0 |
taxonomy |
0.10.1 |
To update |
Metagenomics |
Phylogenetic tree visualisation |
Phylogenetic tree visualisation |
Phylogenomics |
Phylogenomics |
devteam |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps |
t2ps |
Draw phylogeny |
"Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format." - Galaxy tool wrapper |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
64 |
93 |
405 |
479 |
13 |
1240 |
102 |
7952 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8431 |
507 |
1333 |
77 |
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|
|
t2t_report |
t2t_report |
Summarize taxonomy |
2014-01-27 |
https://bitbucket.org/natefoo/taxonomy |
1.0.0 |
taxonomy |
0.10.1 |
To update |
Metagenomics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report |
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0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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0 |
0 |
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1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
55 |
82 |
745 |
1071 |
16 |
1143 |
118 |
7194 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8265 |
863 |
1225 |
71 |
https://usegalaxy.org/published/workflow?id=19c9c8cc3c813bda, https://usegalaxy.org/published/workflow?id=2f7638035fb889ac, https://usegalaxy.org/published/workflow?id=55aa743125c2465d, https://usegalaxy.org/published/workflow?id=59347cc210c4cdbc, https://usegalaxy.org/published/workflow?id=7b67ffcf1b7c2232, https://usegalaxy.org/published/workflow?id=85d825931edf4a64, https://usegalaxy.org/published/workflow?id=896d29573ea3e574, https://usegalaxy.org/published/workflow?id=d851f8436497dd1c |
|
|
t_test_two_samples |
t_test_two_samples |
T Test for Two Samples |
2013-09-25 |
|
1.0.1 |
R |
|
To update |
Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples |
|
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0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
23 |
37 |
54 |
238 |
74 |
290 |
279 |
1220 |
10 |
12 |
1020 |
1390 |
3 |
3 |
4 |
4 |
2852 |
1357 |
342 |
110 |
|
|
|
table_annovar |
table_annovar |
Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered |
2013-12-02 |
|
0.2 |
annovar |
|
To update |
Variant Analysis |
|
|
|
|
devteam |
Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar |
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0 |
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0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
1589 |
7466 |
9066 |
64545 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
64545 |
9066 |
7466 |
1589 |
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|
|
tables_arithmetic_operations |
tables_arithmetic_operations |
Arithmetic Operations on tables |
2014-04-01 |
https://github.com/galaxyproject/gops |
1.0.0 |
perl |
|
To update |
Genomic Interval Operations |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations |
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0 |
0 |
1 |
1 |
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0 |
0 |
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0 |
0 |
1 |
0 |
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0 |
0 |
1 |
1 |
1 |
31 |
42 |
2041 |
2227 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
5 |
79 |
89 |
2316 |
2120 |
47 |
35 |
https://workflowhub.eu/workflows/789?version=1 |
|
|
tabpfn |
tabpfn |
Tabular data prediction using TabPFN using Pytorch. |
2024-10-14 |
https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn |
2.0.9 |
tabpfn |
|
To update |
Machine Learning |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn |
https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn |
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8 |
8 |
218 |
218 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
218 |
218 |
8 |
8 |
https://workflowhub.eu/workflows/1873?version=1 |
statistics/flexynesis_classification |
|
tabular_to_fasta |
tab2fasta |
Tabular-to-FASTA |
2014-05-19 |
|
1.1.1 |
python |
|
To update |
Convert Formats |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta |
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1 |
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1 |
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0 |
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0 |
1 |
1 |
1 |
1849 |
2219 |
342032 |
371433 |
2225 |
9004 |
71824 |
239239 |
331 |
430 |
34115 |
41811 |
50 |
53 |
2907 |
2921 |
655404 |
450878 |
11706 |
4455 |
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genome-annotation/gene-centric, microbiome/metaplasmidome_query, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/database-handling, proteomics/neoantigen-fusion-database-generation, proteomics/neoantigen-non-reference-database-generation, proteomics/neoantigen-peptide-verification, proteomics/neoantigen-variant-annotation, proteomics/proteogenomics-dbcreation, proteomics/proteogenomics-dbsearch, sequence-analysis/Manage_AB1_Sanger |
|
tapscan |
tapscan_classify |
Search for transcription associated proteins (TAPs) |
2024-02-14 |
https://plantcode.cup.uni-freiburg.de/tapscan/ |
4.76+galaxy0 |
hmmer |
3.4 |
To update |
Proteomics |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/tapscan |
https://github.com/bgruening/galaxytools/tree/master/tools/tapscan |
|
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0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
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0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
24 |
24 |
287 |
287 |
5 |
5 |
22 |
22 |
4 |
4 |
39 |
39 |
0 |
0 |
0 |
0 |
348 |
348 |
33 |
33 |
https://usegalaxy.eu/published/workflow?id=21fc597d983f1194, https://workflowhub.eu/workflows/1650?version=1 |
sequence-analysis/tapscan-streptophyte-algae |
|
targetfinder |
targetfinder |
Plant small RNA target prediction tool |
2015-10-23 |
https://github.com/carringtonlab/TargetFinder.git |
1.7 |
targetfinder |
1.7 |
Up-to-date |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder |
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1 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
129 |
137 |
935 |
990 |
99 |
99 |
340 |
340 |
34 |
34 |
1290 |
1290 |
0 |
0 |
0 |
0 |
2620 |
2565 |
270 |
262 |
https://usegalaxy.eu/published/workflow?id=2d2d0c2231babc50, https://workflowhub.eu/workflows/1717?version=2 |
transcriptomics/mirna-target-finder |
|
text_processing |
tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq |
High performance text processing tools using the GNU coreutils, sed, awk and friends. |
2015-02-28 |
https://www.gnu.org/software/ |
9.5 |
coreutils |
8.25 |
To update |
Text Manipulation |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing |
https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing |
|
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0 |
20 |
20 |
20 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
19 |
1 |
19 |
0 |
0 |
0 |
0 |
0 |
20 |
0 |
0 |
0 |
0 |
0 |
0 |
19 |
20 |
19 |
6124 |
7406 |
4349449 |
4523166 |
8936 |
13186 |
710157 |
1085698 |
1273 |
1320 |
131519 |
145869 |
373 |
373 |
30323 |
30492 |
5785225 |
5221448 |
22285 |
16706 |
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assembly/ERGA-post-assembly-QC, assembly/assembly-decontamination, assembly/ecoli_comparison, assembly/metagenomics-assembly, assembly/vgp_genome_assembly, climate/climate-101, climate/fates, computational-chemistry/cheminformatics, computational-chemistry/htmd-analysis, computational-chemistry/md-simulation-gromacs, computational-chemistry/zauberkugel, contributing/create-new-tutorial, data-science/data-manipulation-olympics, digital-humanities/introduction_to_dh, digital-humanities/open-refine-tutorial, digital-humanities/text_mining_chinese, ecology/Ecoregionalization_tutorial, ecology/PAMPA-toolsuite-tutorial, ecology/biodiversity-data-exploration, ecology/ecoregiolifetraits, ecology/obisindicators, ecology/phylogeny-data-prep, ecology/ref-based-rad-seq, ecology/regionalGAM, ecology/species-distribution-modeling, epigenetics/atac-seq, epigenetics/methylation-seq, evolution/mtb_transmission, galaxy-interface/ncbi-sarf, galaxy-interface/workflow-editor, galaxy-interface/workflow-parameters, galaxy-interface/workflow-reports, genome-annotation/bacterial-genome-annotation, genome-annotation/crispr-screen, genome-annotation/hpc-for-lsgc, genome-annotation/lncrna, genome-annotation/secondary-metabolite-discovery, genome-annotation/tnseq, introduction/data-manipulation-olympics, introduction/galaxy-intro-101, introduction/galaxy-intro-101-everyone, introduction/galaxy-intro-peaks2genes, introduction/galaxy-intro-strands, introduction/galaxy-reproduce, metabolomics/qcxms-predictions, microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-3-verification, microbiome/dada-16S, microbiome/metagenomics-assembly, microbiome/metaplasmidome_query, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/mgnify-amplicon, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/biomarker_selection, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-3-verification, proteomics/mass-spectrometry-imaging-loading-exploring-data, proteomics/maxquant-label-free, proteomics/maxquant-msstats-dda-lfq, proteomics/metaquantome-data-creation, proteomics/multiGSEA-tutorial, proteomics/neoantigen-fusion-database-generation, proteomics/neoantigen-non-reference-database-generation, proteomics/neoantigen-predicting-hla-binding, proteomics/protein-quant-sil, proteomics/proteogenomics-dbcreation, proteomics/secretome-prediction, sequence-analysis/human-reads-removal, single-cell/EBI-retrieval, single-cell/bulk-deconvolution-evaluate, single-cell/bulk-music-2-preparescref, single-cell/bulk-music-3-preparebulk, single-cell/pseudobulk-analysis, single-cell/scatac-preprocessing-tenx, single-cell/scrna-case_alevin-combine-datasets, single-cell/scrna-case_cell-cycle, single-cell/scrna-case_monocle3-trajectories, single-cell/scrna-data-ingest, single-cell/scrna-ncbi-anndata, single-cell/scrna-preprocessing, single-cell/scrna-raceid, statistics/flexynesis_cbio_import, statistics/flexynesis_classification, statistics/flexynesis_survival, statistics/fruit_360, transcriptomics/clipseq, transcriptomics/differential-isoform-expression, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-counts-to-genes, transcriptomics/rna-seq-genes-to-pathways, transcriptomics/small_ncrna_clustering, variant-analysis/aiv-analysis, variant-analysis/baculovirus-isolate-variation, variant-analysis/mapping-by-sequencing, variant-analysis/sars-cov-2, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants, variant-analysis/tb-variant-analysis, variant-analysis/trio-analysis |
|
tgsgapcloser |
tgsgapcloser |
TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. |
2021-11-14 |
https://github.com/BGI-Qingdao/TGS-GapCloser |
1.0.3 |
tgsgapcloser |
1.2.1 |
To update |
Assembly |
Genome assembly, Read mapping, Scaffolding, Localised reassembly |
Genome assembly, Read mapping, Scaffolding, Localised reassembly |
Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping |
Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser |
https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser |
TGS-GapCloser |
TGS-GapCloser |
TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
67 |
67 |
587 |
587 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
587 |
587 |
67 |
67 |
|
|
|
tiara |
tiara |
Tool for identification of eukaryotic sequences in the metagenomic datasets. |
2024-05-23 |
https://github.com/ibe-uw/tiara |
1.0.3 |
tiara |
|
To update |
Metagenomics, Sequence Analysis |
Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection |
Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection |
Sequencing, Genomics, DNA polymorphism, DNA structural variation |
Sequencing, Genomics, DNA polymorphism |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/tiara |
https://github.com/bgruening/galaxytools/tree/master/tools/tiara |
Tiara |
TIARA |
Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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0 |
0 |
0 |
0 |
0 |
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33 |
33 |
365 |
365 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
365 |
365 |
33 |
33 |
|
|
|
tmhmm_and_signalp |
promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort |
TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb |
2010-10-21 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis |
0.0.13 |
promoter |
|
To update |
Sequence Analysis |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis |
https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis |
|
|
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0 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
6 |
520 |
587 |
12727 |
14764 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
6 |
14772 |
12729 |
589 |
521 |
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proteomics/secretome-prediction |
|
tophat |
tophat |
Tophat for Illumina |
2014-01-27 |
|
1.5.0 |
samtools |
1.22.1 |
To update |
RNA, Next Gen Mappers |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat |
|
|
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
21 |
7228 |
113 |
66524 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
66525 |
113 |
7229 |
21 |
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|
|
tophat2 |
tophat2 |
Tophat - fast splice junction mapper for RNA-Seq reads |
2014-01-27 |
http://ccb.jhu.edu/software/tophat/index.shtml |
2.1.1 |
bowtie2 |
2.5.4 |
To update |
RNA, Next Gen Mappers |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2 |
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1 |
1 |
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1 |
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1 |
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0 |
1 |
1 |
1 |
924 |
1811 |
12613 |
28442 |
6083 |
28483 |
60708 |
349023 |
271 |
1042 |
3387 |
14476 |
0 |
0 |
0 |
0 |
391941 |
76708 |
31336 |
7278 |
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|
|
tophat_fusion_post |
tophat_fusion_post |
Wrapper for Tophat-Fusion post step |
2014-01-27 |
|
0.1 |
blast+ |
|
To update |
Transcriptomics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post |
|
|
|
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0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
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0 |
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0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
36 |
49 |
191 |
251 |
1 |
191 |
2 |
814 |
4 |
12 |
85 |
120 |
0 |
0 |
0 |
0 |
1185 |
278 |
252 |
41 |
|
|
|
trim_galore |
trim_galore |
Trim Galore adaptive quality and adapter trimmer |
2015-02-28 |
http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
0.6.10 |
trim-galore |
0.6.10 |
Up-to-date |
Sequence Analysis, Fastq Manipulation |
Sequence trimming, Primer removal, Read pre-processing |
Sequence trimming, Primer removal, Read pre-processing |
Sequence analysis |
Sequence analysis |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore |
https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore |
trim_galore |
Trim Galore |
A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
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1 |
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1 |
0 |
0 |
0 |
0 |
0 |
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0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
6966 |
8378 |
297289 |
379413 |
13276 |
20041 |
284172 |
418931 |
1722 |
2020 |
36616 |
41727 |
303 |
305 |
3334 |
3366 |
843437 |
621411 |
30744 |
22267 |
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epigenetics/cut_and_run, epigenetics/estrogen-receptor-binding-site-identification, epigenetics/formation_of_super-structures_on_xi, sequence-analysis/mapping, transcriptomics/mirna-target-finder, transcriptomics/srna, variant-analysis/baculovirus-isolate-variation |
|
trimmer |
trimmer |
Trim leading or trailing characters. |
2012-12-04 |
|
0.0.1 |
|
|
To update |
Text Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer |
|
|
|
|
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
1 |
0 |
1 |
0 |
1 |
1 |
1 |
561 |
669 |
7246 |
10121 |
602 |
3059 |
10190 |
111036 |
69 |
104 |
578 |
1181 |
11 |
12 |
37 |
57 |
122395 |
18051 |
3844 |
1243 |
https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5, https://usegalaxy.eu/published/workflow?id=250e6058f160825f, https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09, https://usegalaxy.eu/published/workflow?id=7c80cd57b2de54d4, https://usegalaxy.eu/published/workflow?id=933ab5e7fe13a8e0, https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06, https://usegalaxy.org/published/workflow?id=08edef22fa132799, https://usegalaxy.org/published/workflow?id=0a3513961f0cf9dd, https://usegalaxy.org/published/workflow?id=14f62361a15f8a24, https://usegalaxy.org/published/workflow?id=3edea70fbdb9dbd9, https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4, https://usegalaxy.org/published/workflow?id=5004f1087f5e87db, https://usegalaxy.org/published/workflow?id=7ca9c5203520ca7e, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9, https://usegalaxy.org/published/workflow?id=e107d8036c064616, https://usegalaxy.org/published/workflow?id=e10859cc568da07c, https://usegalaxy.org/published/workflow?id=e4f1cce653812a22 |
|
|
trna_prediction |
aragorn_trna, trnascan |
Aragorn predicts tRNA and tmRNA in nucleotide sequences. |
2015-02-28 |
http://mbioserv2.mbioekol.lu.se/ARAGORN/ |
0.6 |
aragorn |
1.2.41 |
To update |
RNA |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction |
|
|
|
|
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
513 |
608 |
7300 |
7928 |
0 |
0 |
0 |
0 |
111 |
120 |
2476 |
2875 |
0 |
0 |
0 |
0 |
10803 |
9776 |
728 |
624 |
https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=9275d0c90a8713d6, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178 |
|
|
ucsc_custom_track |
build_ucsc_custom_track_1 |
Build custom track for UCSC genome browser |
2014-07-28 |
|
1.0.1 |
python |
|
To update |
Sequence Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
148 |
182 |
436 |
579 |
586 |
4184 |
2240 |
19093 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
10 |
19682 |
2676 |
4367 |
734 |
https://usegalaxy.eu/published/workflow?id=0ed8817a90caa2b1, https://usegalaxy.eu/published/workflow?id=7878623b7e959284, https://usegalaxy.org/published/workflow?id=4782a4943b6fa990 |
|
|
uniprot_rest_interface |
uniprot |
UniProt ID mapping and sequence retrieval |
2015-10-09 |
https://github.com/jdrudolph/uniprot |
0.7 |
requests |
|
To update |
Proteomics, Sequence Analysis |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface |
https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
387 |
494 |
2533 |
3404 |
532 |
1083 |
2598 |
6109 |
97 |
97 |
1129 |
1129 |
0 |
0 |
0 |
0 |
10642 |
6260 |
1674 |
1016 |
https://usegalaxy.eu/published/workflow?id=cde27d06b74ad2fd, https://usegalaxy.eu/published/workflow?id=d22dac11eba8c5a3, https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c, https://workflowhub.eu/workflows/1417?version=1, https://workflowhub.eu/workflows/1426?version=1 |
proteomics/maxquant-msstats-dda-lfq, proteomics/secretome-prediction |
|
unique |
bg_uniq |
This tool returns all unique lines from a tab-separated file. |
2015-02-28 |
https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation |
0.4 |
python |
|
To update |
Text Manipulation |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation |
https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
537 |
648 |
6125 |
9172 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
83 |
83 |
492 |
492 |
9664 |
6617 |
731 |
620 |
https://usegalaxy.eu/published/workflow?id=2d2d0c2231babc50, https://usegalaxy.eu/published/workflow?id=516b4d4146e4af66, https://usegalaxy.eu/published/workflow?id=6064d1dd87b458be, https://usegalaxy.eu/published/workflow?id=6f4bbed7a320dc2f, https://usegalaxy.eu/published/workflow?id=836cc09d17eaecb0, https://usegalaxy.eu/published/workflow?id=b46b51b2860b63d5, https://usegalaxy.eu/published/workflow?id=c9423228df977254, https://usegalaxy.eu/published/workflow?id=c94a1d028357c81e, https://usegalaxy.eu/published/workflow?id=ca286c2fdc71e960, https://usegalaxy.eu/published/workflow?id=cde27d06b74ad2fd, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://usegalaxy.eu/published/workflow?id=f7a7c72489d6b3d4, https://workflowhub.eu/workflows/117?version=1, https://workflowhub.eu/workflows/1417?version=1, https://workflowhub.eu/workflows/1480?version=1, https://workflowhub.eu/workflows/1631?version=1 |
assembly/metagenomics-assembly, ecology/ENA_Biodiv_submission, genome-annotation/bacterial-comparative-genomics-dataset-construction, microbiome/metagenomics-assembly, proteomics/secretome-prediction |
|
varscan_version_2 |
varscan |
VarScan wrapper |
2013-11-17 |
https://dkoboldt.github.io/varscan/ |
2.4.2 |
varscan |
2.4.6 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2 |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
626 |
819 |
7561 |
9274 |
2644 |
6123 |
14138 |
55924 |
441 |
534 |
2664 |
3327 |
45 |
45 |
153 |
153 |
68678 |
24516 |
7521 |
3756 |
https://usegalaxy.org/published/workflow?id=3d5347f1e8ee7db2, https://usegalaxy.org/published/workflow?id=683a0ab042fa34c9, https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4, https://usegalaxy.org/published/workflow?id=80b12b6e7ac8861f, https://usegalaxy.org/published/workflow?id=9a1b4c9747bf6ae0, https://usegalaxy.org/published/workflow?id=a37961bf3d435918, https://usegalaxy.org/published/workflow?id=a765dc267c6a5c3a, https://usegalaxy.org/published/workflow?id=a7a145c196aa55c9, https://usegalaxy.org/published/workflow?id=a7ee7de93a7fb261, https://usegalaxy.org/published/workflow?id=c4a1246974f279c5, https://usegalaxy.org/published/workflow?id=e2432c4d2b61705a, https://usegalaxy.org/published/workflow?id=ff137b61d4ef1b86 |
|
|
vcf2pgsnp |
vcf2pgSnp |
VCF to pgSnp |
2014-07-28 |
|
1.0.0 |
|
|
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
57 |
72 |
163 |
241 |
172 |
614 |
1040 |
2765 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3006 |
1203 |
686 |
229 |
|
|
|
vcf_annotate |
vcf_annotate |
Annotate a VCF file (dbSNP, hapmap) |
2014-01-27 |
|
1.0.0 |
|
|
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
1 |
0 |
1 |
23 |
54 |
160 |
340 |
0 |
0 |
0 |
0 |
342 |
160 |
56 |
23 |
|
|
|
vcf_extract |
vcf_extract |
Extract reads from a specified region |
2014-01-27 |
|
1.0.0 |
|
|
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
9 |
308 |
569 |
0 |
0 |
0 |
0 |
569 |
308 |
9 |
5 |
|
|
|
vcf_filter |
vcf_filter |
Filter a VCF file |
2014-01-27 |
|
1.0.0 |
|
|
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
183 |
199 |
494 |
630 |
0 |
0 |
0 |
0 |
15 |
56 |
147 |
606 |
0 |
0 |
0 |
0 |
1236 |
641 |
255 |
198 |
|
|
|
vcf_intersect |
vcf_intersect |
Generate the intersection of two VCF files |
2014-01-27 |
|
1.0.0 |
|
|
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
19 |
0 |
0 |
0 |
0 |
16 |
28 |
204 |
463 |
0 |
0 |
0 |
0 |
482 |
204 |
31 |
16 |
|
|
|
vcftools_annotate |
vcftools_annotate |
Annotate VCF using custom/user-defined annotations |
2013-11-24 |
https://vcftools.github.io/ |
0.1 |
echo |
|
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
95 |
127 |
179 |
280 |
640 |
1445 |
2025 |
4484 |
7 |
16 |
75 |
156 |
3 |
3 |
3 |
3 |
4923 |
2282 |
1591 |
745 |
https://usegalaxy.org/published/workflow?id=a7a145c196aa55c9, https://usegalaxy.org/published/workflow?id=e7586d70715207b5, https://usegalaxy.org/published/workflow?id=ff137b61d4ef1b86 |
|
|
vcftools_compare |
vcftools_compare |
Compare VCF files to get overlap and uniqueness statistics |
2013-11-24 |
https://vcftools.github.io/ |
0.1 |
tabix |
1.11 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
138 |
181 |
461 |
726 |
0 |
0 |
0 |
0 |
0 |
12 |
0 |
16 |
0 |
0 |
0 |
0 |
742 |
461 |
193 |
138 |
|
|
|
vcftools_consensus |
vcftools_consensus |
Apply VCF variants to a fasta file to create consensus sequence |
2016-10-16 |
https://vcftools.github.io/ |
0.1.11 |
samtools |
1.22.1 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
vcftools_isec |
vcftools_isec |
Intersect multiple VCF datasets |
2013-11-24 |
https://vcftools.github.io/ |
0.1.1 |
tabix |
1.11 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
110 |
144 |
370 |
622 |
0 |
1 |
0 |
1 |
28 |
50 |
43 |
504 |
0 |
0 |
0 |
0 |
1127 |
413 |
195 |
138 |
https://usegalaxy.org.au/published/workflow?id=3d5deed70ac9bde4 |
|
|
vcftools_merge |
vcftools_merge |
Merge multiple VCF datasets into a single dataset |
2013-11-24 |
https://vcftools.github.io/ |
0.1.11 |
tabix |
1.11 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
285 |
342 |
1115 |
1467 |
1 |
1 |
1 |
1 |
50 |
72 |
112 |
481 |
0 |
0 |
0 |
0 |
1949 |
1228 |
415 |
336 |
https://usegalaxy.eu/published/workflow?id=c00fe92f9a579a15 |
|
|
vcftools_slice |
vcftools_slice |
Subset VCF dataset by genomic regions |
2013-11-24 |
https://vcftools.github.io/ |
0.1 |
echo |
|
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
58 |
73 |
445 |
502 |
127 |
381 |
538 |
8328 |
7 |
19 |
75 |
157 |
0 |
1 |
0 |
5 |
8992 |
1058 |
474 |
192 |
|
|
|
vcftools_subset |
vcftools_subset |
Select samples from a VCF dataset |
2013-11-24 |
https://vcftools.github.io/ |
0.1 |
tabix |
1.11 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset |
https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
40 |
51 |
94 |
147 |
0 |
0 |
0 |
0 |
8 |
19 |
71 |
142 |
0 |
0 |
0 |
0 |
289 |
165 |
70 |
48 |
|
|
|
venn_list |
venn_list |
Draw Venn Diagram (PDF) from lists, FASTA files, etc |
2013-09-26 |
https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list |
0.1.2 |
galaxy_sequence_utils |
1.2.0 |
To update |
Graphics, Sequence Analysis, Visualization |
|
|
|
|
peterjc |
https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list |
https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
764 |
928 |
7475 |
8987 |
955 |
2175 |
9138 |
19328 |
0 |
0 |
0 |
0 |
27 |
27 |
117 |
117 |
28432 |
16730 |
3130 |
1746 |
https://usegalaxy.eu/published/workflow?id=2a123e08436a89f1, https://usegalaxy.eu/published/workflow?id=9e0d784860d6cc91, https://usegalaxy.eu/published/workflow?id=ca286c2fdc71e960 |
|
|
viennarna |
viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup |
ViennaRNA - Prediction and comparison of RNA secondary structures |
2015-02-28 |
http://www.tbi.univie.ac.at/RNA/ |
2.2.10 |
viennarna |
2.7.0 |
To update |
RNA |
|
|
|
|
rnateam |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna |
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna |
|
|
|
|
0 |
0 |
21 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
21 |
21 |
155 |
209 |
2275 |
8658 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8658 |
2275 |
209 |
155 |
https://usegalaxy.eu/published/workflow?id=58fd339165ded462, https://usegalaxy.eu/published/workflow?id=5cd167ed9e159e73, https://usegalaxy.eu/published/workflow?id=9b1b135109072e71, https://usegalaxy.eu/published/workflow?id=bc4155d947ea0808, https://usegalaxy.eu/published/workflow?id=e51f857dd851e7d7 |
|
|
vpt |
vpt_extract, vpt_segment |
Vizgen Post-processing Tool |
2025-04-29 |
https://vizgen.github.io/vizgen-postprocessing/ |
1.3.0 |
|
|
To update |
Single Cell, Spatial Omics, Transcriptomics, Imaging |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/vpt |
https://github.com/bgruening/galaxytools/tree/master/tools/vpt |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
29 |
29 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
29 |
29 |
3 |
3 |
|
|
|
vrhyme |
vrhyme |
Tool for dereplication and binning virus genomes from metagenomes. |
2025-05-14 |
https://github.com/AnantharamanLab/vRhyme |
1.1.0 |
vrhyme |
1.1.0 |
Up-to-date |
Metagenomics |
Scaffolding, Read binning, Read mapping, Sequence trimming |
Scaffolding, Read binning, Read mapping, Sequence trimming |
Metagenomics, Microbial ecology, Model organisms, Machine learning, Sequence assembly |
Metagenomics, Microbial ecology, Model organisms, Machine learning, Sequence assembly |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/vrhyme |
https://github.com/bgruening/galaxytools/tree/master/tools/vrhyme |
vRhyme |
vRhyme |
vRhyme enables binning of viral genomes from metagenomes. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
47 |
47 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
47 |
47 |
6 |
6 |
|
|
|
vt |
vt_@BINARY@, vt_@BINARY@ |
A tool set for short variant discovery in genetic sequence data. |
2015-02-28 |
|
0.2 |
vt |
2015.11.10 |
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
bgruening |
https://github.com/atks/vt |
https://github.com/bgruening/galaxytools/tree/master/tools/vt |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
weightedaverage |
wtavg |
Assign weighted-average of the values of features overlapping an interval |
2014-04-01 |
|
1.0.1 |
galaxy-ops |
1.1.0 |
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
76 |
119 |
2308 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2308 |
119 |
76 |
10 |
|
|
|
whisper |
whisper |
Transcribe audio or video files to text using the OpenAI Whisper. |
2024-04-23 |
https://github.com/bgruening/galaxytools/tree/master/tools/whisper |
20231117 |
|
|
To update |
Machine Learning |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/whisper |
https://github.com/bgruening/galaxytools/tree/master/tools/whisper |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
27 |
27 |
388 |
388 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
388 |
388 |
27 |
27 |
https://usegalaxy.eu/published/workflow?id=a2284469005518e1 |
|
|
whisperx |
whisperx |
Transcribe audio or video files to text using the OpenAI Whisper and speaker diarization using pyannote audio |
2025-07-01 |
https://github.com/bgruening/galaxytools/tree/master/tools/whisperx |
3.4.2 |
|
|
To update |
Machine Learning |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/whisperx |
https://github.com/bgruening/galaxytools/tree/master/tools/whisperx |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
9 |
87 |
87 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
87 |
87 |
9 |
9 |
|
|
|
windowsplitter |
winSplitter |
Make windows |
2014-04-01 |
|
1.0.1 |
bx-python |
0.14.0 |
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
11 |
37 |
335 |
143 |
3983 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3994 |
143 |
337 |
37 |
|
|
|
wordcloud |
wordcloud |
A little word cloud generator in Python. |
2024-12-13 |
https://github.com/amueller/word_cloud |
1.9.4 |
wordcloud |
|
To update |
Visualization |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud |
https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
29 |
29 |
190 |
190 |
0 |
0 |
0 |
0 |
2 |
2 |
46 |
46 |
0 |
0 |
0 |
0 |
236 |
236 |
31 |
31 |
https://usegalaxy.eu/published/workflow?id=0b568c9735c03360, https://usegalaxy.eu/published/workflow?id=3a25999d71a2343a, https://usegalaxy.eu/published/workflow?id=c917db7d7ba7ea6f, https://workflowhub.eu/workflows/1623?version=1, https://workflowhub.eu/workflows/1884?version=1, https://workflowhub.eu/workflows/1953?version=1 |
digital-humanities/introduction_to_dh, digital-humanities/open-refine-tutorial, digital-humanities/text_mining_chinese |
|
wtdbg |
wtdbg |
WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. |
2018-06-12 |
https://github.com/ruanjue/wtdbg2 |
2.5 |
wtdbg |
2.5 |
Up-to-date |
Assembly |
Genome assembly, De-novo assembly |
Genome assembly, De-novo assembly |
Sequence assembly, Sequencing |
Sequence assembly, Sequencing |
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg |
https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg |
wtdbg2 |
wtdbg2 |
Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
366 |
451 |
1313 |
1904 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
28 |
28 |
145 |
145 |
2049 |
1458 |
479 |
394 |
|
|
|
xy_plot |
XY_Plot_1 |
Plotting tool for multiple series and graph types |
2013-09-25 |
|
1.0.2 |
r-base |
|
To update |
Graphics, Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot |
https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
818 |
1006 |
4398 |
6497 |
1927 |
3998 |
5925 |
16639 |
597 |
680 |
2952 |
3388 |
101 |
101 |
344 |
344 |
26868 |
13619 |
5785 |
3443 |
https://usegalaxy.eu/published/workflow?id=17ad465d9515cd25, https://usegalaxy.eu/published/workflow?id=25850714d13f0b0f, https://usegalaxy.eu/published/workflow?id=c1e26abe61c69688, https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19, https://usegalaxy.eu/published/workflow?id=ce21961260fe4351, https://usegalaxy.eu/published/workflow?id=dadca1020f586338, https://usegalaxy.eu/published/workflow?id=f21d6a40a10a8ae8, https://usegalaxy.org.au/published/workflow?id=2717e90438c7fb8c, https://usegalaxy.org.au/published/workflow?id=5877e2d5eba79f36, https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3, https://usegalaxy.org/published/workflow?id=67080f040e855990, https://usegalaxy.org/published/workflow?id=6f090b2c259847d2, https://usegalaxy.org/published/workflow?id=746f4eef47648b26, https://usegalaxy.org/published/workflow?id=775335812a6b7a61, https://usegalaxy.org/published/workflow?id=9cc814d43379c2a6, https://usegalaxy.org/published/workflow?id=bc01b8b203ecc754, https://usegalaxy.org/published/workflow?id=c50f10ecd1ac2ff9, https://usegalaxy.org/published/workflow?id=d653eaefcf6b4697, https://usegalaxy.org/published/workflow?id=e3c1736cca484dda, https://workflowhub.eu/workflows/1412?version=1, https://workflowhub.eu/workflows/1465?version=1, https://workflowhub.eu/workflows/652?version=1 |
microbiome/mothur-miseq-sop, microbiome/mothur-miseq-sop-short |
|
yolo |
json2yolosegment, yolo_predict, yolo_training |
tools for building yolo workflows. |
2025-06-12 |
https://github.com/bgruening/galaxytools |
8.3.0 |
|
|
To update |
Imaging |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools |
https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/yolo |
|
|
|
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
166 |
166 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
166 |
166 |
6 |
6 |
https://usegalaxy.eu/published/workflow?id=751e3e2c338949c0, https://workflowhub.eu/workflows/1840?version=1 |
imaging/yolo-segmentation-training |
|
AMRFinderPlus |
amrfinderplus |
"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms. |
2023-05-12 |
https://github.com/ncbi/amr |
3.12.8 |
ncbi-amrfinderplus |
4.0.23 |
To update |
Sequence Analysis |
Antimicrobial resistance prediction |
Antimicrobial resistance prediction |
Microbiology, Public health and epidemiology, Infectious disease |
Microbiology, Public health and epidemiology, Infectious disease |
iuc |
https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus |
amrfinderplus |
AMRFinderPlus |
AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
953 |
953 |
45130 |
45130 |
689 |
689 |
17362 |
17362 |
0 |
0 |
0 |
0 |
28 |
28 |
1863 |
1863 |
64355 |
64355 |
1670 |
1670 |
https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=32de10b9de8a999a, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=9c0fbd9f51a9857f, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=d3dc805cd43b2737, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=8 |
|
|
Beacon2_Import |
beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence |
Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants. |
2024-07-22 |
https://pypi.org/project/beacon2-import/ |
2.2.4 |
beacon2-import |
2.2.4 |
Up-to-date |
Variant Analysis |
Service discovery, Database search, Genetic variation analysis |
Service discovery, Database search, Genetic variation analysis |
Genetic variation, Population genetics, Data security, Rare diseases |
Genetic variation, Population genetics, Data security, Rare diseases |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import |
ga4gh_beacon |
GA4GH Beacon |
A global search engine for genetic mutations. |
|
0 |
12 |
12 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
61 |
61 |
0 |
0 |
0 |
0 |
1 |
1 |
170 |
170 |
0 |
0 |
0 |
0 |
231 |
231 |
8 |
8 |
|
variant-analysis/beacon_cnv_query, variant-analysis/beaconise_1000hg |
|
ISEScan |
isescan |
"ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements." |
2022-09-01 |
https://github.com/xiezhq/ISEScan |
1.7.3 |
isescan |
1.7.3 |
Up-to-date |
Sequence Analysis |
Structural variation detection |
Structural variation detection |
Genomics, DNA structural variation, Sequence analysis, Genetic variation |
Genomics, Sequence analysis, Genetic variation |
iuc |
https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan |
ISEScan |
ISEScan |
Automated identification of insertion sequence elements in prokaryotic genomes. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
392 |
392 |
67516 |
67516 |
237 |
237 |
1535 |
1535 |
116 |
116 |
7464 |
7464 |
37 |
37 |
1759 |
1759 |
78274 |
78274 |
782 |
782 |
https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=b1afc8d1e81fc904, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.eu/published/workflow?id=fd63b9884fda75b6, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=3940186d02245b1d, https://usegalaxy.org/published/workflow?id=49da012e2839c046, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=649cdc14757e5755, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=12, https://workflowhub.eu/workflows/1513?version=1 |
genome-annotation/bacterial-genome-annotation |
|
abricate |
abricate, abricate_list, abricate_summary |
Mass screening of contigs for antiobiotic resistance genes |
2016-07-29 |
https://github.com/tseemann/abricate |
1.0.1 |
abricate |
1.0.1 |
Up-to-date |
Sequence Analysis |
Antimicrobial resistance prediction |
Antimicrobial resistance prediction |
Genomics, Microbiology |
Genomics, Microbiology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate |
ABRicate |
ABRicate |
Mass screening of contigs for antimicrobial resistance or virulence genes. |
|
0 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
4522 |
4679 |
799841 |
821957 |
3401 |
3468 |
401550 |
405363 |
1867 |
2216 |
578174 |
600408 |
85 |
85 |
19178 |
19178 |
1846906 |
1798743 |
10448 |
9875 |
https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=32de10b9de8a999a, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=6984990d0ac2e1e6, https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=77e5bbd317750915, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=abe85758e77c78e6, https://usegalaxy.eu/published/workflow?id=b203dec6ee6da2fd, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=e37cc0b64774561b, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=f30f8e7dcd50cd0d, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d78f885b4b86635f, https://usegalaxy.org.au/published/workflow?id=e20172eb0f30d6cd, https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2, https://usegalaxy.org/published/workflow?id=00596e862edb23f2, https://usegalaxy.org/published/workflow?id=2078a54de1f2628d, https://usegalaxy.org/published/workflow?id=2b4b1fe82258f303, https://usegalaxy.org/published/workflow?id=3c177fdf38311118, https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5, https://usegalaxy.org/published/workflow?id=562bcaa9b4d2e8a4, https://usegalaxy.org/published/workflow?id=69d8863d40524120, https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1, https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8, https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665, https://usegalaxy.org/published/workflow?id=9ba6da7dae465d3e, https://usegalaxy.org/published/workflow?id=9c0fbd9f51a9857f, https://usegalaxy.org/published/workflow?id=aaf8e740b3f8e2c0, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=cce88bc57b180d09, https://usegalaxy.org/published/workflow?id=d3dc805cd43b2737, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://usegalaxy.org/published/workflow?id=ef187f85b103d858, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be, https://usegalaxy.org/published/workflow?id=fde774a049875466, https://workflowhub.eu/workflows/1049?version=8, https://workflowhub.eu/workflows/1062?version=1, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1495?version=1, https://workflowhub.eu/workflows/470?version=1 |
microbiome/pathogen-detection-from-nanopore-foodborne-data |
|
abritamr |
abritamr |
A pipeline for running AMRfinderPlus and collating results into functional classes |
2023-04-03 |
https://zenodo.org/record/7370628 |
1.0.19 |
abritamr |
1.0.19 |
Up-to-date |
Sequence Analysis |
Antimicrobial resistance prediction |
Antimicrobial resistance prediction |
Microbiology, Public health and epidemiology, Infectious disease, Antimicrobial resistance |
Microbiology, Public health and epidemiology, Infectious disease |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr |
abritamr |
abriTAMR |
an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
319 |
319 |
2633 |
2633 |
0 |
0 |
0 |
0 |
97 |
97 |
880 |
880 |
3 |
3 |
5 |
5 |
3518 |
3518 |
419 |
419 |
https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://workflowhub.eu/workflows/634?version=1 |
|
|
abyss |
abyss-pe |
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler |
2015-04-14 |
http://www.bcgsc.ca/platform/bioinfo/software/abyss |
2.3.10 |
abyss |
2.3.10 |
Up-to-date |
Assembly |
Genome assembly, De-novo assembly, Scaffolding |
Genome assembly, De-novo assembly, Scaffolding |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss |
abyss |
ABySS |
De novo genome sequence assembler using short reads. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1258 |
1368 |
7148 |
7779 |
183 |
414 |
505 |
1305 |
398 |
398 |
2608 |
2608 |
11 |
11 |
16 |
16 |
11708 |
10277 |
2191 |
1850 |
|
|
|
adapter_removal |
adapter_removal |
Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. |
2022-05-04 |
https://github.com/MikkelSchubert/adapterremoval |
2.3.4 |
adapterremoval |
2.3.4 |
Up-to-date |
Fasta Manipulation, Sequence Analysis |
Sequence trimming, Sequence merging, Primer removal |
Sequence trimming, Sequence merging, Primer removal |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal |
adapterremoval |
AdapterRemoval |
AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
108 |
108 |
841 |
841 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
841 |
841 |
108 |
108 |
|
|
|
add_input_name_as_column |
addName |
Add input name as column on an existing tabular file |
2020-03-24 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column |
0.2.0 |
python |
|
To update |
Text Manipulation |
|
|
|
|
mvdbeek |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
260 |
306 |
87241 |
99370 |
296 |
466 |
27850 |
30946 |
34 |
34 |
2760 |
2760 |
0 |
0 |
0 |
0 |
133076 |
117851 |
806 |
590 |
https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=098f43ded1b5fa7f, https://usegalaxy.eu/published/workflow?id=16418e8b023ff226, https://usegalaxy.eu/published/workflow?id=1f3f6757de60d3cf, https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.eu/published/workflow?id=31c6dcd3a25620df, https://usegalaxy.eu/published/workflow?id=389d992ff7268247, https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc, https://usegalaxy.eu/published/workflow?id=89ed570bc0703472, https://usegalaxy.eu/published/workflow?id=8d00a8b70b0c019c, https://usegalaxy.eu/published/workflow?id=9aa290ce1927d700, https://usegalaxy.eu/published/workflow?id=9c5a0596956064a6, https://usegalaxy.eu/published/workflow?id=9e497c5c9e64d9b3, https://usegalaxy.eu/published/workflow?id=cc385bd4376a907c, https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21, https://usegalaxy.eu/published/workflow?id=df99c8a88309918e, https://usegalaxy.eu/published/workflow?id=f4a55ef0d4c2cd97, https://usegalaxy.org.au/published/workflow?id=2df1d32f78974528, https://usegalaxy.org.au/published/workflow?id=2fee25e188531691, https://usegalaxy.org.au/published/workflow?id=446ba22c3d2f3367, https://usegalaxy.org.au/published/workflow?id=499245b3a113e06d, https://usegalaxy.org.au/published/workflow?id=518d27f68e05a356, https://usegalaxy.org.au/published/workflow?id=66e530368fd40abd, https://usegalaxy.org.au/published/workflow?id=9016b2be61f89053, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=cf775b8ff0745456, https://usegalaxy.org.au/published/workflow?id=e2c49586dc941f38, https://usegalaxy.org.au/published/workflow?id=e6552643a3713b50, https://usegalaxy.org/published/workflow?id=1e264fc06d87899f, https://usegalaxy.org/published/workflow?id=44bcae0e352563f9, https://usegalaxy.org/published/workflow?id=450c2181f89e6b23, https://usegalaxy.org/published/workflow?id=48dd4a4cb5536670, https://usegalaxy.org/published/workflow?id=682b1c7e2ad9d443, https://usegalaxy.org/published/workflow?id=768cee70d9aa8cc6, https://usegalaxy.org/published/workflow?id=b1b4fc510099d592, https://usegalaxy.org/published/workflow?id=bf79271a438ffa54, https://usegalaxy.org/published/workflow?id=e50e36a25bae863c, https://usegalaxy.org/published/workflow?id=f18e6fa5270fcd37, https://workflowhub.eu/workflows/1057?version=9, https://workflowhub.eu/workflows/1564?version=1 |
evolution/mtb_transmission |
|
aegean |
aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval |
AEGeAn toolkit wrappers |
2021-01-03 |
https://github.com/BrendelGroup/AEGeAn |
0.16.0 |
aegean |
0.16.0 |
Up-to-date |
Transcriptomics, Sequence Analysis |
Sequence annotation |
Sequence annotation |
Sequence analysis, Gene structure |
Sequence analysis, Gene structure |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean |
gaeval |
GAEVAL |
Gene Annotation EVAluation. |
|
0 |
4 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
4 |
0 |
69 |
69 |
291 |
291 |
57 |
57 |
117 |
117 |
33 |
33 |
2747 |
2747 |
22 |
22 |
52 |
52 |
3207 |
3207 |
181 |
181 |
https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.org.au/published/workflow?id=4e161a8f5098cc49, https://workflowhub.eu/workflows/1525?version=1, https://workflowhub.eu/workflows/754?version=1 |
genome-annotation/funannotate |
|
aldex2 |
aldex2 |
Performs analysis Of differential abundance taking sample variation into account |
2022-06-29 |
https://github.com/ggloor/ALDEx_bioc |
1.26.0 |
bioconductor-aldex2 |
1.38.0 |
To update |
Metagenomics |
Statistical inference |
Statistical inference |
Gene expression, Statistics and probability |
Gene expression, Statistics and probability |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 |
aldex2 |
ALDEx2 |
A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
64 |
64 |
356 |
356 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
356 |
356 |
64 |
64 |
|
|
|
allegro |
allegro |
Linkage and haplotype analysis from deCODE |
2017-11-19 |
http://www.decode.com/software/ |
2 |
allegro |
3 |
To update |
Variant Analysis |
Sequence motif discovery |
Sequence motif discovery |
Sequence analysis, Transcription factors and regulatory sites, DNA |
Sequence analysis, Transcription factors and regulatory sites, DNA |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro |
allegro |
Allegro |
It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
amplican |
amplican |
AmpliCan is an analysis tool for genome editing. |
2021-09-22 |
https://github.com/valenlab/amplican |
1.14.0 |
bioconductor-amplican |
1.28.0 |
To update |
Sequence Analysis |
Alignment, Standardisation and normalisation |
Alignment, Standardisation and normalisation |
PCR experiment, Statistics and probability |
PCR experiment, Statistics and probability |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican |
amplican |
amplican |
It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
18 |
18 |
85 |
85 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
85 |
85 |
18 |
18 |
|
|
|
ampligone |
ampligone |
AmpliGone is a tool which accurately finds and removes primer sequences from NGS reads in an amplicon experiment. |
2025-07-29 |
https://rivm-bioinformatics.github.io/AmpliGone/latest/ |
2.0.1 |
AmpliGone |
2.0.1 |
Up-to-date |
Sequence Analysis, Fastq Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampligone |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampligone |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
ampvis2 |
ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_export_otu, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn |
ampvis2 |
2022-04-04 |
https://github.com/MadsAlbertsen/ampvis2/ |
2.8.9 |
|
|
To update |
Metagenomics |
Analysis, Visualisation |
Analysis, Visualisation |
Biodiversity |
Biodiversity |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 |
ampvis |
ampvis |
ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. |
|
0 |
0 |
20 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
19 |
0 |
56 |
56 |
3292 |
3292 |
15 |
15 |
28 |
28 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3320 |
3320 |
71 |
71 |
https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=b4ed2a3690da0196, https://usegalaxy.eu/published/workflow?id=e91def3fc9738ebb, https://usegalaxy.org/published/workflow?id=82973143b28bb767, https://usegalaxy.org/published/workflow?id=b76c55dafd44b305, https://workflowhub.eu/workflows/1275?version=2, https://workflowhub.eu/workflows/1855?version=1 |
microbiome/mgnify-amplicon |
|
ancombc |
ancombc |
Performs analysis of compositions of microbiomes with bias correction. |
2022-07-16 |
https://github.com/FrederickHuangLin/ANCOMBC |
1.4.0 |
bioconductor-ancombc |
2.8.0 |
To update |
Metagenomics |
DNA barcoding |
DNA barcoding |
Microbial ecology, Metagenomics, Taxonomy |
Microbial ecology, Metagenomics, Taxonomy |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc |
ancombc |
ANCOMBC |
Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
20 |
20 |
64 |
64 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
64 |
64 |
20 |
20 |
|
|
|
anndata |
anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom |
Import, Export, Inspect and Manipulate Anndata and Loom objects |
2019-03-21 |
https://anndata.readthedocs.io |
0.10.9 |
anndata |
0.6.22.post1 |
To update |
Single Cell, Spatial Omics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata |
anndata |
anndata |
From https://anndata.readthedocs.io/en/latest/"Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray." |
|
0 |
5 |
5 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
5 |
787 |
890 |
47423 |
51315 |
459 |
467 |
23370 |
23451 |
139 |
141 |
11736 |
12386 |
2 |
2 |
56 |
56 |
87208 |
82585 |
1500 |
1387 |
https://usegalaxy.eu/published/workflow?id=030e978022e19375, https://usegalaxy.eu/published/workflow?id=0e6e181234b48121, https://usegalaxy.eu/published/workflow?id=171d6fca2c3339e2, https://usegalaxy.eu/published/workflow?id=21315ffd2df2f159, https://usegalaxy.eu/published/workflow?id=35c092316cdc27d1, https://usegalaxy.eu/published/workflow?id=37e51e215684bdcc, https://usegalaxy.eu/published/workflow?id=3adf77a0576af98c, https://usegalaxy.eu/published/workflow?id=3fe3b9a57762841e, https://usegalaxy.eu/published/workflow?id=409ac72c9906f16a, https://usegalaxy.eu/published/workflow?id=4756053b2596b6cf, https://usegalaxy.eu/published/workflow?id=49a6ddcba35bf085, https://usegalaxy.eu/published/workflow?id=5b8e4ae3447934d9, https://usegalaxy.eu/published/workflow?id=704e6c9bc51db49f, https://usegalaxy.eu/published/workflow?id=715ca378c1d68de3, https://usegalaxy.eu/published/workflow?id=73aa794916b91bb2, https://usegalaxy.eu/published/workflow?id=767f8c990316b66a, https://usegalaxy.eu/published/workflow?id=77e85bde57477194, https://usegalaxy.eu/published/workflow?id=78dc6fca5b58ec05, https://usegalaxy.eu/published/workflow?id=7d22eea4278570e8, https://usegalaxy.eu/published/workflow?id=921cab3e6faf30be, https://usegalaxy.eu/published/workflow?id=9a657909d6191203, https://usegalaxy.eu/published/workflow?id=9a9bbd8046da7b19, https://usegalaxy.eu/published/workflow?id=9d15b328d8408715, https://usegalaxy.eu/published/workflow?id=b5627201bb4f6943, https://usegalaxy.eu/published/workflow?id=d1a1e6070c0a36ca, https://usegalaxy.eu/published/workflow?id=d20fbb95f15386f5, https://usegalaxy.eu/published/workflow?id=d70dc4cfeedb690b, https://usegalaxy.eu/published/workflow?id=ddced7b107e4707a, https://usegalaxy.eu/published/workflow?id=decd6ad0b41289ef, https://usegalaxy.eu/published/workflow?id=e2391c40d24d403f, https://usegalaxy.eu/published/workflow?id=e472096116cbe392, https://usegalaxy.eu/published/workflow?id=e4e969e9943cdaa5, https://usegalaxy.eu/published/workflow?id=f05754467a439134, https://usegalaxy.eu/published/workflow?id=f689faf267fbe504, https://usegalaxy.org.au/published/workflow?id=102eb726f63f3190, https://usegalaxy.org.au/published/workflow?id=218ffb4438833bdd, https://usegalaxy.org.au/published/workflow?id=471615c412b305f2, https://usegalaxy.org.au/published/workflow?id=57321b64220d5835, https://usegalaxy.org.au/published/workflow?id=8055596d732590d6, https://usegalaxy.org.au/published/workflow?id=94241afd07e8a8b7, https://usegalaxy.org/published/workflow?id=dd43ae9a5b303086, https://usegalaxy.org/published/workflow?id=ea3257e0ef9f505a, https://usegalaxy.org/published/workflow?id=f35ccb693cd874c1, https://workflowhub.eu/workflows/1077?version=1, https://workflowhub.eu/workflows/1078?version=1, https://workflowhub.eu/workflows/1256?version=1, https://workflowhub.eu/workflows/1356?version=1, https://workflowhub.eu/workflows/1362?version=1, https://workflowhub.eu/workflows/1485?version=1, https://workflowhub.eu/workflows/1490?version=1, https://workflowhub.eu/workflows/1496?version=1, https://workflowhub.eu/workflows/1501?version=1, https://workflowhub.eu/workflows/1506?version=1, https://workflowhub.eu/workflows/1519?version=1, https://workflowhub.eu/workflows/1520?version=1, https://workflowhub.eu/workflows/1523?version=1, https://workflowhub.eu/workflows/1524?version=1, https://workflowhub.eu/workflows/1527?version=1, https://workflowhub.eu/workflows/1529?version=1, https://workflowhub.eu/workflows/1531?version=1, https://workflowhub.eu/workflows/1537?version=1, https://workflowhub.eu/workflows/1539?version=1, https://workflowhub.eu/workflows/1543?version=1, https://workflowhub.eu/workflows/1548?version=1, https://workflowhub.eu/workflows/1550?version=1, https://workflowhub.eu/workflows/1551?version=1, https://workflowhub.eu/workflows/1556?version=1, https://workflowhub.eu/workflows/1561?version=1, https://workflowhub.eu/workflows/1565?version=1, https://workflowhub.eu/workflows/1574?version=1, https://workflowhub.eu/workflows/1745?version=2, https://workflowhub.eu/workflows/468?version=3, https://workflowhub.eu/workflows/512?version=2, https://workflowhub.eu/workflows/513?version=3, https://workflowhub.eu/workflows/646?version=2 |
single-cell/bulk-music-2-preparescref, single-cell/pseudobulk-analysis, single-cell/scatac-batch-correction-snapatac2, single-cell/scatac-preprocessing-tenx, single-cell/scatac-standard-processing-snapatac2, single-cell/scrna-case_alevin, single-cell/scrna-case_alevin-combine-datasets, single-cell/scrna-case_basic-pipeline, single-cell/scrna-case_cell-cycle, single-cell/scrna-case_monocle3-trajectories, single-cell/scrna-case_trajectories, single-cell/scrna-data-ingest, single-cell/scrna-ncbi-anndata, single-cell/scrna-plant, single-cell/scrna-scanpy-pbmc3k |
|
anndata2ri |
anndata2ri |
Convert between Anndata and SingCellExperiment objects |
2025-02-12 |
https://github.com/theislab/anndata2ri |
1.3.2 |
anndata2ri |
2.0 |
To update |
Single Cell, Convert Formats |
Data handling |
Data handling |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata2ri/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata2ri |
anndata2ri |
anndata2ri |
RPy2 converter from AnnData to SingleCellExperiment and back. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
12 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
8 |
8 |
|
|
|
annotatemyids |
annotatemyids |
annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages |
2017-11-17 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids |
3.18.0 |
bioconductor-org.hs.eg.db |
3.20.0 |
To update |
Genome annotation |
Annotation |
Annotation |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids |
annotatemyids |
annotatemyids |
This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3392 |
3780 |
31980 |
37238 |
6704 |
7867 |
62133 |
78958 |
1250 |
1315 |
6352 |
7039 |
25 |
25 |
181 |
181 |
123416 |
100646 |
12987 |
11371 |
https://usegalaxy.eu/published/workflow?id=030e978022e19375, https://usegalaxy.eu/published/workflow?id=0f7acf235096b708, https://usegalaxy.eu/published/workflow?id=227d97974573aaf2, https://usegalaxy.eu/published/workflow?id=2ae4a83327615155, https://usegalaxy.eu/published/workflow?id=2f7c04ad219a9d2d, https://usegalaxy.eu/published/workflow?id=3386856a60b35897, https://usegalaxy.eu/published/workflow?id=36eefcc25ab1fe15, https://usegalaxy.eu/published/workflow?id=6d47a24218d08930, https://usegalaxy.eu/published/workflow?id=a6290cdfa12d34ad, https://usegalaxy.eu/published/workflow?id=ca286c2fdc71e960, https://usegalaxy.eu/published/workflow?id=d9f8c5d575da02b1, https://usegalaxy.eu/published/workflow?id=f98f0e0c18222cc0, https://usegalaxy.eu/published/workflow?id=f9ddc4dd9140b293, https://usegalaxy.eu/published/workflow?id=fe6c64676be56ee9, https://usegalaxy.org.au/published/workflow?id=bdb498b1f0e8944f, https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6, https://usegalaxy.org/published/workflow?id=93bfbd7db42db543, https://workflowhub.eu/workflows/1542?version=1, https://workflowhub.eu/workflows/1548?version=1, https://workflowhub.eu/workflows/1684?version=1, https://workflowhub.eu/workflows/1703?version=1, https://workflowhub.eu/workflows/689?version=1 |
single-cell/bulk-deconvolution-evaluate, single-cell/bulk-music-2-preparescref, single-cell/bulk-music-3-preparebulk, transcriptomics/minerva-pathways, transcriptomics/rna-seq-counts-to-genes |
|
argnorm |
argnorm |
argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database |
2024-08-28 |
https://github.com/BigDataBiology/argNorm |
1.0.0 |
argnorm |
1.1.0 |
To update |
Genome annotation |
Gene functional annotation |
Gene functional annotation |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm |
argnorm |
argNorm |
argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
48 |
48 |
211 |
211 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
91 |
91 |
302 |
302 |
51 |
51 |
|
|
|
arriba |
arriba, arriba_draw_fusions, arriba_get_filters |
Arriba detects fusion genes in RNA-Seq data after running RNA-STAR |
2022-07-27 |
https://github.com/suhrig/arriba |
2.5.1 |
arriba |
2.5.1 |
Up-to-date |
Sequence Analysis, Transcriptomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba |
|
|
|
|
0 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
75 |
75 |
4142 |
4142 |
20 |
20 |
254 |
254 |
16 |
16 |
503 |
503 |
0 |
0 |
0 |
0 |
4899 |
4899 |
111 |
111 |
https://usegalaxy.eu/published/workflow?id=d0a809f0880d7ec0, https://usegalaxy.org.au/published/workflow?id=0dff588f31f1dfd6, https://usegalaxy.org.au/published/workflow?id=65250d6b30d4bc7c, https://usegalaxy.org.au/published/workflow?id=d5a3fd1faa3f0a41, https://usegalaxy.org/published/workflow?id=39810594e5c332d5, https://usegalaxy.org/published/workflow?id=b28789b6a0e1f5c9, https://workflowhub.eu/workflows/1442?version=1, https://workflowhub.eu/workflows/1792?version=1 |
proteomics/neoantigen-fusion-database-generation |
|
art |
art_454, art_illumina, art_solid |
Simulator for Illumina, 454, and SOLiD sequencing data |
2015-02-11 |
http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ |
2014.11.03.0 |
art |
2016.06.05 |
To update |
Sequence Analysis, Data Source |
Conversion |
Conversion |
Bioinformatics |
Bioinformatics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/art |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/art |
art |
ART |
ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD |
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
36 |
36 |
398 |
398 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
400 |
400 |
37 |
37 |
|
|
|
artic |
artic_guppyplex, artic_minion |
The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building |
2020-04-17 |
https://github.com/artic-network/fieldbioinformatics |
1.7.3 |
artic |
1.8.4 |
To update |
Sequence Analysis |
Sequence alignment |
Sequence alignment |
Genomics |
Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic |
artic |
ARTIC |
A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore |
|
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
2 |
1 |
206 |
206 |
13444 |
13459 |
0 |
0 |
0 |
0 |
34 |
34 |
1812 |
1812 |
0 |
0 |
0 |
0 |
15271 |
15256 |
240 |
240 |
https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3, https://workflowhub.eu/workflows/521?version=1 |
|
|
assembly_stats |
assembly_stats |
Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. |
2023-06-21 |
https://github.com/rjchallis/assembly-stats |
17.02 |
rjchallis-assembly-stats |
17.02 |
Up-to-date |
Assembly |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
18 |
18 |
32 |
32 |
32 |
32 |
18 |
18 |
|
|
|
astral |
astral |
Tool for estimating an unrooted species tree given a set of unrooted gene trees |
2024-08-28 |
https://github.com/smirarab/ASTRAL |
5.7.8 |
astral-tree |
5.7.8 |
Up-to-date |
Phylogenetics |
|
|
|
|
iuc |
https://github.com/usegalaxy-be/galaxytools/tree/main/astral |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
151 |
151 |
0 |
0 |
0 |
0 |
151 |
151 |
5 |
5 |
https://workflowhub.eu/workflows/359?version=1 |
|
|
augustus |
augustus, augustus_training |
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. |
2017-10-05 |
http://bioinf.uni-greifswald.de/augustus/ |
3.5.0 |
augustus |
3.5.0 |
Up-to-date |
Sequence Analysis |
Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation |
Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation |
Gene transcripts, Gene and protein families |
Gene transcripts, Gene and protein families |
bgruening |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus |
augustus |
AUGUSTUS |
AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
1917 |
2188 |
16670 |
19094 |
2787 |
2897 |
18204 |
19188 |
496 |
496 |
8640 |
8666 |
49 |
49 |
4693 |
4693 |
51641 |
48207 |
5630 |
5249 |
https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org/published/workflow?id=ec3cc032a90c44f1, https://workflowhub.eu/workflows/1504?version=1 |
genome-annotation/annotation-with-maker |
|
autobigs |
autobigs-cli |
Automated MLST typing from PubMLST and InstitutPasteur. |
2025-02-24 |
https://github.com/Syph-and-VPD-Lab/autoBIGS.cli |
0.6.2 |
autobigs-cli |
0.6.5 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/Syph-and-VPD-Lab/autoBIGS.cli |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/autobigs |
AutoBIGS.CLI |
AutoBIGS.CLI |
A command-line interface (CLI) based program that allows quickly batched requests for obtaining MLST profiles on multiple FASTA sequences and exporting it as a convenient CSV. Capable of querying a variety of MLST databases from both Institut Pasteur and PubMLST. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
31 |
31 |
53 |
53 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
53 |
53 |
31 |
31 |
|
|
|
b2btools |
b2btools_single_sequence |
This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. |
2022-08-09 |
https://bio2byte.be |
3.0.5+galaxy0 |
b2btools |
3.0.7 |
To update |
Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology |
Protein disorder prediction, Protein secondary structure prediction, Protein feature detection |
Protein disorder prediction, Protein secondary structure prediction |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools |
b2btools |
b2bTools |
The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
22 |
22 |
380 |
380 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
380 |
380 |
22 |
22 |
|
|
|
bakta |
bakta |
"Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis." |
2022-09-01 |
https://github.com/oschwengers/bakta |
1.9.4 |
bakta |
1.11.4 |
To update |
Sequence Analysis |
Genome annotation |
Genome annotation |
Genomics, Sequence analysis, Bioinformatics |
Genomics, Sequence analysis, Bioinformatics |
iuc |
https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta |
bakta |
Bakta |
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1503 |
1503 |
67465 |
67465 |
1017 |
1017 |
14351 |
14351 |
399 |
399 |
33530 |
33530 |
84 |
84 |
3664 |
3664 |
119010 |
119010 |
3003 |
3003 |
https://usegalaxy.eu/published/workflow?id=29c565eff0080e42, https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=4f9f7065975b3f97, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=968f0ac2617aa524, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=b1afc8d1e81fc904, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.eu/published/workflow?id=fd63b9884fda75b6, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org.au/published/workflow?id=b6bad1f167257248, https://usegalaxy.org/published/workflow?id=00596e862edb23f2, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=3940186d02245b1d, https://usegalaxy.org/published/workflow?id=49da012e2839c046, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=562bcaa9b4d2e8a4, https://usegalaxy.org/published/workflow?id=649cdc14757e5755, https://usegalaxy.org/published/workflow?id=69d8863d40524120, https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1, https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=9c0fbd9f51a9857f, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=12, https://workflowhub.eu/workflows/1352?version=3, https://workflowhub.eu/workflows/1488?version=1, https://workflowhub.eu/workflows/1513?version=1 |
genome-annotation/amr-gene-detection, genome-annotation/bacterial-genome-annotation |
|
bam2fastx |
bam2fastx |
Convert PacBio Bam File to fasta or fastq file |
2024-03-11 |
https://github.com/PacificBiosciences/pbtk |
3.5.0 |
pbtk |
3.5.0 |
Up-to-date |
Convert Formats, Fasta Manipulation, Fastq Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
53 |
53 |
180 |
180 |
69 |
69 |
372 |
372 |
14 |
14 |
80 |
80 |
0 |
0 |
0 |
0 |
632 |
632 |
136 |
136 |
|
|
|
bam_to_scidx |
bam_to_scidx |
Contains a tool that converts a BAM file to an ScIdx file. |
2015-12-07 |
https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx |
1.0.1 |
openjdk |
|
To update |
Convert Formats |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
10 |
21 |
26 |
132 |
37 |
213 |
186 |
791 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
923 |
212 |
234 |
47 |
|
|
|
bamtools |
bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag |
Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. |
2017-06-09 |
https://github.com/pezmaster31/bamtools |
2.5.2 |
bamtools |
2.5.3 |
To update |
Sequence Analysis, SAM |
Data handling, Sequence alignment analysis |
Data handling, Sequence alignment analysis |
Sequencing, Data management, Sequence analysis |
Sequencing, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split |
bamtools |
BamTools |
BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. |
|
0 |
3 |
4 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
385 |
385 |
42883 |
42883 |
247 |
247 |
6842 |
6842 |
24 |
24 |
379 |
379 |
3 |
3 |
16 |
16 |
50120 |
50120 |
659 |
659 |
https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b, https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=574e42683dc3961b, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://usegalaxy.org/published/workflow?id=a8b9252fad5fe06a, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/1061?version=1, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/1492?version=2 |
microbiome/pathogen-detection-from-nanopore-foodborne-data, variant-analysis/aiv-analysis |
|
bamtools |
bamtools |
Operate on and transform BAM datasets in various ways using bamtools |
2017-06-09 |
https://github.com/pezmaster31/bamtools |
2.5.2 |
bamtools |
2.5.3 |
To update |
Sequence Analysis, SAM |
Data handling, Sequence alignment analysis |
Data handling, Sequence alignment analysis |
Sequencing, Data management, Sequence analysis |
Sequencing, Sequence analysis |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools |
bamtools |
BamTools |
BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
583 |
746 |
13272 |
15936 |
1177 |
5735 |
56981 |
102230 |
6 |
6 |
283 |
283 |
14 |
14 |
56 |
56 |
118505 |
70592 |
6501 |
1780 |
https://usegalaxy.eu/published/workflow?id=36a4646959829018, https://usegalaxy.eu/published/workflow?id=99022559adf01c4a, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://workflowhub.eu/workflows/1480?version=1, https://workflowhub.eu/workflows/1631?version=1 |
assembly/metagenomics-assembly, microbiome/metagenomics-assembly |
|
bamtools_filter |
bamFilter |
Filter BAM datasets on various attributes using bamtools filter |
2017-06-09 |
https://github.com/pezmaster31/bamtools |
2.5.2 |
bamtools |
2.5.3 |
To update |
Sequence Analysis, SAM |
Data handling, Sequence alignment analysis |
Data handling, Sequence alignment analysis |
Sequencing, Data management, Sequence analysis |
Sequencing, Sequence analysis |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter |
bamtools |
BamTools |
BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3441 |
4000 |
113566 |
150142 |
6066 |
11844 |
91327 |
161400 |
565 |
622 |
8452 |
9127 |
521 |
523 |
2536 |
2611 |
323280 |
215881 |
16989 |
10593 |
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epigenetics/atac-seq, epigenetics/cut_and_run, sequence-analysis/mapping, single-cell/scrna-preprocessing, variant-analysis/non-dip, variant-analysis/somatic-variants |
|
bamutil |
bamutil_clip_overlap, bamutil_diff |
bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. |
2021-03-29 |
https://github.com/statgen/bamUtil |
|
bamutil |
1.0.15 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
23 |
23 |
51 |
51 |
23 |
23 |
71 |
71 |
1 |
1 |
408 |
408 |
0 |
0 |
0 |
0 |
530 |
530 |
47 |
47 |
|
|
|
bandage |
bandage_image, bandage_info |
Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily |
2018-09-06 |
https://github.com/rrwick/Bandage |
2022.09 |
bandage_ng |
2025.6.1 |
To update |
Visualization |
Sequence assembly visualisation |
Sequence assembly visualisation |
Genomics, Sequence assembly |
Genomics, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage |
bandage |
Bandage |
GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
5065 |
5359 |
74766 |
78507 |
4846 |
5038 |
63998 |
65491 |
3140 |
3234 |
25266 |
26126 |
317 |
319 |
9763 |
9780 |
179904 |
173793 |
13950 |
13368 |
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assembly/ERGA-post-assembly-QC, assembly/assembly-with-preprocessing, assembly/chloroplast-assembly, assembly/largegenome, assembly/metagenomics-assembly, assembly/mrsa-illumina, assembly/mrsa-nanopore, microbiome/metagenomics-assembly, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/plasmid-metagenomics-nanopore |
|
barcode_splitter |
barcode_splitter |
A utility to split sequence files using multiple sets of barcodes |
2019-02-21 |
https://bitbucket.org/princeton_genomics/barcode_splitter/ |
0.18.4.0 |
barcode_splitter |
0.18.6 |
To update |
Fastq Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
baredsc |
baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d |
baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. |
2023-09-06 |
https://github.com/lldelisle/baredSC |
1.1.3 |
baredsc |
1.1.3 |
Up-to-date |
Single Cell, Transcriptomics, Visualization |
Data retrieval, Expression correlation analysis, Differential gene expression profiling |
Data retrieval, Expression correlation analysis, Differential gene expression profiling |
RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability |
RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc |
baredsc |
baredSC |
The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. |
|
0 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
6 |
6 |
115 |
115 |
12 |
12 |
180 |
180 |
1 |
1 |
336 |
336 |
0 |
0 |
0 |
0 |
631 |
631 |
19 |
19 |
https://usegalaxy.eu/published/workflow?id=2da3c41ad5c11c3b, https://usegalaxy.eu/published/workflow?id=3410a75a2a4899dc, https://usegalaxy.eu/published/workflow?id=4025b5dca188e6a4, https://usegalaxy.eu/published/workflow?id=49d913cefc5daaf3, https://usegalaxy.eu/published/workflow?id=4eb8aec8a5be98b3, https://usegalaxy.eu/published/workflow?id=72c03f7b5bc9fb9d, https://usegalaxy.eu/published/workflow?id=7341ca7572447d60, https://usegalaxy.eu/published/workflow?id=967f890c0883f72a, https://usegalaxy.eu/published/workflow?id=b3d38025c7ff72ed, https://usegalaxy.eu/published/workflow?id=cdf782de6c67477a, https://usegalaxy.eu/published/workflow?id=da41880826c3d758, https://usegalaxy.eu/published/workflow?id=fb08922b0bd812a9, https://usegalaxy.org.au/published/workflow?id=2436bc493e76f438, https://usegalaxy.org.au/published/workflow?id=31a664d151978dc6, https://usegalaxy.org.au/published/workflow?id=481c666fbc7ffa02, https://usegalaxy.org.au/published/workflow?id=51aaafbd00b91717, https://usegalaxy.org.au/published/workflow?id=579da54989f5d55c, https://usegalaxy.org.au/published/workflow?id=5e3ff382ab802baf, https://usegalaxy.org.au/published/workflow?id=ac4799c5009f98d3, https://usegalaxy.org.au/published/workflow?id=b73280eaeb77a0a9, https://usegalaxy.org.au/published/workflow?id=d01ff75a4943fa79, https://usegalaxy.org.au/published/workflow?id=d6521e6c247eeaaf, https://usegalaxy.org.au/published/workflow?id=ecafc3d43b4c63f7, https://usegalaxy.org.au/published/workflow?id=ffeef94c4539c3e5, https://usegalaxy.org/published/workflow?id=0f6bb7847f8769af, https://usegalaxy.org/published/workflow?id=1a08efa0bf83d225, https://usegalaxy.org/published/workflow?id=3d0f92e7f63978b6, https://usegalaxy.org/published/workflow?id=6cad14c78ec330ac, https://usegalaxy.org/published/workflow?id=6f1da4e0830e6051, https://usegalaxy.org/published/workflow?id=84112c29ee53a5db, https://usegalaxy.org/published/workflow?id=92b67534076ae889, https://usegalaxy.org/published/workflow?id=a8fa62e35610d85e, https://usegalaxy.org/published/workflow?id=e3366346808b1f55, https://usegalaxy.org/published/workflow?id=ebdf324634e7243c, https://usegalaxy.org/published/workflow?id=fd511165e30cb62c, https://usegalaxy.org/published/workflow?id=fda56c998bb88e2a, https://usegalaxy.org/published/workflow?id=ff84d87fd3638a3f, https://workflowhub.eu/workflows/615?version=6 |
|
|
barrnap |
barrnap |
Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. |
2017-08-25 |
https://github.com/tseemann/barrnap |
1.2.2 |
barrnap |
0.9 |
To update |
Sequence Analysis |
Gene prediction |
Gene prediction |
Genomics, Model organisms, Model organisms |
Genomics, Model organisms, Model organisms |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap |
barrnap |
Barrnap |
Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
719 |
719 |
11908 |
11908 |
0 |
0 |
0 |
0 |
281 |
417 |
7921 |
9428 |
21 |
21 |
420 |
420 |
21756 |
20249 |
1157 |
1021 |
https://usegalaxy.eu/published/workflow?id=e8eb80ee09159bac, https://usegalaxy.eu/published/workflow?id=fe43cf59e48bf556 |
|
|
basil |
basil |
Breakpoint detection, including large insertions |
2019-05-22 |
https://github.com/seqan/anise_basil |
1.2.0 |
anise_basil |
1.2.0 |
Up-to-date |
Variant Analysis |
|
|
|
|
iuc |
|
https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
94 |
106 |
253 |
368 |
114 |
121 |
471 |
516 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
884 |
724 |
227 |
208 |
https://usegalaxy.org/published/workflow?id=e67b6da41e1e6932 |
|
|
bax2bam |
bax2bam |
BAX to BAM converter |
2019-10-12 |
https://github.com/pacificbiosciences/bax2bam/ |
0.0.11 |
bax2bam |
0.0.11 |
Up-to-date |
Convert Formats, Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
16 |
26 |
28 |
208 |
29 |
32 |
124 |
213 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
421 |
152 |
58 |
45 |
|
|
|
bayescan |
BayeScan |
Detecting natural selection from population-based genetic data |
2017-03-09 |
http://cmpg.unibe.ch/software/BayeScan/index.html |
2.1 |
bayescan |
2.0.1 |
To update |
Sequence Analysis |
Statistical inference |
Statistical inference |
Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism |
Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan |
bayescan |
BayeScan |
BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
28 |
35 |
109 |
136 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
136 |
109 |
35 |
28 |
|
|
|
bbgbigwig |
bbgtobigwig |
Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file. |
2024-06-14 |
https://www.encodeproject.org/software/bedgraphtobigwig/ |
0.1 |
ucsc-bedgraphtobigwig |
482 |
To update |
Convert Formats |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://www.encodeproject.org/software/bedgraphtobigwig/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
71 |
71 |
339 |
339 |
204 |
204 |
1348 |
1348 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1687 |
1687 |
275 |
275 |
https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=e522be58f0bac656 |
epigenetics/formation_of_super-structures_on_xi |
|
bbtools |
bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole |
BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. |
2021-10-04 |
https://jgi.doe.gov/data-and-tools/bbtools/ |
39.08 |
bbmap |
39.33 |
To update |
Sequence Analysis |
RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment |
RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment |
Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq |
RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools |
bbmap |
BBMap |
BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. |
|
0 |
3 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
6 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
413 |
413 |
25287 |
25287 |
562 |
562 |
10487 |
10487 |
172 |
172 |
3537 |
3537 |
5 |
5 |
134 |
134 |
39445 |
39445 |
1152 |
1152 |
https://usegalaxy.org.au/published/workflow?id=25f65a29ce3c3ee0, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/519?version=1 |
|
|
bcftools |
bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@ |
BCFtools toolkit wrappers |
2015-08-12 |
https://samtools.github.io/bcftools/ |
1.15.1 |
bcftools |
1.22 |
To update |
Variant Analysis |
Data handling, Variant calling |
Data handling, Variant calling |
Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment |
DNA polymorphism, GWAS study, Genotyping experiment |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools |
bcftools |
BCFtools |
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
bctools |
bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events |
bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 |
2017-10-05 |
https://github.com/dmaticzka/bctools |
0.2.2 |
bctools |
0.2.2 |
Up-to-date |
Sequence Analysis, Transcriptomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools |
|
|
|
|
0 |
0 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
7 |
7 |
124 |
157 |
1759 |
3227 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3227 |
1759 |
157 |
124 |
https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c, https://workflowhub.eu/workflows/1706?version=1 |
transcriptomics/clipseq |
|
beacon2 |
beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff |
beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). |
2023-08-11 |
https://github.com/EGA-archive/beacon2-ri-tools/tree/main |
2.0.0 |
beacon2-ri-tools |
2.0.5 |
To update |
Variant Analysis |
Service discovery, Database search, Genetic variation analysis |
Service discovery, Database search, Genetic variation analysis |
Genetic variation, Population genetics, Data security, Rare diseases |
Genetic variation, Population genetics, Data security, Rare diseases |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2 |
ga4gh_beacon |
GA4GH Beacon |
A global search engine for genetic mutations. |
|
0 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
13 |
13 |
64 |
64 |
0 |
0 |
0 |
0 |
2 |
2 |
37 |
37 |
1 |
1 |
2 |
2 |
103 |
103 |
16 |
16 |
|
|
|
beagle |
beagle |
Beagle is a program for phasing and imputing missing genotypes. |
2021-07-03 |
https://faculty.washington.edu/browning/beagle/beagle.html |
5.4_29Oct24.c8e |
beagle |
5.4_22Jul22.46e |
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
43 |
43 |
252 |
252 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
4 |
4 |
256 |
256 |
45 |
45 |
https://usegalaxy.fr/published/workflow?id=4ec0bc782472fa10 |
|
|
bedops_sortbed |
bedops-sort-bed |
BEDOPS: high-performance genomic feature operations |
2023-08-08 |
https://bedops.readthedocs.io/en/latest/ |
2.4.42 |
bedops |
2.4.42 |
Up-to-date |
Genomic Interval Operations |
|
|
|
|
iuc |
https://bedops.readthedocs.io/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
95 |
95 |
277 |
277 |
116 |
116 |
451 |
451 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
728 |
728 |
211 |
211 |
|
|
|
bedtools |
bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed |
bedtools is a powerful toolset for genome arithmetic |
2014-09-13 |
https://github.com/arq5x/bedtools2 |
2.31.1 |
bedtools |
2.31.1 |
Up-to-date |
Genomic Interval Operations, Text Manipulation |
Mapping |
Mapping |
Genomics |
Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools |
bedtools |
BEDTools |
BEDTools is an extensive suite of utilities for comparing genomic features in BED format. |
|
0 |
37 |
37 |
37 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
37 |
37 |
37 |
0 |
0 |
0 |
0 |
0 |
37 |
0 |
0 |
0 |
0 |
0 |
0 |
37 |
37 |
37 |
5261 |
5753 |
986602 |
1069403 |
7556 |
10120 |
422356 |
735272 |
1153 |
1223 |
93992 |
110440 |
336 |
337 |
10193 |
10644 |
1925759 |
1513143 |
17433 |
14306 |
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assembly/ecoli_comparison, assembly/vgp_genome_assembly, epigenetics/atac-seq, epigenetics/cut_and_run, epigenetics/formation_of_super-structures_on_xi, epigenetics/tal1-binding-site-identification, genome-annotation/repeatmasker, introduction/galaxy-intro-101, microbiome/mgnify-amplicon, microbiome/pathogen-detection-from-nanopore-foodborne-data, single-cell/scatac-preprocessing-tenx, transcriptomics/clipseq |
|
bellavista |
bellavista_prepare |
Open-Source Visualization for Imaging-Based Spatial Transcriptomics |
2025-05-02 |
https://github.com/pkosurilab/BellaVista |
0.0.2 |
|
|
To update |
Single Cell, Spatial Omics, Transcriptomics, Imaging |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bellavista |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellavista |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
2 |
2 |
|
|
|
bellerophon |
bellerophon |
Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. |
2021-05-28 |
https://github.com/davebx/bellerophon |
1.0 |
bellerophon |
1.0 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/davebx/bellerophon |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
350 |
350 |
2265 |
2265 |
110 |
110 |
1644 |
1644 |
41 |
41 |
843 |
843 |
0 |
0 |
0 |
0 |
4752 |
4752 |
501 |
501 |
https://usegalaxy.eu/published/workflow?id=069d99391a69baf4, https://usegalaxy.eu/published/workflow?id=0c3ce9feb83f7920, https://usegalaxy.eu/published/workflow?id=0cf3c2114ab65858, https://usegalaxy.eu/published/workflow?id=3010ecad1a342331, https://usegalaxy.eu/published/workflow?id=31f8c7c46207432f, https://usegalaxy.eu/published/workflow?id=3b57fc81001667b5, https://usegalaxy.eu/published/workflow?id=4949751217c0e211, https://usegalaxy.eu/published/workflow?id=652433160b04b232, https://usegalaxy.eu/published/workflow?id=792b24fc23bd3071, https://usegalaxy.eu/published/workflow?id=a37d1e0db16cfb67, https://usegalaxy.eu/published/workflow?id=a53f78aa6866b811, https://usegalaxy.eu/published/workflow?id=b287bb779cf686ef, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=bc8ccd13a07bd9ec, https://usegalaxy.eu/published/workflow?id=c8f94a2e838fc0f1, https://usegalaxy.eu/published/workflow?id=feeb1fa358ccf328, https://usegalaxy.org.au/published/workflow?id=0aa316f8c6cff444, https://usegalaxy.org.au/published/workflow?id=0dbb85f727302a72, https://usegalaxy.org.au/published/workflow?id=29f0c07c8a24b542, https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=455e68f185fec41b, https://usegalaxy.org.au/published/workflow?id=6c1c11a81a2ab1b8, https://usegalaxy.org.au/published/workflow?id=6ec5728eec9c26d7, https://usegalaxy.org.au/published/workflow?id=7028436ef03171cc, https://usegalaxy.org.au/published/workflow?id=77b2fcf8c805ad5d, https://usegalaxy.org.au/published/workflow?id=7a97e8ccc332c1e8, https://usegalaxy.org.au/published/workflow?id=86eb0ea9dc230f04, https://usegalaxy.org.au/published/workflow?id=ae6a03240680712a, https://usegalaxy.org.au/published/workflow?id=b9e89401313a0cca, https://usegalaxy.org.au/published/workflow?id=be35847680078c90, https://usegalaxy.org.au/published/workflow?id=cac0b8a09d59044b, https://usegalaxy.org.au/published/workflow?id=e07866576cc2f467, https://usegalaxy.org.au/published/workflow?id=fdec6e2fcd5e2cf5, https://usegalaxy.org/published/workflow?id=155839aeb6340f54, https://usegalaxy.org/published/workflow?id=28dbbfb3d480f4b1, https://usegalaxy.org/published/workflow?id=28ddea356ae57da1, https://usegalaxy.org/published/workflow?id=3d805d7e0f34c727, https://usegalaxy.org/published/workflow?id=3db51822f04f4ff7, https://usegalaxy.org/published/workflow?id=6341c384ceaf47ed, https://usegalaxy.org/published/workflow?id=88327cb2e0fe3c25, https://usegalaxy.org/published/workflow?id=903e35b62946ed76, https://usegalaxy.org/published/workflow?id=9f4c4038d1c519e2, https://usegalaxy.org/published/workflow?id=a4a6d6846c1692f9, https://usegalaxy.org/published/workflow?id=afa89bb0e8966753, https://usegalaxy.org/published/workflow?id=f09033420c6267ab, https://workflowhub.eu/workflows/1054?version=1, https://workflowhub.eu/workflows/1607?version=1, https://workflowhub.eu/workflows/1641?version=1, https://workflowhub.eu/workflows/608?version=1, https://workflowhub.eu/workflows/702?version=1 |
assembly/ERGA-post-assembly-QC, assembly/vgp_genome_assembly |
|
berokka |
berokka |
Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. |
2019-03-08 |
https://github.com/tseemann/berokka |
0.2.3 |
berokka |
0.2.3 |
Up-to-date |
Fasta Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka |
|
|
|
|
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
85 |
85 |
1250 |
1250 |
0 |
0 |
0 |
0 |
1250 |
1250 |
85 |
85 |
|
|
|
bigscape |
bigscape |
Construct sequence similarity networks of BGCs and groups them into GCF |
2024-02-18 |
https://github.com/medema-group/BiG-SCAPE |
1.1.9 |
bigscape |
1.1.9 |
Up-to-date |
Metagenomics |
Clustering, Global alignment, Fold recognition |
Clustering, Global alignment, Fold recognition |
Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families |
Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape |
BiG-SCAPE |
BiG-SCAPE |
A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
95 |
95 |
2449 |
2449 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2449 |
2449 |
95 |
95 |
|
|
|
bigwig_outlier_bed |
bigwig_outlier_bed |
pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files |
2024-07-05 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed |
0.2.4 |
python |
|
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed |
bigtools |
bigtools |
Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
19 |
19 |
912 |
912 |
54 |
54 |
867 |
867 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1779 |
1779 |
73 |
73 |
https://usegalaxy.eu/published/workflow?id=3b94f511c52da835 |
|
|
binette |
binette |
Binning refinement tool |
2025-01-14 |
https://github.com/genotoul-bioinfo/Binette |
1.1.2 |
binette |
1.1.2 |
Up-to-date |
Metagenomics |
Read binning |
Read binning |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/binette/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/binette |
binette |
Binette |
Binette is a fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
11 |
359 |
359 |
8 |
8 |
17 |
17 |
0 |
0 |
0 |
0 |
1 |
1 |
49 |
49 |
425 |
425 |
20 |
20 |
https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/1352?version=3 |
|
|
binning_refiner |
bin_refiner |
Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. |
2022-02-18 |
https://github.com/songweizhi/Binning_refiner |
1.4.3 |
binning_refiner |
1.4.3 |
Up-to-date |
Metagenomics |
Read binning, Sequence clustering |
Read binning, Sequence clustering |
Metagenomics, Sequence assembly, Microbial ecology |
Metagenomics, Sequence assembly, Microbial ecology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner |
binning_refiner |
Binning_refiner |
Improving genome bins through the combination of different binning programs |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
64 |
64 |
236 |
236 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
236 |
236 |
64 |
64 |
|
|
|
bio_hansel |
bio_hansel |
Heidelberg and Enteritidis SNP Elucidation |
2017-09-29 |
https://github.com/phac-nml/bio_hansel |
2.6.1 |
bio_hansel |
2.6.1 |
Up-to-date |
Sequence Analysis |
Genotyping, SNP detection, Genome assembly |
Genotyping, SNP detection, Genome assembly |
Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science |
Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel |
Biohansel |
BioHansel |
BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
36 |
39 |
312 |
397 |
57 |
63 |
538 |
592 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
989 |
850 |
102 |
93 |
|
|
|
bioext |
bioext_bam2msa, bioext_bealign |
A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! |
2016-11-03 |
https://pypi.python.org/pypi/biopython-extensions/ |
0.21.9 |
python-bioext |
0.21.9 |
Up-to-date |
Next Gen Mappers |
|
|
|
|
iuc |
https://github.com/davebx/bioext-gx/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
833 |
833 |
33209 |
33209 |
1366 |
1366 |
22291 |
22291 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
55502 |
55502 |
2200 |
2200 |
https://usegalaxy.eu/published/workflow?id=90f993a1b245eb68, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.org/published/workflow?id=4884918895db9af0, https://usegalaxy.org/published/workflow?id=63adc811e3ae529d, https://usegalaxy.org/published/workflow?id=c03c18813a3380b3 |
|
|
bioinformatics_cafe |
fasta_regex_finder |
Miscellanea of scripts for bioinformatics |
2023-01-25 |
https://github.com/dariober/bioinformatics-cafe/ |
0.1.0 |
python |
|
To update |
Sequence Analysis |
|
|
|
|
mbernt |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
130 |
130 |
1691 |
1691 |
126 |
126 |
1430 |
1430 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3121 |
3121 |
256 |
256 |
https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a, https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539 |
variant-analysis/pox-tiled-amplicon, variant-analysis/sars-cov-2-variant-discovery |
|
biomformat |
biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table |
The biom-format package provides a command line interface and Python API for working with BIOM files. |
2016-06-07 |
https://github.com/biocore/biom-format |
2.1.15 |
biom-format |
2.1.7 |
To update |
Metagenomics |
Formatting |
Formatting |
Laboratory information management, Sequence analysis |
Laboratory information management, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format |
biomformat |
biomformat |
This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. |
|
0 |
2 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
342 |
356 |
16688 |
16852 |
374 |
593 |
2736 |
5533 |
166 |
235 |
2283 |
2833 |
0 |
0 |
0 |
0 |
25218 |
21707 |
1184 |
882 |
https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.eu/published/workflow?id=fb806b88850f3427, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org.au/published/workflow?id=20d472fc5563a640, https://usegalaxy.org.au/published/workflow?id=4f837b7f90d5ebac, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://usegalaxy.org.au/published/workflow?id=ca6f29110df8dadc, https://usegalaxy.org/published/workflow?id=45f959d5bf505b15, https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1273?version=2, https://workflowhub.eu/workflows/142?version=1, https://workflowhub.eu/workflows/1842?version=1, https://workflowhub.eu/workflows/1856?version=1, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1 |
microbiome/mgnify-amplicon |
|
biotradis |
bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites |
Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. |
2020-01-17 |
https://www.sanger.ac.uk/science/tools/bio-tradis |
1.4.5 |
biotradis |
1.4.5 |
Up-to-date |
Genome annotation |
Sequence analysis |
Sequence analysis |
Mobile genetic elements, Workflows |
Mobile genetic elements, Workflows |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis |
biotradis |
biotradis |
The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
165 |
176 |
6369 |
6769 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6769 |
6369 |
176 |
165 |
|
|
|
biscot |
biscot |
Bionano scaffolding correction tool |
2023-01-06 |
https://github.com/institut-de-genomique/biscot |
2.3.3 |
biscot |
2.3.3 |
Up-to-date |
Assembly |
|
|
|
|
iuc |
https://github.com/bgruening/iuc/tree/master/tools/biscot |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
2 |
2 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
2 |
2 |
|
|
|
blastxml_to_gapped_gff3 |
blastxml_to_gapped_gff3 |
BlastXML to gapped GFF3 |
2015-05-25 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 |
1.1 |
bcbiogff |
0.6.6 |
To update |
Convert Formats, Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 |
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|
|
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0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
121 |
128 |
908 |
952 |
69 |
77 |
156 |
193 |
18 |
18 |
185 |
185 |
0 |
0 |
0 |
0 |
1330 |
1249 |
223 |
208 |
https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=44189803f223acd1, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6 |
|
|
bowtie2 |
bowtie2 |
Bowtie2: Fast and sensitive read alignment |
2017-05-08 |
http://bowtie-bio.sourceforge.net/bowtie2 |
2.5.4 |
bowtie2 |
2.5.4 |
Up-to-date |
Next Gen Mappers |
Read mapping |
Read mapping |
Mapping, Genomics, Mapping |
Mapping, Genomics, Mapping |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 |
bowtie2 |
Bowtie 2 |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. |
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0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
14402 |
16726 |
416270 |
533359 |
34023 |
59018 |
582611 |
1027362 |
4158 |
5085 |
66910 |
84030 |
1570 |
1574 |
28821 |
28955 |
1673706 |
1094612 |
82403 |
54153 |
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assembly/assembly-with-preprocessing, assembly/metagenomics-assembly, contributing/create-new-tutorial, epigenetics/atac-seq, epigenetics/cut_and_run, epigenetics/estrogen-receptor-binding-site-identification, epigenetics/formation_of_super-structures_on_xi, epigenetics/hicexplorer, genome-annotation/amr-gene-detection, microbiome/metagenomics-assembly, sequence-analysis/mapping |
|
bp_genbank2gff3 |
bp_genbank2gff3 |
Converts GenBank format files to GFF3 |
2015-08-14 |
https://bioperl.org/ |
1.1 |
perl-bioperl |
1.7.8 |
To update |
Sequence Analysis |
Data handling, Service invocation |
Data handling, Service invocation |
Genomics, Software engineering, Data management |
Genomics, Software engineering |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl |
bioperl |
BioPerl |
A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
638 |
721 |
10572 |
11606 |
974 |
1075 |
10887 |
11385 |
180 |
207 |
8997 |
9165 |
22 |
22 |
309 |
309 |
32465 |
30765 |
2025 |
1814 |
|
genome-annotation/secondary-metabolite-discovery |
|
bracken |
est_abundance |
Bayesian Reestimation of Abundance with KrakEN |
2019-10-15 |
https://github.com/jenniferlu717/Bracken/releases |
3.1 |
bracken |
3.1 |
Up-to-date |
Sequence Analysis, Metagenomics |
Statistical calculation |
Statistical calculation |
Metagenomics, Microbial ecology |
Metagenomics, Microbial ecology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken |
bracken |
Bracken |
Bracken is a companion program to Kraken 1, KrakenUniq, or Kraken 2 While Kraken classifies reads to multiple levels in the taxonomic tree, Bracken allows estimation of abundance at a single level using those classifications (e.g. Bracken can estimate abundance of species within a sample). |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1714 |
1714 |
108307 |
108307 |
804 |
804 |
27569 |
27569 |
265 |
265 |
8873 |
8873 |
59 |
59 |
12432 |
12432 |
157181 |
157181 |
2842 |
2842 |
https://usegalaxy.eu/published/workflow?id=0a82eb8b44d9d502, https://usegalaxy.eu/published/workflow?id=0abd32dbc5207b88, https://usegalaxy.eu/published/workflow?id=0c47571d20535426, https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d, https://usegalaxy.eu/published/workflow?id=47e14222073e7192, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=884a4415b669690c, https://usegalaxy.eu/published/workflow?id=aafcfcb585c5ca75, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=bb63b5bb983fd49c, https://usegalaxy.eu/published/workflow?id=c14d2e8b3c191bc4, https://usegalaxy.eu/published/workflow?id=c930a54a30dcc7e3, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=ebb131f2a6172081, https://usegalaxy.fr/published/workflow?id=3d3b40398d1cd1ae, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=a335b9c9103b57ad, https://usegalaxy.org/published/workflow?id=1be5c982c2d36a6c, https://usegalaxy.org/published/workflow?id=2a782ad24271f570, https://usegalaxy.org/published/workflow?id=323c651ca583c9e5, https://usegalaxy.org/published/workflow?id=4f698eaeef30e364, https://usegalaxy.org/published/workflow?id=623fc80c7f91a33a, https://usegalaxy.org/published/workflow?id=9ba6da7dae465d3e, https://usegalaxy.org/published/workflow?id=9f68718f025bed30, https://usegalaxy.org/published/workflow?id=b6a795834009ce06, https://usegalaxy.org/published/workflow?id=de9bf4c1024f8d53, https://usegalaxy.org/published/workflow?id=dfd73857c0eb2a21, https://usegalaxy.org/published/workflow?id=f378960ee55f567e, https://workflowhub.eu/workflows/1052?version=11, https://workflowhub.eu/workflows/1199?version=2, https://workflowhub.eu/workflows/1470?version=1, https://workflowhub.eu/workflows/1644?version=1, https://workflowhub.eu/workflows/1674?version=1, https://workflowhub.eu/workflows/1881?version=1, https://workflowhub.eu/workflows/1882?version=2 |
ecology/bacterial-isolate-species-contamination-checking, microbiome/taxonomic-profiling, sequence-analysis/quality-contamination-control |
|
breseq |
breseq |
Predicts mutations in microbial genomes |
2019-10-21 |
https://github.com/barricklab/breseq |
0.35.5 |
breseq |
0.39.0 |
To update |
Variant Analysis |
Polymorphism detection |
Polymorphism detection |
Sequencing, Sequence analysis, DNA mutation |
Sequencing, Sequence analysis, DNA mutation |
iuc |
|
https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq |
breseq |
breseq |
Runs Breseq software on a set of fastq files. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
198 |
198 |
4455 |
4455 |
0 |
0 |
0 |
0 |
71 |
83 |
896 |
1004 |
0 |
0 |
0 |
0 |
5459 |
5351 |
281 |
269 |
|
|
|
brew3r_r |
brew3r_r |
Extend 3' end of a GTF using another GTF as a template |
2024-06-11 |
https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html |
1.0.2 |
|
|
To update |
Transcriptomics, RNA |
Genome annotation |
Genome annotation |
Transcriptomics, Genomics |
Transcriptomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r |
brew3r.r |
BREW3R.r |
This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
75 |
75 |
4 |
4 |
22 |
22 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
97 |
97 |
9 |
9 |
https://usegalaxy.eu/published/workflow?id=a6d36048d545bca7, https://usegalaxy.eu/published/workflow?id=efe6d8a65226505e, https://usegalaxy.org/published/workflow?id=38f06c4c6dd4eb62, https://usegalaxy.org/published/workflow?id=5a5d0dc4cd2f1ebd, https://workflowhub.eu/workflows/1051?version=2 |
|
|
busco |
busco |
BUSCO assess genome and annotation completeness |
2017-01-12 |
https://gitlab.com/ezlab/busco/-/releases |
5.8.0 |
busco |
6.0.0 |
To update |
Sequence Analysis |
Sequence assembly validation |
Sequence assembly validation |
Sequence assembly, Genomics, Transcriptomics, Sequence analysis |
Sequence assembly, Transcriptomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco |
busco |
BUSCO |
Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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1 |
1 |
5636 |
5838 |
134029 |
137202 |
5194 |
5212 |
58403 |
58497 |
3096 |
3288 |
49227 |
52147 |
262 |
262 |
8860 |
8866 |
256712 |
250519 |
14600 |
14188 |
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assembly/ERGA-post-assembly-QC, assembly/assembly-quality-control, assembly/hifi-assembly, assembly/largegenome, assembly/vgp_genome_assembly, ecology/phylogeny-data-prep, genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short, genome-annotation/braker3, genome-annotation/comparison-braker-helixer-annotation, genome-annotation/funannotate, genome-annotation/helixer |
|
bwa |
bwa_mem, bwa |
Wrapper for bwa mem, aln, sampe, and samse |
2017-11-21 |
http://bio-bwa.sourceforge.net/ |
0.7.19 |
bwa |
0.7.19 |
Up-to-date |
Next Gen Mappers |
Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment |
Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment |
Mapping |
Mapping |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa |
bwa |
BWA |
Fast, accurate, memory-efficient aligner for short and long sequencing reads |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
11730 |
13297 |
948091 |
1092022 |
23003 |
36519 |
419994 |
745074 |
3413 |
4520 |
101030 |
123169 |
314 |
317 |
6918 |
7008 |
1967273 |
1476033 |
54653 |
38460 |
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admin/reference-genomes, assembly/chloroplast-assembly, ecology/ref-based-rad-seq, epigenetics/tal1-binding-site-identification, galaxy-interface/collections, introduction/galaxy-intro-ngs-data-managment, sequence-analysis/human-reads-removal, sequence-analysis/sars-with-galaxy-on-anvil, single-cell/scatac-preprocessing-tenx, single-cell/scatac-standard-processing-snapatac2, variant-analysis/aiv-analysis, variant-analysis/baculovirus-isolate-variation, variant-analysis/dunovo, variant-analysis/exome-seq, variant-analysis/non-dip, variant-analysis/pox-tiled-amplicon, variant-analysis/sars-cov-2, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants |
|
bwa_mem2 |
bwa_mem2_idx, bwa_mem2 |
Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. |
2021-10-08 |
https://github.com/bwa-mem2/bwa-mem2 |
2.3 |
bwa-mem2 |
2.3 |
Up-to-date |
Next Gen Mappers |
Sequence alignment |
Sequence alignment |
Mapping |
Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 |
bwa-mem2 |
Bwa-mem2 |
Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
0 |
4165 |
4165 |
95467 |
95467 |
4910 |
4910 |
69756 |
69756 |
1058 |
1058 |
31125 |
31125 |
67 |
67 |
578 |
578 |
196926 |
196926 |
10200 |
10200 |
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assembly/ERGA-post-assembly-QC, assembly/mrsa-nanopore, assembly/vgp_genome_assembly, introduction/galaxy-intro-ngs-data-managment |
|
bwameth |
bwameth |
Fast and accurate alignment of BS-seq reads |
2016-09-14 |
https://github.com/brentp/bwa-meth |
0.2.9 |
bwameth |
0.2.9 |
Up-to-date |
Sequence Analysis, Next Gen Mappers |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
691 |
1020 |
10937 |
16134 |
862 |
907 |
12645 |
13009 |
176 |
176 |
1696 |
1700 |
2 |
2 |
2 |
2 |
30845 |
25280 |
2105 |
1731 |
https://usegalaxy.org.au/published/workflow?id=91c8daa5f2bcf7c0, https://usegalaxy.org/published/workflow?id=e20e1371e50bdcee, https://usegalaxy.org/published/workflow?id=eb4f7dbca0114270, https://workflowhub.eu/workflows/1566?version=1 |
epigenetics/methylation-seq |
|
cactus |
cactus_cactus, cactus_export |
Cactus is a reference-free whole-genome multiple alignment program |
2022-01-28 |
https://github.com/ComparativeGenomicsToolkit/cactus |
2.7.1 |
|
|
To update |
Sequence Analysis |
Multiple sequence alignment, Genome alignment |
Multiple sequence alignment, Genome alignment |
Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics |
Genomics, Sequence assembly, Mapping, Phylogenetics |
galaxy-australia |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus |
cactus |
Cactus |
Cactus is a reference-free whole-genome multiple alignment program. |
|
0 |
2 |
2 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
92 |
92 |
575 |
575 |
0 |
0 |
0 |
0 |
96 |
96 |
2883 |
2883 |
4 |
4 |
12 |
12 |
3470 |
3470 |
192 |
192 |
|
|
|
calculate_contrast_threshold |
calculate_contrast_threshold |
Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. |
2019-08-26 |
https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold |
1.0.0 |
numpy |
|
To update |
Visualization, Genomic Interval Operations, SAM |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
calculate_numeric_param |
calculate_numeric_param |
Calculate a numeric parameter value using integer and float values. |
2021-05-04 |
|
0.1.0 |
|
|
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
21 |
21 |
2700 |
2700 |
7 |
7 |
379 |
379 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3079 |
3079 |
28 |
28 |
https://usegalaxy.eu/published/workflow?id=40d2c7ac42bd5302, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://workflowhub.eu/workflows/1876?version=1 |
|
|
cami_amber |
biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert |
Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments |
2024-05-20 |
https://github.com/CAMI-challenge/AMBER |
2.0.7 |
cami-amber |
2.0.7 |
Up-to-date |
Metagenomics |
Read binning |
Read binning |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber |
cami-amber |
AMBER |
AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. The provided metrics were used in the first community benchmarking challenge of the initiative for the Critical Assessment of Metagenomic Interpretation. |
|
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
10522 |
10522 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10522 |
10522 |
8 |
8 |
https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=17d2e76147fc940c, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1 |
|
|
cd_hit |
cd_hit |
Cluster or compare biological sequence datasets |
2018-02-26 |
http://weizhongli-lab.org/cd-hit/ |
4.8.1 |
cd-hit |
4.8.1 |
Up-to-date |
Sequence Analysis, Fasta Manipulation |
Sequence clustering |
Sequence clustering |
Sequencing |
Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit |
cd-hit |
cd-hit |
Cluster a nucleotide dataset into representative sequences. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
899 |
899 |
20148 |
20148 |
1 |
1 |
2 |
2 |
1 |
1 |
2 |
2 |
57 |
57 |
1174 |
1174 |
21326 |
21326 |
958 |
958 |
https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5 |
|
|
cemitool |
cemitool |
Gene co-expression network analysis tool |
2022-10-10 |
https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html |
1.30.0 |
bioconductor-cemitool |
1.30.0 |
Up-to-date |
Transcriptomics, RNA, Statistics, Single Cell |
Enrichment analysis, Pathway or network analysis |
Enrichment analysis, Pathway or network analysis |
Gene expression, Transcriptomics, Microarray experiment |
Transcriptomics, Microarray experiment |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool |
cemitool |
CEMiTool |
It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
45 |
45 |
354 |
354 |
87 |
87 |
584 |
584 |
6 |
6 |
154 |
154 |
0 |
0 |
0 |
0 |
1092 |
1092 |
138 |
138 |
|
|
|
charts |
charts |
Enables advanced visualization options in Galaxy Charts |
2018-01-30 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ |
1.0.1 |
r-getopt |
|
To update |
Visualization |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2016 |
2636 |
4166 |
5631 |
3945 |
8272 |
8242 |
16754 |
8 |
145 |
13 |
350 |
58 |
58 |
111 |
111 |
22846 |
12532 |
11111 |
6027 |
https://usegalaxy.eu/published/workflow?id=f30c8054f064ac9f, https://usegalaxy.org/published/workflow?id=cb03300161109123 |
|
|
checkm |
checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa |
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes |
2022-07-29 |
https://github.com/Ecogenomics/CheckM |
1.2.4 |
checkm-genome |
1.2.4 |
Up-to-date |
Metagenomics |
Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation |
Sequence assembly validation, Sequence composition calculation, Statistical calculation |
Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management |
Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm |
checkm |
CheckM |
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. |
|
0 |
10 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
0 |
717 |
717 |
12189 |
12189 |
179 |
179 |
1510 |
1510 |
96 |
96 |
2254 |
2254 |
50 |
50 |
1469 |
1469 |
17422 |
17422 |
1042 |
1042 |
https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/1352?version=3 |
microbiome/metagenomics-binning |
|
checkm2 |
checkm2 |
Rapid assessment of genome bin quality using machine learning |
2024-11-08 |
https://github.com/chklovski/CheckM2 |
1.0.2 |
checkm2 |
1.1.0 |
To update |
Metagenomics |
Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation |
Sequence assembly validation, Sequence composition calculation, Statistical calculation |
Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management |
Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management |
iuc |
https://github.com/galaxyproject/tools-iuc/blob/main/tools/checkm2/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm2 |
checkm |
CheckM |
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
228 |
228 |
1602 |
1602 |
187 |
187 |
1322 |
1322 |
0 |
0 |
0 |
0 |
15 |
15 |
1268 |
1268 |
4192 |
4192 |
430 |
430 |
https://usegalaxy.eu/published/workflow?id=3303a04887a47675, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=ba1fda2318046543, https://usegalaxy.eu/published/workflow?id=e532d98f4b368666, https://usegalaxy.org/published/workflow?id=524602abe59b18f7, https://usegalaxy.org/published/workflow?id=5cd56232e873beab, https://usegalaxy.org/published/workflow?id=b76a9ce44ea019f1, https://workflowhub.eu/workflows/1352?version=3, https://workflowhub.eu/workflows/1882?version=2 |
genome-annotation/bacterial-genome-quality-control |
|
cherri |
cherri_eval, cherri_train |
Computational Help Evaluating RNA-RNA interactions |
2022-12-09 |
https://github.com/BackofenLab/Cherri |
0.7 |
cherri |
0.8 |
To update |
Transcriptomics, RNA |
|
|
Molecular interactions, pathways and networks, Structure analysis, Machine learning |
Molecular interactions, pathways and networks, Structure analysis, Machine learning |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri |
cherri |
cherri |
CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
1 |
1 |
207 |
207 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
207 |
207 |
1 |
1 |
|
|
|
chewbbaca |
chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema |
BSR-Based Allele Calling Algorithm |
2024-04-13 |
https://github.com/B-UMMI/chewBBACA/tree/master |
|
chewbbaca |
3.4.2 |
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca |
|
|
|
|
0 |
0 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
100 |
100 |
9644 |
9644 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9644 |
9644 |
100 |
100 |
|
|
|
chira |
chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify |
Chimeric Read Annotator for RNA-RNA interactome data |
2020-01-19 |
https://github.com/pavanvidem/chira |
1.4.3 |
chira |
1.4.3 |
Up-to-date |
RNA, Transcriptomics, Sequence Analysis |
|
|
RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA |
Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira |
chira |
ChiRA |
ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. |
|
0 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
5 |
128 |
137 |
39830 |
42352 |
95 |
95 |
21742 |
21742 |
17 |
17 |
585 |
585 |
0 |
0 |
0 |
0 |
64679 |
62157 |
249 |
240 |
https://usegalaxy.eu/published/workflow?id=25a209bda998412f, https://usegalaxy.eu/published/workflow?id=26c4882e320ed7b3, https://usegalaxy.eu/published/workflow?id=66834f10c86362b9, https://workflowhub.eu/workflows/1681?version=1, https://workflowhub.eu/workflows/66?version=1, https://workflowhub.eu/workflows/67?version=1 |
transcriptomics/rna-interactome |
|
chopin2 |
chopin2 |
Domain-Agnostic Supervised Learning with Hyperdimensional Computing |
2023-01-18 |
https://github.com/cumbof/chopin2 |
1.0.9.post1 |
chopin2 |
|
To update |
Machine Learning |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
21 |
21 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
21 |
21 |
8 |
8 |
|
statistics/hyperdimensional_computing |
|
chopper |
chopper |
Filtering and trimming of fastq files with long read sequencing such as PacBio or ONT. |
2025-07-22 |
https://github.com/wdecoster/chopper |
0.11.0 |
chopper |
0.11.0 |
Up-to-date |
Sequence Analysis, Fastq Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
6 |
6 |
https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67 |
|
|
chromeister |
chromeister |
ultra-fast pairwise genome comparisons |
2020-09-30 |
https://github.com/estebanpw/chromeister |
1.5.a |
chromeister |
1.5.a |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
550 |
550 |
10141 |
10141 |
0 |
0 |
0 |
0 |
277 |
277 |
1883 |
1883 |
56 |
56 |
2443 |
2443 |
14467 |
14467 |
883 |
883 |
https://usegalaxy.org.au/published/workflow?id=478c79365fc9677f, https://usegalaxy.org.au/published/workflow?id=7f37c5366bce5489, https://usegalaxy.org.au/published/workflow?id=d06665e4bc7fff6d, https://usegalaxy.org.au/published/workflow?id=d957bfeb3cd03db0, https://workflowhub.eu/workflows/1545?version=1, https://workflowhub.eu/workflows/1646?version=1 |
assembly/assembly-quality-control, genome-annotation/hpc-for-lsgc |
|
cialign |
cialign |
Tool to clean, visualise and analyse a multiple sequence alignment |
2025-08-04 |
https://github.com/KatyBrown/CIAlign |
1.1.4 |
cialign |
1.1.4 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
3 |
3 |
|
|
|
circexplorer2 |
circexplorer2 |
Comprehensive and integrative circular RNA analysis toolset. |
2022-08-26 |
https://github.com/YangLab/CIRCexplorer2 |
2.3.8 |
circexplorer2 |
2.3.8 |
Up-to-date |
RNA, Assembly |
|
|
RNA splicing, Gene transcripts, Literature and language |
RNA splicing, Gene transcripts, Literature and language |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 |
circexplorer2 |
CIRCexplorer2 |
Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
39 |
39 |
833 |
833 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
833 |
833 |
39 |
39 |
|
|
|
circos |
circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile |
Build Circos Plots in Galaxy |
2017-08-07 |
http://circos.ca/ |
0.69.8 |
circos |
0.69.9 |
To update |
Graphics |
Sequence visualisation |
Sequence visualisation |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos |
galactic_circos |
Galactic Circos |
Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. |
|
0 |
11 |
11 |
11 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
11 |
11 |
0 |
0 |
0 |
0 |
0 |
11 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
11 |
11 |
1387 |
1476 |
30286 |
32934 |
1656 |
1808 |
33780 |
36943 |
409 |
515 |
10963 |
28143 |
24 |
25 |
586 |
588 |
98608 |
75615 |
3824 |
3476 |
https://usegalaxy.eu/published/workflow?id=0de5fcc38ef1501d, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=29c565eff0080e42, https://usegalaxy.eu/published/workflow?id=2c3d05023c02113e, https://usegalaxy.eu/published/workflow?id=2d0400b5d05c6c10, https://usegalaxy.eu/published/workflow?id=4f9f7065975b3f97, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=6ed1016dfdf9f928, https://usegalaxy.eu/published/workflow?id=75e88603745e069e, https://usegalaxy.eu/published/workflow?id=b1d1694b95ed10e1, https://usegalaxy.eu/published/workflow?id=b556b0a67ad979da, https://usegalaxy.org.au/published/workflow?id=0f9a29e8eac2075c, https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org.au/published/workflow?id=6588e175004aba38, https://usegalaxy.org.au/published/workflow?id=6a58898d37da5c83, https://usegalaxy.org.au/published/workflow?id=f85353f93461d180, https://workflowhub.eu/workflows/1413?version=1, https://workflowhub.eu/workflows/1415?version=1, https://workflowhub.eu/workflows/1419?version=1, https://workflowhub.eu/workflows/1651?version=1, https://workflowhub.eu/workflows/676?version=1 |
assembly/ecoli_comparison, variant-analysis/somatic-variant-discovery, visualisation/circos, visualisation/circos-microbial |
|
cite_seq_count |
cite_seq_count |
Count CMO/HTO |
2023-01-18 |
https://github.com/Hoohm/CITE-seq-Count |
1.4.4 |
cite-seq-count |
1.4.5 |
To update |
Single Cell, Transcriptomics, Proteomics |
RNA-Seq quantification |
RNA-Seq quantification |
Transcriptomics, Immunoproteins and antigens |
Transcriptomics, Immunoproteins and antigens |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count |
CITE-seq-Count |
CITE-seq-Count |
Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
5 |
5 |
23 |
23 |
6 |
6 |
21 |
21 |
1 |
1 |
290 |
290 |
0 |
0 |
0 |
0 |
334 |
334 |
12 |
12 |
https://usegalaxy.eu/published/workflow?id=4cb8f782994763a4, https://usegalaxy.eu/published/workflow?id=5009d8d7a907a825, https://usegalaxy.eu/published/workflow?id=6ed089fe65347272, https://usegalaxy.eu/published/workflow?id=865715636d40b798, https://usegalaxy.eu/published/workflow?id=a18615f77ed3f371, https://usegalaxy.eu/published/workflow?id=a72e3cb6eb656102, https://usegalaxy.eu/published/workflow?id=c4327bccfa623f7e, https://usegalaxy.eu/published/workflow?id=e296e4ac941bf0de, https://usegalaxy.org.au/published/workflow?id=0f01e24e6c33a834, https://usegalaxy.org.au/published/workflow?id=109f0c68e617e104, https://usegalaxy.org.au/published/workflow?id=aa387984ac9e2f71, https://usegalaxy.org.au/published/workflow?id=b09530351a9e9ffb, https://usegalaxy.org.au/published/workflow?id=b88036506d0be117, https://usegalaxy.org.au/published/workflow?id=bcdbefda8e15e547, https://usegalaxy.org.au/published/workflow?id=d66f1a1c1ffd6275, https://usegalaxy.org/published/workflow?id=1d19cf599e1d4a0f, https://usegalaxy.org/published/workflow?id=3b88ab63573edb0f, https://usegalaxy.org/published/workflow?id=41c40e7aa6b24f51, https://usegalaxy.org/published/workflow?id=586b923221fb5da4, https://usegalaxy.org/published/workflow?id=73a8b48cbd6f1d8c, https://usegalaxy.org/published/workflow?id=90ac9dc2bd9d8092, https://usegalaxy.org/published/workflow?id=a737766dd083b280, https://workflowhub.eu/workflows/694?version=8 |
|
|
clair3 |
clair3 |
Symphonizing pileup and full-alignment for high-performance long-read variant calling |
2022-06-15 |
https://github.com/HKU-BAL/Clair3 |
1.0.10 |
clair3 |
1.2.0 |
To update |
Sequence Analysis, Variant Analysis |
Variant calling |
Variant calling |
Molecular genetics |
Molecular genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 |
clair3 |
Clair3 |
Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
328 |
328 |
5269 |
5269 |
52 |
52 |
1858 |
1858 |
13 |
13 |
246 |
246 |
2 |
2 |
54 |
54 |
7427 |
7427 |
395 |
395 |
https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, https://usegalaxy.eu/published/workflow?id=3f0b104a74acf869, https://usegalaxy.eu/published/workflow?id=60e0b2a28a900178, https://usegalaxy.eu/published/workflow?id=64abcddeb516a712, https://usegalaxy.eu/published/workflow?id=6aa2891bd2b41f32, https://usegalaxy.eu/published/workflow?id=cb54883452a73019, https://usegalaxy.eu/published/workflow?id=cdf2f02428f5f83f, https://usegalaxy.eu/published/workflow?id=d215a2e554fd83bc, https://usegalaxy.org.au/published/workflow?id=0e11619979c2830c, https://usegalaxy.org.au/published/workflow?id=244ea5e94237ebad, https://usegalaxy.org.au/published/workflow?id=76a0a3af8de11622, https://usegalaxy.org.au/published/workflow?id=857e482acfcb2dba, https://usegalaxy.org/published/workflow?id=29ba77708cdafe0f, https://usegalaxy.org/published/workflow?id=38911ba6f66d80f6, https://usegalaxy.org/published/workflow?id=3e703abaeb870f6f, https://usegalaxy.org/published/workflow?id=6d778eeb176d563c, https://usegalaxy.org/published/workflow?id=cb810cdaa4915f4b, https://workflowhub.eu/workflows/1063?version=5, https://workflowhub.eu/workflows/1479?version=1 |
microbiome/pathogen-detection-from-nanopore-foodborne-data |
|
clustalw |
clustalw |
ClustalW multiple sequence alignment program for DNA or proteins |
2022-10-02 |
http://www.clustal.org/clustal2/ |
2.1 |
clustalw |
2.1 |
Up-to-date |
Phylogenetics, Sequence Analysis |
Multiple sequence alignment |
Multiple sequence alignment |
Phylogeny, Sequence analysis |
Phylogeny, Sequence analysis |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw |
clustal2 |
Clustal 2 (Clustal W, Clustal X) |
Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2268 |
2506 |
114395 |
117339 |
3966 |
8263 |
54653 |
99642 |
837 |
966 |
11073 |
13924 |
42 |
43 |
726 |
730 |
231635 |
180847 |
11778 |
7113 |
https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=3e0246389fb70340, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=042758b8a8c5ac80, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3d7baebefa7c9b81, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=75c2cf36253194c2, https://usegalaxy.org/published/workflow?id=7b68f97bf88f99b9, https://usegalaxy.org/published/workflow?id=87685c6247521b54, https://usegalaxy.org/published/workflow?id=8b7e03f09b0183d9, https://usegalaxy.org/published/workflow?id=b2fb90873471f4e7, https://usegalaxy.org/published/workflow?id=be9bd7286d38c210, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/1541?version=1, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1 |
ecology/phylogeny-data-prep, genome-annotation/hpc-for-lsgc, microbiome/pathogen-detection-from-nanopore-foodborne-data |
|
clustering_from_distmat |
clustering_from_distmat |
Distance matrix-based hierarchical clustering using SciPy |
2024-08-08 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ |
1.1.1 |
python |
|
To update |
Statistics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
69 |
69 |
305 |
305 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
305 |
305 |
69 |
69 |
https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6 |
evolution/mtb_transmission |
|
cnv-vcf2json |
cnv_vcf2json |
cnv-vcf2json Converts structural variants VCF file to JSON. |
2024-02-27 |
https://pypi.org/project/cnv-phenopacket/ |
2.0.0 |
cnv-vcf2json |
|
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
11 |
69 |
69 |
0 |
0 |
0 |
0 |
1 |
1 |
12 |
12 |
0 |
0 |
0 |
0 |
81 |
81 |
12 |
12 |
https://usegalaxy.eu/published/workflow?id=07b440eec3ac7c2e |
variant-analysis/beaconise_1000hg |
|
cnv_phenopacket |
cnv_phenopacket |
cnv-phenopacket Converts TSV metadata file to JSON. |
2024-02-27 |
https://pypi.org/project/cnv-phenopacket/ |
1.0.2 |
cnv-phenopacket |
|
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
13 |
13 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
13 |
13 |
7 |
7 |
|
variant-analysis/beaconise_1000hg |
|
cnvkit |
cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_export_bed, cnvkit_breaks, cnvkit_call, cnvkit_export_cdt, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_export_jtv, cnvkit_export_nexus_basic, cnvkit_export_nexus_ogt, cnvkit_reference, cnvkit_scatter, cnvkit_export_seg, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target, cnvkit_theta, cnvkit_export_vcf |
detecting copy number variants and alterations genome-wide from high-throughput sequencing |
2023-03-14 |
https://github.com/etal/cnvkit |
0.9.12 |
cnvkit |
0.9.12 |
Up-to-date |
Variant Analysis |
Variant calling |
Variant calling |
DNA structural variation |
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit |
cnvkit |
CNVkit |
CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. |
|
0 |
25 |
25 |
25 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
17 |
0 |
59 |
59 |
3401 |
3401 |
0 |
0 |
0 |
0 |
3 |
3 |
430 |
430 |
0 |
0 |
0 |
0 |
3831 |
3831 |
62 |
62 |
https://usegalaxy.eu/published/workflow?id=07b440eec3ac7c2e |
|
|
codeml |
codeml |
Detects positive selection |
2017-07-19 |
http://abacus.gene.ucl.ac.uk/software/paml.html |
4.9 |
paml |
4.10.9 |
To update |
Phylogenetics |
Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis |
Probabilistic sequence generation |
Phylogenetics, Sequence analysis |
Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml |
paml |
PAML |
Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
72 |
84 |
62891 |
63000 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
63000 |
62891 |
84 |
72 |
|
|
|
cojac |
cooc_mutbamscan, cooc_pubmut, cooc_tabmut |
co-occurrence of mutations on amplicons |
2022-08-11 |
https://github.com/cbg-ethz/cojac |
0.9.3 |
cojac |
0.9.3 |
Up-to-date |
Metagenomics, Sequence Analysis |
|
|
Genetic variation |
Genetic variation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac |
cojac |
COJAC |
CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. |
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
13 |
13 |
2763 |
2763 |
7 |
7 |
20 |
20 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2783 |
2783 |
20 |
20 |
https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b |
|
|
colabfold |
colabfold_alphafold, colabfold_msa |
Protein prediction based on AlphaFold2 |
2024-03-24 |
https://github.com/sokrypton/ColabFold |
1.5.5 |
|
|
To update |
Proteomics, Graphics |
Database search, Protein structure prediction, Fold recognition |
Database search, Protein structure prediction, Fold recognition |
Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics |
Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics |
iuc |
https://github.com/sokrypton/ColabFold |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold |
Colabfold |
ColabFold |
ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
233 |
233 |
10606 |
10606 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10606 |
10606 |
233 |
233 |
|
|
|
colibread |
commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak |
Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome |
2017-10-02 |
https://colibread.inria.fr/ |
24.7.14 |
commet |
24.7.14 |
Up-to-date |
Sequence Analysis, Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
47 |
52 |
1393 |
1457 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
68 |
68 |
259 |
262 |
1719 |
1652 |
120 |
115 |
|
|
|
collection_column_join |
collection_column_join |
Column Join on Collections |
2016-05-26 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join |
0.0.3 |
coreutils |
8.25 |
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
4863 |
5343 |
27514 |
31287 |
5333 |
6304 |
23001 |
29705 |
862 |
938 |
3486 |
4038 |
891 |
892 |
5039 |
5055 |
70085 |
59040 |
13477 |
11949 |
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https://usegalaxy.org/published/workflow?id=fb903de4aa4d5090, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1061?version=1, https://workflowhub.eu/workflows/1199?version=2, https://workflowhub.eu/workflows/123?version=1, https://workflowhub.eu/workflows/1269?version=2, https://workflowhub.eu/workflows/1275?version=2, https://workflowhub.eu/workflows/1296?version=2, https://workflowhub.eu/workflows/1352?version=3, https://workflowhub.eu/workflows/1390?version=2, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/1491?version=1, https://workflowhub.eu/workflows/1492?version=2, https://workflowhub.eu/workflows/1571?version=1, https://workflowhub.eu/workflows/1634?version=1, https://workflowhub.eu/workflows/1684?version=1, https://workflowhub.eu/workflows/1692?version=1, https://workflowhub.eu/workflows/1851?version=1, https://workflowhub.eu/workflows/1855?version=1, https://workflowhub.eu/workflows/689?version=1 |
assembly/metagenomics-assembly, assembly/vgp_genome_assembly, microbiome/metagenomics-assembly, microbiome/mgnify-amplicon, microbiome/pathogen-detection-from-nanopore-foodborne-data, single-cell/bulk-deconvolution-evaluate, single-cell/scrna-preprocessing, transcriptomics/minerva-pathways, transcriptomics/rna-seq-reads-to-counts |
|
collection_element_identifiers |
collection_element_identifiers |
Extract element identifiers of a collection |
2018-06-13 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers |
0.0.2 |
|
|
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers |
|
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0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
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0 |
0 |
0 |
0 |
0 |
1 |
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1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2213 |
2274 |
12646 |
13068 |
2624 |
2659 |
10358 |
10479 |
367 |
368 |
1829 |
1840 |
308 |
308 |
3128 |
3128 |
28515 |
27961 |
5609 |
5512 |
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https://workflowhub.eu/workflows/1078?version=1, https://workflowhub.eu/workflows/1199?version=2, https://workflowhub.eu/workflows/1207?version=2, https://workflowhub.eu/workflows/1259?version=1, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1273?version=2, https://workflowhub.eu/workflows/1395?version=2, https://workflowhub.eu/workflows/1495?version=1, https://workflowhub.eu/workflows/1561?version=1, https://workflowhub.eu/workflows/1635?version=1, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/1713?version=1, https://workflowhub.eu/workflows/1745?version=2, https://workflowhub.eu/workflows/1842?version=1, https://workflowhub.eu/workflows/1856?version=1, https://workflowhub.eu/workflows/439?version=3 |
ecology/ENA_Biodiv_submission, microbiome/dada-16S, microbiome/mgnify-amplicon, microbiome/pathogen-detection-from-nanopore-foodborne-data, sequence-analysis/Manage_AB1_Sanger, single-cell/scatac-batch-correction-snapatac2, transcriptomics/differential-isoform-expression, transcriptomics/ref-based |
|
column_maker |
Add_a_column1 |
Compute an expression on every row |
2019-06-24 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker |
2.1 |
python |
|
To update |
Text Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker |
|
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0 |
1 |
1 |
1 |
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0 |
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1 |
1 |
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0 |
0 |
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0 |
0 |
1 |
1 |
1 |
6569 |
7917 |
2959895 |
3934273 |
6681 |
15326 |
265585 |
753337 |
1099 |
1306 |
98471 |
100332 |
253 |
259 |
11349 |
11525 |
4799467 |
3335300 |
24808 |
14602 |
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https://usegalaxy.org/published/workflow?id=f58c90061c31bd48, https://usegalaxy.org/published/workflow?id=f60027545d40b82d, https://usegalaxy.org/published/workflow?id=f6ee07c7edf170fb, https://usegalaxy.org/published/workflow?id=f7d1c6be4e4c3357, https://usegalaxy.org/published/workflow?id=f93a4f6b5f3aaaed, https://usegalaxy.org/published/workflow?id=fa26fd51caea53c7, https://usegalaxy.org/published/workflow?id=fbf75fbb72b488bd, https://usegalaxy.org/published/workflow?id=fc7b14aafa0b421e, https://usegalaxy.org/published/workflow?id=fcbe12fc4eaae12e, https://usegalaxy.org/published/workflow?id=fd155fcba9bed7ff, https://usegalaxy.org/published/workflow?id=fd40e50c9f1545ce, https://usegalaxy.org/published/workflow?id=fdfe38dc92e51611, https://usegalaxy.org/published/workflow?id=ff3ade25b35f4893, https://workflowhub.eu/workflows/1057?version=9, https://workflowhub.eu/workflows/1061?version=1, https://workflowhub.eu/workflows/109?version=9, https://workflowhub.eu/workflows/111?version=5, https://workflowhub.eu/workflows/1327?version=6, https://workflowhub.eu/workflows/138?version=9, https://workflowhub.eu/workflows/1395?version=2, https://workflowhub.eu/workflows/1448?version=1, https://workflowhub.eu/workflows/1469?version=1, https://workflowhub.eu/workflows/1486?version=1, https://workflowhub.eu/workflows/1492?version=2, https://workflowhub.eu/workflows/1518?version=1, https://workflowhub.eu/workflows/1530?version=1, https://workflowhub.eu/workflows/1567?version=1, https://workflowhub.eu/workflows/1571?version=1, https://workflowhub.eu/workflows/1601?version=1, https://workflowhub.eu/workflows/1607?version=1, https://workflowhub.eu/workflows/1623?version=1, https://workflowhub.eu/workflows/1632?version=1, https://workflowhub.eu/workflows/1684?version=1, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/1699?version=1, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1713?version=1, https://workflowhub.eu/workflows/1874?version=1, https://workflowhub.eu/workflows/354?version=1, https://workflowhub.eu/workflows/356?version=1, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/603?version=2, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/612?version=24, https://workflowhub.eu/workflows/629?version=1, https://workflowhub.eu/workflows/633?version=22, https://workflowhub.eu/workflows/641?version=29, https://workflowhub.eu/workflows/642?version=24, https://workflowhub.eu/workflows/689?version=1, https://workflowhub.eu/workflows/698?version=1, https://workflowhub.eu/workflows/751?version=17, https://workflowhub.eu/workflows/789?version=1, https://workflowhub.eu/workflows/794?version=2 |
assembly/vgp_genome_assembly, data-science/data-manipulation-olympics, digital-humanities/text_mining_chinese, genome-annotation/gene-centric, genome-annotation/tnseq, introduction/data-manipulation-olympics, introduction/galaxy-intro-peaks2genes, microbiome/dada-16S, microbiome/metaplasmidome_query, microbiome/mgnify-amplicon, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/maxquant-label-free, single-cell/bulk-deconvolution-evaluate, statistics/flexynesis_survival, transcriptomics/differential-isoform-expression, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-genes-to-pathways, variant-analysis/pox-tiled-amplicon |
|
column_order_header_sort |
column_order_header_sort |
Sort Column Order by heading |
2017-04-04 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort |
0.0.1 |
python |
|
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
291 |
369 |
4668 |
5579 |
342 |
434 |
1768 |
2044 |
0 |
0 |
0 |
0 |
13 |
13 |
21 |
21 |
7644 |
6457 |
816 |
646 |
https://usegalaxy.eu/published/workflow?id=1d2e17a4f71f2455, https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=dd8b55e7768843b1, https://usegalaxy.eu/published/workflow?id=f28459c5b16549b7, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.org/published/workflow?id=173ecc0c88090d0e, https://usegalaxy.org/published/workflow?id=6d0a3f36d2736087, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=93650de42fb8c015, https://usegalaxy.org/published/workflow?id=a89def2c2462674a, https://usegalaxy.org/published/workflow?id=aac2ae0419f7d515, https://usegalaxy.org/published/workflow?id=b094b6e1e7d48416, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8 |
|
|
column_remove_by_header |
column_remove_by_header |
Remove columns by header |
2017-04-04 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header |
1.0 |
python |
|
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
787 |
891 |
9614 |
10501 |
815 |
908 |
5129 |
5911 |
48 |
48 |
2147 |
2147 |
46 |
46 |
219 |
219 |
18778 |
17109 |
1893 |
1696 |
https://usegalaxy.eu/published/workflow?id=04df470a38b10e94, https://usegalaxy.eu/published/workflow?id=1b72af1870c540d6, https://usegalaxy.eu/published/workflow?id=2ae4a83327615155, https://usegalaxy.eu/published/workflow?id=409ac72c9906f16a, https://usegalaxy.eu/published/workflow?id=9791e8aae12d6e63, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=c7b9fb6872444809, https://usegalaxy.eu/published/workflow?id=d1b3b62e7f91e217, https://usegalaxy.eu/published/workflow?id=e04be1ab5a16eb9f, https://usegalaxy.org.au/published/workflow?id=5fe66b29dcfb22ab, https://usegalaxy.org/published/workflow?id=13a3954b8894e1b1, https://usegalaxy.org/published/workflow?id=347571ba3b281bf4, https://usegalaxy.org/published/workflow?id=3cb4fd9ff755d36e, https://workflowhub.eu/workflows/1207?version=2, https://workflowhub.eu/workflows/1542?version=1, https://workflowhub.eu/workflows/1556?version=1, https://workflowhub.eu/workflows/888?version=2 |
ecology/ecoregiolifetraits, single-cell/bulk-music-3-preparebulk, single-cell/pseudobulk-analysis |
|
comebin |
comebin |
Binning of metagenomic contigs using COntrastive Multi-viEw representation learning |
2025-07-03 |
https://github.com/ziyewang/COMEBin |
1.0.4 |
comebin |
1.0.4 |
Up-to-date |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
1 |
1 |
|
|
|
compleasm |
compleasm |
Compleasm: a faster and more accurate reimplementation of BUSCO |
2023-12-04 |
https://github.com/huangnengCSU/compleasm |
0.2.6 |
compleasm |
0.2.7 |
To update |
Sequence Analysis |
Sequence assembly validation |
Sequence assembly validation |
Sequence assembly, Genomics, Transcriptomics, Sequence analysis |
Sequence assembly, Transcriptomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm |
compleasm |
Compleasm |
Compleasm: a faster and more accurate reimplementation of BUSCO.It provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
99 |
99 |
675 |
675 |
92 |
92 |
638 |
638 |
20 |
20 |
269 |
269 |
18 |
18 |
449 |
449 |
2031 |
2031 |
229 |
229 |
https://usegalaxy.eu/published/workflow?id=082bfd9b36e921e8, https://usegalaxy.eu/published/workflow?id=122da0054fd40adf, https://usegalaxy.eu/published/workflow?id=194a05d42687b524, https://usegalaxy.eu/published/workflow?id=1cba6eb4aff8dc61, https://usegalaxy.eu/published/workflow?id=1d1ae39386b5c318, https://usegalaxy.eu/published/workflow?id=1da7ac8eaf891f39, https://usegalaxy.eu/published/workflow?id=1e7f4ba6261f979c, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=3e255a5b7026d26e, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=45ae834d842302c3, https://usegalaxy.eu/published/workflow?id=475ea16f943cc013, https://usegalaxy.eu/published/workflow?id=54590ccd11ffbf65, https://usegalaxy.eu/published/workflow?id=56523b41ff7eec76, https://usegalaxy.eu/published/workflow?id=6573f3b1606b7f09, 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|
|
compose_text_param |
compose_text_param |
Compose a text parameter value using text, integer and float values |
2019-05-09 |
|
0.1.1 |
|
|
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
939 |
944 |
51227 |
51246 |
555 |
555 |
20402 |
20402 |
142 |
142 |
1655 |
1655 |
14 |
14 |
2809 |
2809 |
76112 |
76093 |
1655 |
1650 |
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https://workflowhub.eu/workflows/356?version=1, https://workflowhub.eu/workflows/400?version=12, https://workflowhub.eu/workflows/401?version=13, https://workflowhub.eu/workflows/439?version=3, https://workflowhub.eu/workflows/519?version=1, https://workflowhub.eu/workflows/612?version=24, https://workflowhub.eu/workflows/622?version=11, https://workflowhub.eu/workflows/625?version=26, https://workflowhub.eu/workflows/628?version=1, https://workflowhub.eu/workflows/629?version=1, https://workflowhub.eu/workflows/632?version=11, https://workflowhub.eu/workflows/633?version=22, https://workflowhub.eu/workflows/642?version=24, https://workflowhub.eu/workflows/738?version=4, https://workflowhub.eu/workflows/751?version=17 |
digital-humanities/open-refine-tutorial, galaxy-interface/workflow-automation, microbiome/pathogen-detection-from-nanopore-foodborne-data, variant-analysis/pox-tiled-amplicon |
|
compress_file |
compress_file |
Compress files. |
2022-02-04 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file |
0.1.0 |
gzip |
|
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
439 |
439 |
10916 |
10916 |
523 |
523 |
7826 |
7826 |
101 |
101 |
13887 |
13887 |
0 |
0 |
0 |
0 |
32629 |
32629 |
1063 |
1063 |
https://usegalaxy.eu/published/workflow?id=2062c7e1c50b05f3, https://usegalaxy.eu/published/workflow?id=32a0c4bbe6f9add9, https://usegalaxy.eu/published/workflow?id=c0c8228673b7191f, https://usegalaxy.eu/published/workflow?id=c7f34c67c9054234, https://usegalaxy.eu/published/workflow?id=e71ae1076d5f0584, https://usegalaxy.org.au/published/workflow?id=2f49a0a03d99c57a, https://usegalaxy.org.au/published/workflow?id=614898119cf0dabf, https://usegalaxy.org.au/published/workflow?id=8004dce1906ec057, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=fc74419b109527b2, https://usegalaxy.org/published/workflow?id=40be58638e230ab5, https://usegalaxy.org/published/workflow?id=5f621330d6339655, https://usegalaxy.org/published/workflow?id=67b9046dc5dbc009, https://usegalaxy.org/published/workflow?id=982a3eb2b4c4f5ae, https://workflowhub.eu/workflows/1648?version=1, https://workflowhub.eu/workflows/738?version=4 |
assembly/mitochondrion-assembly |
|
concoct |
concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering |
CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. |
2022-02-18 |
https://github.com/BinPro/CONCOCT |
1.1.0 |
concoct |
1.1.0 |
Up-to-date |
Metagenomics |
Sequence clustering, Read binning |
Sequence clustering, Read binning |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct |
concoct |
CONCOCT |
A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. |
|
0 |
0 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
107 |
107 |
9955 |
9955 |
19 |
19 |
187 |
187 |
0 |
0 |
0 |
0 |
4 |
4 |
3085 |
3085 |
13227 |
13227 |
130 |
130 |
https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=58f779d238d569dc, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://workflowhub.eu/workflows/1352?version=3 |
|
|
contig_annotation_tool |
cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise |
Contig Annotation Tool (CAT) |
2019-11-27 |
https://github.com/dutilh/CAT |
5.2.3 |
cat |
6.0.1 |
To update |
Metagenomics |
Taxonomic classification, Sequence assembly, Coding region prediction |
Taxonomic classification, Sequence assembly, Coding region prediction |
Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly |
Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly |
iuc |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat |
cat_bins |
CAT and BAT |
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. |
|
0 |
2 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
5 |
257 |
267 |
17418 |
17676 |
216 |
231 |
1590 |
1750 |
84 |
85 |
848 |
875 |
0 |
0 |
0 |
0 |
20301 |
19856 |
583 |
557 |
https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef |
|
|
control_freec |
control_freec |
Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. |
2020-07-22 |
http://boevalab.inf.ethz.ch/FREEC/ |
11.6 |
gawk |
|
To update |
Variant Analysis |
Copy number estimation, Variant calling, Genome alignment |
Copy number estimation, Variant calling, Genome alignment |
DNA structural variation, Oncology, Human genetics, Data mining |
Oncology, Human genetics, Data mining |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec |
freec |
FREEC |
A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
118 |
118 |
1565 |
1575 |
0 |
0 |
0 |
0 |
4 |
4 |
201 |
201 |
1 |
1 |
17 |
17 |
1793 |
1783 |
123 |
123 |
https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=2c3d05023c02113e, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=6ed1016dfdf9f928, https://usegalaxy.eu/published/workflow?id=75e88603745e069e, https://usegalaxy.eu/published/workflow?id=7cc253b53379b727, https://usegalaxy.eu/published/workflow?id=b1d1694b95ed10e1, https://workflowhub.eu/workflows/1651?version=1, https://workflowhub.eu/workflows/676?version=1 |
variant-analysis/somatic-variant-discovery |
|
coreprofiler |
coreprofiler_allele_calling |
CoreProfiler, a tool for cgMLST allele calling from bacterial genome assemblies |
2025-07-22 |
https://gitlab.com/ifb-elixirfr/abromics/coreprofiler |
1.1.4 |
coreprofiler |
1.1.4 |
Up-to-date |
Variant Analysis |
Multilocus sequence typing |
Multilocus sequence typing |
Microbiology, Bioinformatics, Phylogenetics |
Microbiology, Bioinformatics, Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/coreprofiler |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/coreprofiler |
coreprofiler |
CoreProfiler |
CoreProfiler is a cgMLST (core genome multilocus sequence typing) software that identifies alleles in bacterial genome assemblies by comparing them to a reference allele scheme. It detects both exact matches to known alleles and potential novel alleles using a two-step BLAST-based approach, enabling robust and reproducible strain genotyping. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
cosg |
cosg |
Marker gene identification for single-cell sequencing data using COSG. |
2024-05-29 |
https://github.com/genecell/COSG |
1.0.1 |
cosg |
1.0.3 |
To update |
Transcriptomics, Sequence Analysis, Single Cell |
Nucleic acid sequence analysis |
Nucleic acid sequence analysis |
Bioinformatics |
Bioinformatics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg |
cosg |
COSG |
COSG is a cosine similarity-based method for more accurate and scalable marker gene identification. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
https://usegalaxy.eu/published/workflow?id=9adf0402b641042c |
|
|
coverage_report |
CoverageReport2 |
Generate Detailed Coverage Report from BAM file |
2017-10-16 |
https://github.com/galaxyproject/tools-iuc |
0.0.4 |
perl-number-format |
1.76 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
coverm |
coverm_contig, coverm_genome |
CoverM genome and contig wrappers |
2022-04-26 |
https://github.com/wwood/CoverM |
0.7.0 |
coverm |
0.7.0 |
Up-to-date |
Sequence Analysis |
Local alignment |
Local alignment |
Metagenomics, Sequence analysis |
Metagenomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tools/coverm |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm |
coverm |
CoverM |
Read coverage calculator for metagenomics |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
147 |
147 |
3594 |
3594 |
14 |
14 |
414 |
414 |
11 |
11 |
125 |
125 |
7 |
7 |
565 |
565 |
4698 |
4698 |
179 |
179 |
https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://workflowhub.eu/workflows/1352?version=3, https://workflowhub.eu/workflows/1390?version=2 |
assembly/metagenomics-assembly, microbiome/metagenomics-assembly |
|
cramino |
cramino |
A tool for quick quality assessment of cram and bam files, intended for long read sequencing. |
2025-06-17 |
https://github.com/wdecoster/cramino |
1.1.0 |
cramino |
1.1.0 |
Up-to-date |
Statistics, Nanopore |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cramino/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cramino |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
crispr_studio |
crispr_studio |
CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. |
2019-08-13 |
https://github.com/moineaulab/CRISPRStudio |
1+galaxy0 |
crispr_studio |
1 |
To update |
Sequence Analysis |
Visualisation |
Visualisation |
Sequence analysis, Genomics, Data visualisation |
Sequence analysis, Genomics, Data visualisation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio |
crisprstudio |
CRISPRStudio |
CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
94 |
103 |
2795 |
2880 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2880 |
2795 |
103 |
94 |
|
|
|
crosscontamination_barcode_filter |
crosscontamination_barcode_filter |
Barcode contamination discovery tool |
2018-07-27 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter |
0.3 |
r-ggplot2 |
2.2.1 |
To update |
Transcriptomics, Visualization, Single Cell |
Filtering, Sequence contamination filtering, Sequencing quality control, RNA-Seq analysis |
Filtering, Sequence contamination filtering, RNA-Seq analysis |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter |
cross-contamination_barcode_filter |
Cross-contamination Barcode Filter |
This tool produces plots enabling the discovery of cross-contamination of samples across the full selection of barcodes used in a sequencing plate. It also filters false barcodes from each batch and retains only the 'real' barcodes. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
68 |
99 |
146 |
415 |
48 |
49 |
82 |
144 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
559 |
228 |
148 |
116 |
|
|
|
crossmap |
crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig |
CrossMap converts genome coordinates or annotation files between genome assemblies |
2016-04-04 |
http://crossmap.sourceforge.net/ |
0.7.3 |
crossmap |
0.7.3 |
Up-to-date |
Convert Formats, Genomic Interval Operations |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap |
|
|
|
|
0 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
6 |
5 |
84 |
104 |
2277 |
2776 |
222 |
254 |
4500 |
5654 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8430 |
6777 |
358 |
306 |
https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4 |
|
|
cuffcompare |
cuffcompare |
Galaxy wrappers for the Cuffcompare tool. |
2020-06-08 |
http://cole-trapnell-lab.github.io/cufflinks/ |
2.2.1 |
cufflinks |
2.2.1 |
Up-to-date |
Transcriptomics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
177 |
329 |
710 |
1264 |
569 |
5791 |
1726 |
25159 |
29 |
98 |
186 |
496 |
65 |
66 |
294 |
329 |
27248 |
2916 |
6284 |
840 |
https://usegalaxy.org/published/workflow?id=2ae1b71ea4634d1e, https://usegalaxy.org/published/workflow?id=2b1c98865a3ce11a, https://usegalaxy.org/published/workflow?id=52a2cca52985cdc7, https://usegalaxy.org/published/workflow?id=61b7ad6588f7db41, https://usegalaxy.org/published/workflow?id=712d9ae42b45c4b9, https://usegalaxy.org/published/workflow?id=7c3b5398dd05a6a5, https://usegalaxy.org/published/workflow?id=82681bd5f059e39a, https://usegalaxy.org/published/workflow?id=930dfd894899173e, https://usegalaxy.org/published/workflow?id=a57db139837dd24c, https://usegalaxy.org/published/workflow?id=b4174fd0cf4f865c, https://usegalaxy.org/published/workflow?id=eae740bac11ecc91, https://usegalaxy.org/published/workflow?id=f47f0b25c1405128, https://usegalaxy.org/published/workflow?id=fcce98489c8ca7a3 |
|
|
cuffdiff |
cuffdiff |
Galaxy wrappers for the Cuffdiff tool. |
2020-06-08 |
http://cole-trapnell-lab.github.io/cufflinks/ |
2.2.1 |
cufflinks |
2.2.1 |
Up-to-date |
Transcriptomics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff |
|
|
|
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0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
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0 |
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0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
567 |
854 |
3184 |
6491 |
3733 |
20588 |
18787 |
118461 |
6 |
616 |
28 |
4231 |
1 |
1 |
4 |
4 |
129187 |
22003 |
22059 |
4307 |
https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=60f2a8721e203057, https://usegalaxy.org.au/published/workflow?id=0427bd5f28789a1f, https://usegalaxy.org.au/published/workflow?id=115896e8f4059e44, https://usegalaxy.org.au/published/workflow?id=126116a92f2e9a68, https://usegalaxy.org.au/published/workflow?id=1624a678c6791ca6, https://usegalaxy.org.au/published/workflow?id=189c584ea4bde59a, https://usegalaxy.org.au/published/workflow?id=1ac197bae296b2bf, https://usegalaxy.org.au/published/workflow?id=39bb22274ede7500, https://usegalaxy.org.au/published/workflow?id=427e27f87b8048a3, https://usegalaxy.org.au/published/workflow?id=50fdbdb8f807c021, https://usegalaxy.org.au/published/workflow?id=52d2fb868defa474, https://usegalaxy.org.au/published/workflow?id=581c455f74aa55a4, https://usegalaxy.org.au/published/workflow?id=60c5675ed2f4a7d8, https://usegalaxy.org.au/published/workflow?id=73854e391eec51d0, 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https://usegalaxy.org/published/workflow?id=fa9cb11930ef8297, https://usegalaxy.org/published/workflow?id=fcce98489c8ca7a3, https://workflowhub.eu/workflows/40?version=1 |
|
|
cufflinks |
cufflinks |
Galaxy wrappers for the Cufflinks tool. |
2020-06-08 |
http://cole-trapnell-lab.github.io/cufflinks/ |
2.2.1 |
cufflinks |
2.2.1 |
Up-to-date |
Transcriptomics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks |
|
|
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0 |
1 |
1 |
1 |
0 |
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0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
893 |
1397 |
24563 |
35224 |
5434 |
27612 |
57968 |
356362 |
281 |
854 |
2678 |
10520 |
43 |
47 |
977 |
1058 |
403164 |
86186 |
29910 |
6651 |
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|
|
cuffmerge |
cuffmerge |
Galaxy wrappers for the Cuffmerge tool. |
2020-06-08 |
http://cole-trapnell-lab.github.io/cufflinks/ |
2.2.1 |
cufflinks |
2.2.1 |
Up-to-date |
Transcriptomics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
355 |
714 |
2092 |
3626 |
2472 |
13902 |
16686 |
68295 |
96 |
573 |
635 |
3101 |
57 |
57 |
128 |
128 |
75150 |
19541 |
15246 |
2980 |
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|
|
cuffnorm |
cuffnorm |
The Cuffnorm tool |
2020-06-08 |
http://cole-trapnell-lab.github.io/cufflinks/ |
2.2.1 |
cufflinks |
2.2.1 |
Up-to-date |
Transcriptomics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
66 |
117 |
302 |
707 |
202 |
1179 |
713 |
13525 |
49 |
71 |
287 |
367 |
0 |
0 |
0 |
0 |
14599 |
1302 |
1367 |
317 |
|
|
|
cuffquant |
cuffquant |
The Cuffquant tool |
2020-06-08 |
http://cole-trapnell-lab.github.io/cufflinks/ |
2.2.1 |
cufflinks |
2.2.1 |
Up-to-date |
Transcriptomics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
49 |
79 |
352 |
767 |
192 |
1326 |
1070 |
15964 |
22 |
47 |
257 |
426 |
0 |
0 |
0 |
0 |
17157 |
1679 |
1452 |
263 |
https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.org/published/workflow?id=8b2c8c8ce121177d, https://workflowhub.eu/workflows/40?version=1 |
|
|
cutadapt |
cutadapt |
Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). |
2018-02-20 |
https://cutadapt.readthedocs.org/en/stable/ |
5.1 |
cutadapt |
5.1 |
Up-to-date |
Fasta Manipulation, Fastq Manipulation, Sequence Analysis |
Sequence trimming, Primer removal, Read pre-processing |
Sequence trimming, Primer removal, Read pre-processing |
Genomics, Probes and primers, Sequencing |
Genomics, Probes and primers, Sequencing |
lparsons |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt |
cutadapt |
Cutadapt |
Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
14131 |
16253 |
330892 |
364942 |
22476 |
26008 |
409500 |
482165 |
4256 |
4631 |
79748 |
86014 |
1579 |
1582 |
59464 |
59550 |
992671 |
879604 |
48474 |
42442 |
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assembly/metagenomics-assembly, assembly/vgp_genome_assembly, contributing/create-new-tutorial, ecology/ENA_Biodiv_submission, epigenetics/atac-seq, genome-annotation/crispr-screen, genome-annotation/tnseq, microbiome/metagenomics-assembly, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, sequence-analysis/quality-control, transcriptomics/clipseq, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-interactome, transcriptomics/rna-seq-reads-to-counts |
|
cutesv |
cutesv |
Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. |
2020-09-23 |
https://github.com/tjiangHIT/cuteSV |
2.1.3 |
cutesv |
2.1.3 |
Up-to-date |
Variant Analysis |
Split read mapping, Genotyping, Structural variation detection |
Split read mapping, Genotyping, Structural variation detection |
DNA structural variation, Sequencing, Computer science |
Sequencing, Computer science |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv |
cuteSV |
cuteSV |
Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
58 |
58 |
344 |
344 |
0 |
0 |
0 |
0 |
11 |
11 |
166 |
166 |
0 |
0 |
0 |
0 |
510 |
510 |
69 |
69 |
|
|
|
cwpair2 |
cwpair2 |
Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. |
2015-12-18 |
|
1.1.1 |
matplotlib |
|
To update |
ChIP-seq |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
33 |
85 |
60 |
283 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
283 |
60 |
85 |
33 |
|
|
|
dada2 |
dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_primerCheck, dada2_removeBimeraDenovo, dada2_seqCounts |
DADA2 wrappers |
2019-07-05 |
https://benjjneb.github.io/dada2/index.html |
1.34.0 |
bioconductor-dada2 |
1.34.0 |
Up-to-date |
Metagenomics |
Variant calling, DNA barcoding |
Variant calling, DNA barcoding |
Sequencing, Genetic variation, Microbial ecology, Metagenomics |
Sequencing, Genetic variation, Microbial ecology, Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 |
dada2 |
dada2 |
This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. |
|
0 |
10 |
11 |
11 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
10 |
865 |
885 |
205808 |
209081 |
1301 |
1344 |
254475 |
270135 |
179 |
179 |
52639 |
52639 |
72 |
72 |
38131 |
38131 |
569986 |
551053 |
2480 |
2417 |
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microbiome/dada-16S |
|
das_tool |
Fasta_to_Contig2Bin, das_tool |
DAS Tool for genome resolved metagenomics |
2022-06-23 |
https://github.com/cmks/DAS_Tool |
1.1.7 |
das_tool |
1.1.7 |
Up-to-date |
Metagenomics |
Read binning |
Read binning |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool |
dastool |
dastool |
DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. |
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0 |
0 |
2 |
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0 |
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0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
77 |
77 |
6906 |
6906 |
12 |
12 |
283 |
283 |
0 |
0 |
0 |
0 |
3 |
3 |
1185 |
1185 |
8374 |
8374 |
92 |
92 |
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|
|
data_manager_homer_preparse |
homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide |
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. |
2021-08-08 |
http://homer.ucsd.edu/homer/index.html |
4.11 |
homer |
5.1 |
To update |
Sequence Analysis |
Sequence motif discovery |
Sequence motif discovery |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer |
homer |
homer |
HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. |
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0 |
0 |
5 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
293 |
293 |
11363 |
11363 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
23 |
24 |
388 |
534 |
11897 |
11751 |
317 |
316 |
https://usegalaxy.eu/published/workflow?id=d3a4e6cc1b4565e5 |
|
|
data_source_iris_tcga |
data_source_iris_tcga |
IRIS-TCGA Data source tool |
2016-02-18 |
|
1.0.0 |
python |
|
To update |
Data Source |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga |
|
|
|
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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|
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datamash |
datamash_ops, datamash_reverse, datamash_transpose |
GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. |
2015-08-03 |
https://www.gnu.org/software/datamash/ |
1.9 |
datamash |
1.1.0 |
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash |
|
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0 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
6000 |
6432 |
876492 |
892401 |
5184 |
5885 |
114632 |
134970 |
2485 |
2521 |
24641 |
25144 |
249 |
250 |
5920 |
5956 |
1058471 |
1021685 |
15088 |
13918 |
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assembly/ecoli_comparison, climate/climate-101, data-science/data-manipulation-olympics, digital-humanities/open-refine-tutorial, digital-humanities/text_mining_chinese, ecology/PAMPA-toolsuite-tutorial, epigenetics/cut_and_run, galaxy-interface/workflow-reports, introduction/data-manipulation-olympics, introduction/galaxy-intro-101, introduction/galaxy-intro-101-everyone, introduction/galaxy-reproduce, microbiome/nanopore-16S-metagenomics, proteomics/maxquant-msstats-dda-lfq, single-cell/bulk-deconvolution-evaluate, single-cell/bulk-music-2-preparescref, single-cell/scrna-case_monocle3-trajectories, single-cell/scrna-data-ingest, single-cell/scrna-raceid, single-cell/scrna-scanpy-pbmc3k, statistics/flexynesis_classification, statistics/flexynesis_survival, transcriptomics/rna-seq-viz-with-heatmap2, variant-analysis/pox-tiled-amplicon, variant-analysis/sars-cov-2-variant-discovery |
|
decontam |
decontam |
Removes decontamination features (ASVs/OTUs) using control samples |
2024-09-13 |
https://github.com/benjjneb/decontam |
1.22.0 |
bioconductor-decontam |
1.26.0 |
To update |
Metagenomics |
Classification |
Classification |
Metagenomics, Microbial ecology, Sequencing |
Metagenomics, Microbial ecology, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontam |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam |
decontam |
decontam |
Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data. Requires DNA quantitation data or sequenced negative control samples. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
32 |
32 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
32 |
32 |
8 |
8 |
https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 |
|
|
decontaminator |
decontaminator |
Deep Learning method for novel virus detection in sequencing data |
2023-01-09 |
https://github.com/cbib/decontaminator |
1.0.0 |
numpy |
|
To update |
Machine Learning |
Filtering |
Filtering |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator |
decontaminator |
decontaminator |
Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
41 |
41 |
349 |
349 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
349 |
349 |
41 |
41 |
|
|
|
deeparg |
deeparg_predict, deeparg_short_reads |
A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes |
2024-10-07 |
https://github.com/gaarangoa/deeparg |
1.0.4 |
deeparg |
1.0.4 |
Up-to-date |
Sequence Analysis |
Antimicrobial resistance prediction, Antimicrobial resistance prediction |
Antimicrobial resistance prediction, Antimicrobial resistance prediction |
Microbiology |
Microbiology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/deeparg |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/deeparg |
deeparg |
DeepARG |
A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes. |
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
20 |
20 |
108 |
108 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
65 |
65 |
173 |
173 |
24 |
24 |
|
|
|
deepmicro |
deepmicro |
Representation learning and classification framework |
2023-03-16 |
https://github.com/paulzierep/DeepMicro |
1.4 |
deepmicro |
1.4 |
Up-to-date |
Machine Learning |
Essential dynamics, Splitting, Community profiling |
Essential dynamics, Splitting |
Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics |
Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics |
iuc |
https://github.com/paulzierep/DeepMicro |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro |
DeepMicro |
DeepMicro |
Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
9 |
9 |
560 |
560 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
560 |
560 |
9 |
9 |
|
|
|
deepsig |
deepsig |
Predictor of signal peptides in proteins based on deep learning |
2023-04-28 |
https://github.com/BolognaBiocomp/deepsig |
1.2.5 |
deepsig |
1.2.5 |
Up-to-date |
Genome annotation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
131 |
131 |
388 |
388 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
11 |
45 |
45 |
433 |
433 |
142 |
142 |
https://usegalaxy.eu/published/workflow?id=a018307be3563f28 |
|
|
deepvariant |
deepvariant |
DeepVariant is a deep learning-based variant caller |
2021-09-06 |
https://github.com/google/deepvariant |
1.5.0 |
|
|
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
546 |
546 |
5121 |
5121 |
789 |
789 |
6696 |
6696 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11817 |
11817 |
1335 |
1335 |
https://usegalaxy.org/published/workflow?id=39753cc73284963f, https://usegalaxy.org/published/workflow?id=b1a98a2d5ebda1c5, https://usegalaxy.org/published/workflow?id=e7586d70715207b5 |
|
|
deg_annotate |
deg_annotate |
Annotate DESeq2/DEXSeq output tables |
2018-11-22 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate |
1.1.0+galaxy1 |
bedtools |
2.31.1 |
To update |
Transcriptomics, Single Cell |
RNA-Seq analysis, Gene functional annotation |
RNA-Seq analysis, Gene functional annotation |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate |
deg_annotate |
DEG Annotate |
This tool appends the output table of DESeq2 or DEXSeq with gene symbols, biotypes, positions etc. The information you want to add is configurable. This information should present in the input GTF/GFF file as attributes of feature you choose. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
5016 |
5484 |
28041 |
30372 |
6635 |
6880 |
40314 |
41985 |
1207 |
1251 |
6149 |
6366 |
185 |
186 |
649 |
665 |
79388 |
75153 |
13801 |
13043 |
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transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz |
|
delly |
delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge |
Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. |
2020-09-28 |
https://github.com/dellytools/delly |
0.9.1 |
delly |
1.5.0 |
To update |
Variant Analysis |
Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis |
Indel detection, Structural variation detection, Genotyping |
DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases |
Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly |
delly2 |
Delly2 |
Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. |
|
0 |
0 |
6 |
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185 |
185 |
3117 |
3117 |
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0 |
0 |
0 |
0 |
0 |
0 |
3117 |
3117 |
185 |
185 |
|
|
|
deseq2 |
deseq2 |
Differential gene expression analysis based on the negative binomial distribution |
2014-12-03 |
https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html |
2.11.40.8 |
bioconductor-deseq2 |
1.46.0 |
To update |
Transcriptomics, RNA, Statistics, Single Cell |
Differential gene expression analysis, RNA-Seq analysis |
Differential gene expression analysis, RNA-Seq analysis |
RNA-Seq |
RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 |
DESeq2 |
DESeq2 |
R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. |
|
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15994 |
110682 |
133936 |
27214 |
37996 |
191581 |
286575 |
2980 |
3614 |
19899 |
24448 |
820 |
824 |
4511 |
4530 |
449489 |
326673 |
58428 |
44721 |
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transcriptomics/de-novo, transcriptomics/mirna-target-finder, transcriptomics/network-analysis-with-heinz, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/srna |
|
dexseq |
dexseq, dexseq_count, plotdexseq |
Inference of differential exon usage in RNA-Seq |
2015-09-25 |
https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html |
1.48.0 |
bioconductor-dexseq |
1.52.0 |
To update |
Transcriptomics, RNA, Statistics, Single Cell |
Enrichment analysis, Exonic splicing enhancer prediction |
Enrichment analysis, Exonic splicing enhancer prediction |
RNA-Seq |
RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq |
dexseq |
DEXSeq |
The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. |
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0 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
274 |
481 |
14442 |
18733 |
646 |
1620 |
16356 |
30696 |
65 |
101 |
2756 |
4812 |
8 |
9 |
97 |
98 |
54339 |
33651 |
2211 |
993 |
https://usegalaxy.org/published/workflow?id=82681bd5f059e39a |
transcriptomics/ref-based |
|
diamond |
bg_diamond, bg_diamond_makedb, bg_diamond_view |
DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. |
2021-03-21 |
https://github.com/bbuchfink/diamond |
2.1.13 |
diamond |
2.1.13 |
Up-to-date |
Sequence Analysis |
Sequence alignment analysis |
Sequence alignment analysis |
Sequence analysis, Proteins |
Sequence analysis, Proteins |
bgruening |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond |
diamond |
Diamond |
Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. |
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1 |
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0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
1620 |
1706 |
112648 |
114376 |
665 |
1048 |
35921 |
43599 |
446 |
448 |
65850 |
66062 |
125 |
125 |
2180 |
2208 |
226245 |
216599 |
3327 |
2856 |
https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=ff4d5beb6ce1809d, https://usegalaxy.org.au/published/workflow?id=0a3fb089674de144, https://usegalaxy.org/published/workflow?id=b0f85c802c1ea7f8, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1518?version=1, https://workflowhub.eu/workflows/1641?version=1 |
assembly/ERGA-post-assembly-QC, genome-annotation/functional, genome-annotation/gene-centric, sequence-analysis/ncbi-blast-against-the-madland |
|
diffbind |
diffbind |
Diffbind provides functions for processing ChIP-Seq data. |
2018-01-21 |
http://bioconductor.org/packages/release/bioc/html/DiffBind.html |
3.12.0 |
bioconductor-diffbind |
3.16.0 |
To update |
ChIP-seq |
Differential binding analysis |
Differential binding analysis |
ChIP-seq |
ChIP-seq |
bgruening |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind |
diffbind |
DiffBind |
Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. |
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0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
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0 |
0 |
0 |
1 |
1 |
667 |
792 |
9452 |
11112 |
1268 |
2073 |
13935 |
20417 |
80 |
101 |
1868 |
2386 |
69 |
69 |
130 |
130 |
34045 |
25385 |
3035 |
2084 |
https://usegalaxy.eu/published/workflow?id=719314fa5263b501, https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf |
|
|
diffdock |
diffdock |
Diffusion Steps, Twists, and Turns for Molecular Docking. |
2025-06-27 |
https://github.com/gcorso/DiffDock |
1.1.3 |
|
|
To update |
Computational chemistry |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffdock/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffdock |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
18 |
18 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
18 |
18 |
6 |
6 |
|
|
|
dimet |
dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ |
DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. |
2023-07-19 |
https://github.com/cbib/DIMet |
0.2.4 |
dimet |
0.2.4 |
Up-to-date |
Metabolomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
disco |
disco |
DISCO is a overlap-layout-consensus (OLC) metagenome assembler |
2017-10-26 |
http://disco.omicsbio.org/ |
|
disco |
1.3 |
To update |
Metagenomics, Assembly |
Protein sequence analysis |
Protein sequence analysis |
Structure determination |
Structure determination |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco |
disco |
DISCO |
DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
127 |
163 |
280 |
453 |
406 |
435 |
1525 |
1690 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2143 |
1805 |
598 |
533 |
|
|
|
dnabot |
dnabot |
DNA assembly using BASIC on OpenTrons |
2022-04-17 |
https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT |
3.1.0 |
dnabot |
|
To update |
Synthetic Biology |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
https://workflowhub.eu/workflows/1576?version=1 |
synthetic-biology/basic_assembly_analysis |
|
dnaweaver |
dnaweaver |
Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. |
2022-12-08 |
https://github.com/Edinburgh-Genome-Foundry/DnaWeaver |
1.0.2 |
dnaweaver_synbiocad |
1.0.2 |
Up-to-date |
Synthetic Biology |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
dos2unix |
dos2unix |
dos2unix convert text files with DOS or Mac line breaks to Unix line breaks and vice versa. |
2025-07-11 |
https://waterlan.home.xs4all.nl/dos2unix.html |
7.5.2 |
dos2unix |
|
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/dos2unix/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/dos2unix |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
18 |
18 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
18 |
18 |
7 |
7 |
|
|
|
dram |
dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer |
DRAM for distilling microbial metabolism to automate the curation of microbiome function |
2022-09-01 |
https://github.com/WrightonLabCSU/DRAM |
1.5.0 |
dram |
1.5.0 |
Up-to-date |
Metagenomics |
Gene functional annotation |
Gene functional annotation |
Metagenomics, Biological databases, Molecular genetics |
Metagenomics, Biological databases, Molecular genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram |
dram |
DRAM |
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes |
|
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
120 |
120 |
13633 |
13633 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
13633 |
13633 |
120 |
120 |
|
|
|
drep |
drep_compare, drep_dereplicate |
dRep compares and dereplicates genome sets |
2020-01-06 |
https://github.com/MrOlm/drep |
3.6.2 |
drep |
3.6.2 |
Up-to-date |
Metagenomics |
Genome comparison |
Genome comparison |
Metagenomics, Genomics, Sequence analysis |
Metagenomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep |
drep |
dRep |
Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. |
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
113 |
115 |
1708 |
1749 |
13 |
13 |
47 |
47 |
0 |
0 |
0 |
0 |
38 |
38 |
1273 |
1273 |
3069 |
3028 |
166 |
164 |
https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://workflowhub.eu/workflows/1352?version=3 |
genome-annotation/bacterial-genome-quality-control |
|
dropletutils |
dropletutils |
DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data |
2019-06-04 |
https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html |
1.10.0 |
bioconductor-dropletutils |
1.26.0 |
To update |
Single Cell, Sequence Analysis |
Loading, Community profiling |
|
Gene expression, RNA-seq, Sequencing, Transcriptomics |
Sequencing, Transcriptomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils |
dropletutils |
DropletUtils |
Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
450 |
517 |
4128 |
4902 |
381 |
385 |
5328 |
5345 |
42 |
46 |
2038 |
2190 |
34 |
34 |
110 |
110 |
12547 |
11604 |
982 |
907 |
https://usegalaxy.eu/published/workflow?id=0f563f176bb245af, https://usegalaxy.eu/published/workflow?id=3403d5a8a71e0c3c, https://usegalaxy.eu/published/workflow?id=49a6ddcba35bf085, https://usegalaxy.eu/published/workflow?id=6a6e2c2335051fb5, https://usegalaxy.eu/published/workflow?id=704e6c9bc51db49f, https://usegalaxy.eu/published/workflow?id=7d22eea4278570e8, https://usegalaxy.eu/published/workflow?id=83ae28e23099a3f6, https://usegalaxy.eu/published/workflow?id=90a32c95b60f5221, https://usegalaxy.eu/published/workflow?id=a1cfb476e849fce3, https://usegalaxy.eu/published/workflow?id=a3cb75fd31ba0689, https://usegalaxy.eu/published/workflow?id=af7c349497a75314, https://usegalaxy.eu/published/workflow?id=b5627201bb4f6943, https://usegalaxy.eu/published/workflow?id=d79309343e2a5d62, https://usegalaxy.eu/published/workflow?id=e7494f29c8672f34, https://usegalaxy.eu/published/workflow?id=e7a9e1a7728848cd, https://usegalaxy.eu/published/workflow?id=fa960b78dfc0c2f8, https://usegalaxy.eu/published/workflow?id=fd61d070d9744f95, https://usegalaxy.org.au/published/workflow?id=00da6615bca12a3c, https://usegalaxy.org.au/published/workflow?id=0458ecd2761307d1, https://usegalaxy.org.au/published/workflow?id=10296e860e9ef4bb, https://usegalaxy.org.au/published/workflow?id=281ea78467e73147, https://usegalaxy.org.au/published/workflow?id=3fd10af90a07f771, https://usegalaxy.org.au/published/workflow?id=41b115a9be4b6002, https://usegalaxy.org.au/published/workflow?id=471615c412b305f2, https://usegalaxy.org.au/published/workflow?id=644d8e4c78df8e36, https://usegalaxy.org.au/published/workflow?id=738350fc2ca69c0b, https://usegalaxy.org.au/published/workflow?id=c64dcc1e6a67f3e4, https://usegalaxy.org.au/published/workflow?id=f627023a3401bf9b, https://usegalaxy.org/published/workflow?id=4bbe4c8a6c52d03a, https://usegalaxy.org/published/workflow?id=516a2181b41af94e, https://usegalaxy.org/published/workflow?id=69712265fdb10ed5, https://usegalaxy.org/published/workflow?id=7aa36b1722ff4c11, https://usegalaxy.org/published/workflow?id=8e6d24a14d2908c2, https://usegalaxy.org/published/workflow?id=a6d6a2e8867fa566, https://usegalaxy.org/published/workflow?id=b73e416c06790ac5, https://usegalaxy.org/published/workflow?id=be7dab2274c1acdd, https://usegalaxy.org/published/workflow?id=cdb6c9c7037a95b2, https://workflowhub.eu/workflows/1523?version=1, https://workflowhub.eu/workflows/1527?version=1, https://workflowhub.eu/workflows/1546?version=1 |
single-cell/scrna-data-ingest, single-cell/scrna-preprocessing-tenx |
|
drug2cell |
drug2cell |
Collection of utility functions for gene group activity evaluation in scanpy. |
2025-01-21 |
https://github.com/Teichlab/drug2cell |
0.1.2 |
drug2cell |
0.1.2 |
Up-to-date |
Single Cell |
|
|
|
|
iuc |
https://github.com/Teichlab/drug2cell |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/drug2cell |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
1 |
1 |
|
|
|
duplex_family_size_distribution |
fsd, fsd_beforevsafter, fsd_regions, td |
Tool that plots a histogram of sizes of read families |
2019-10-24 |
|
1.0.2 |
matplotlib |
|
To update |
Graphics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
13 |
326 |
612 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
612 |
326 |
13 |
12 |
|
|
|
ebi_tools |
ebi_search_rest_results |
Tools to query and download data from several EMBL-EBI databases |
2016-11-29 |
http://www.ebi.ac.uk/services/all |
0.1.1 |
six |
|
To update |
Web Services, Data Source |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
121 |
180 |
187 |
431 |
449 |
587 |
1055 |
1533 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
1965 |
1243 |
768 |
571 |
|
|
|
edger |
edger |
Perform RNA-Seq differential expression analysis using edgeR pipeline |
2017-09-11 |
http://bioconductor.org/packages/release/bioc/html/edgeR.html |
3.36.0 |
bioconductor-edger |
4.4.0 |
To update |
Transcriptomics, RNA, Statistics, Single Cell |
Differential gene expression analysis |
Differential gene expression analysis |
Genetics, RNA-Seq, ChIP-seq |
Genetics, RNA-Seq, ChIP-seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger |
edger |
edgeR |
Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2767 |
3276 |
20681 |
25641 |
6109 |
8376 |
43822 |
64826 |
928 |
1075 |
7956 |
10252 |
29 |
30 |
172 |
173 |
100892 |
72631 |
12757 |
9833 |
https://usegalaxy.eu/published/workflow?id=0229f3f3835c2d53, https://usegalaxy.eu/published/workflow?id=04df470a38b10e94, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=c7b9fb6872444809, https://usegalaxy.eu/published/workflow?id=d1b3b62e7f91e217, https://usegalaxy.eu/published/workflow?id=e04be1ab5a16eb9f, https://usegalaxy.org.au/published/workflow?id=0cfc1408fd9ea4e7, https://usegalaxy.org.au/published/workflow?id=0fc7c14c4d1ac8f5, https://usegalaxy.org.au/published/workflow?id=5fe66b29dcfb22ab, https://usegalaxy.org.au/published/workflow?id=863eee1b041b6c58, https://usegalaxy.org/published/workflow?id=03258e0321162584, https://usegalaxy.org/published/workflow?id=13a3954b8894e1b1, https://usegalaxy.org/published/workflow?id=ce232859a466c75c, https://usegalaxy.org/published/workflow?id=d761637d43ee0324, https://workflowhub.eu/workflows/1207?version=2, https://workflowhub.eu/workflows/1556?version=1 |
single-cell/pseudobulk-analysis |
|
ega_download_client |
pyega3 |
EGA python client uses the EGA REST API to download authorized datasets and files. |
2020-09-02 |
https://github.com/EGA-archive/ega-download-client |
5.0.2 |
pyega3 |
5.2.0 |
To update |
Data Source |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
138 |
138 |
2852 |
2852 |
55 |
55 |
208 |
208 |
5 |
5 |
459 |
459 |
0 |
0 |
0 |
0 |
3519 |
3519 |
198 |
198 |
https://usegalaxy.eu/published/workflow?id=b3c0eba755f269b2, https://workflowhub.eu/workflows/1636?version=1, https://workflowhub.eu/workflows/363?version=2 |
variant-analysis/trio-analysis |
|
egsea |
egsea |
This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing |
2017-12-28 |
https://bioconductor.org/packages/release/bioc/html/EGSEA.html |
1.20.0 |
bioconductor-egsea |
1.34.0 |
To update |
Transcriptomics, RNA, Statistics, Single Cell |
Gene set testing |
Gene set testing |
Systems biology |
Systems biology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea |
egsea |
EGSEA |
This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
365 |
467 |
2481 |
3462 |
783 |
865 |
5041 |
5849 |
259 |
282 |
2025 |
2377 |
0 |
0 |
0 |
0 |
11688 |
9547 |
1614 |
1407 |
https://usegalaxy.eu/published/workflow?id=12bf85cdc8102bb5, https://usegalaxy.eu/published/workflow?id=63c91ea322cd2819, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=8b1e2fe9f4a07de0, https://usegalaxy.org.au/published/workflow?id=9f6e62f465589ca3, https://workflowhub.eu/workflows/1699?version=1 |
transcriptomics/rna-seq-genes-to-pathways |
|
emboss |
emboss_needle, emboss_needleall |
Galaxy wrappers for EMBOSS6 tools |
2025-01-17 |
http://emboss.open-bio.org/ |
6.6.0 |
emboss |
6.6.0 |
Up-to-date |
Sequence Analysis, Fasta Manipulation |
Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment |
Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment |
Molecular biology, Sequence analysis, Biology |
Molecular biology, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss |
emboss |
EMBOSS |
Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
62 |
62 |
419 |
419 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
419 |
419 |
62 |
62 |
|
|
|
emboss_5 |
EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 |
Galaxy wrappers for EMBOSS version 5.0.0 tools |
2017-01-11 |
http://emboss.open-bio.org/ |
5.0.0 |
emboss |
6.6.0 |
To update |
Sequence Analysis, Fasta Manipulation |
Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment |
Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment |
Molecular biology, Sequence analysis, Biology |
Molecular biology, Sequence analysis |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 |
emboss |
EMBOSS |
Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. |
|
0 |
107 |
107 |
107 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
107 |
0 |
0 |
0 |
0 |
0 |
107 |
0 |
0 |
0 |
0 |
0 |
0 |
107 |
107 |
107 |
444 |
513 |
264479 |
273772 |
1350 |
2518 |
169846 |
325994 |
557 |
810 |
29757 |
35329 |
51 |
51 |
997 |
1037 |
636132 |
465079 |
3892 |
2402 |
https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5, https://usegalaxy.eu/published/workflow?id=0ed8817a90caa2b1, https://usegalaxy.eu/published/workflow?id=1031e4c4f18e020e, https://usegalaxy.eu/published/workflow?id=1f88311a8e365c17, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=402b14906a03b2ef, https://usegalaxy.eu/published/workflow?id=6e1fe7372e93fae0, https://usegalaxy.eu/published/workflow?id=90f993a1b245eb68, https://usegalaxy.eu/published/workflow?id=9275d0c90a8713d6, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=a31100610fba17a1, https://usegalaxy.eu/published/workflow?id=ada52ba09b462567, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=b77e3b08092fa73e, https://usegalaxy.eu/published/workflow?id=d22dac11eba8c5a3, https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd, https://usegalaxy.eu/published/workflow?id=eaf3c4d97399e673, https://usegalaxy.fr/published/workflow?id=297b71156b297a73, https://usegalaxy.fr/published/workflow?id=b3974acb70608e38, https://usegalaxy.org.au/published/workflow?id=42137e36791652bc, https://usegalaxy.org.au/published/workflow?id=6b1b0a945d367b4c, https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a, https://usegalaxy.org.au/published/workflow?id=b432a1312859edd2, https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33, https://usegalaxy.org.au/published/workflow?id=f21446cc44da50ce, https://usegalaxy.org/published/workflow?id=00381bbae3fd7e78, https://usegalaxy.org/published/workflow?id=2d1ca299c1b058f6, https://usegalaxy.org/published/workflow?id=3b37e1cb61ec6f8e, https://usegalaxy.org/published/workflow?id=3c7349268d74c576, https://usegalaxy.org/published/workflow?id=4884918895db9af0, https://usegalaxy.org/published/workflow?id=63adc811e3ae529d, https://usegalaxy.org/published/workflow?id=6b4ad51307a28c7f, https://usegalaxy.org/published/workflow?id=6f836f4b71d399e7, https://usegalaxy.org/published/workflow?id=8d8e8927d63803ef, https://usegalaxy.org/published/workflow?id=8e1c6ad6ff623015, https://usegalaxy.org/published/workflow?id=94da3d448bb8a137, https://usegalaxy.org/published/workflow?id=956987e628530c79, https://usegalaxy.org/published/workflow?id=a666aaaa32f62487, https://usegalaxy.org/published/workflow?id=cc6ee582a6e5cae2, https://usegalaxy.org/published/workflow?id=cdf5dffbed938d49, https://usegalaxy.org/published/workflow?id=d3a69b0b826331ef, https://usegalaxy.org/published/workflow?id=e1dcdc125122f561, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://usegalaxy.org/published/workflow?id=f737593a1db217c8, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1632?version=1, https://workflowhub.eu/workflows/1647?version=1, https://workflowhub.eu/workflows/439?version=3 |
sequence-analysis/viral_primer_design, variant-analysis/pox-tiled-amplicon, variant-analysis/tb-variant-analysis |
|
ena_upload |
ena_upload |
Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). |
2020-06-10 |
https://github.com/usegalaxy-eu/ena-upload-cli |
0.9.0 |
ena-upload-cli |
0.9.0 |
Up-to-date |
Data Export |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
48 |
48 |
418 |
418 |
0 |
0 |
0 |
0 |
15 |
15 |
1833 |
1833 |
0 |
0 |
0 |
0 |
2251 |
2251 |
63 |
63 |
https://usegalaxy.eu/published/workflow?id=924edc19e0653870, https://workflowhub.eu/workflows/1409?version=1 |
galaxy-interface/upload-data-to-ena |
|
ena_webin_cli |
ena_webin_cli |
Submits a genome assembly to the European Nucleotide Archive (ENA) using the Webin-CLI Submission tool. |
2025-02-27 |
https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html |
8.1.1 |
ena-webin-cli |
9.0.1 |
To update |
Data Export |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
enasearch |
enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data |
A Python library for interacting with ENA's API |
2017-08-05 |
https://github.com/bebatut/enasearch |
|
enasearch |
0.2.2 |
To update |
Data Source |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch |
|
|
|
|
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
161 |
221 |
1661 |
2454 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2454 |
1661 |
221 |
161 |
|
|
|
ensembl_vep |
ensembl_vep |
Ensembl VEP: Annotate VCFs with variant effect predictions |
2022-05-11 |
https://github.com/Ensembl/ensembl-vep |
115.1 |
ensembl-vep |
115.2 |
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
269 |
269 |
3860 |
3860 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3860 |
3860 |
269 |
269 |
https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e, https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=99ad31bf3970ade4, https://usegalaxy.eu/published/workflow?id=ce1712139b4a4273, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1 |
|
|
episcanpy |
episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess |
EpiScanpy – Epigenomics single cell analysis in python |
2023-03-13 |
https://github.com/colomemaria/epiScanpy |
0.3.2 |
episcanpy |
0.4.0 |
To update |
Single Cell, Epigenetics |
Enrichment analysis, Imputation |
Enrichment analysis, Imputation |
Epigenomics, Cell biology, DNA |
Epigenomics, Cell biology, DNA |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy |
episcanpy |
epiScanpy |
Epigenomics Single Cell Analysis in Python. |
|
0 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
53 |
53 |
1075 |
1075 |
53 |
53 |
406 |
406 |
2 |
2 |
766 |
766 |
0 |
0 |
0 |
0 |
2247 |
2247 |
108 |
108 |
https://workflowhub.eu/workflows/1502?version=1, https://workflowhub.eu/workflows/1506?version=1 |
single-cell/scatac-preprocessing-tenx |
|
ete_treeviewer |
ete_treeviewer |
A toolkit for the analysis and visualization of trees. |
2024-11-25 |
http://etetoolkit.org |
3.1.3 |
curl |
|
To update |
Phylogenetics |
Phylogenetic analysis, Phylogenetic tree editing |
Phylogenetic tree editing |
Phylogenetics |
Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ete-toolkit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ete-toolkit |
ete |
ete |
The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
130 |
130 |
1626 |
1626 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
5 |
5 |
1631 |
1631 |
134 |
134 |
https://workflowhub.eu/workflows/1650?version=1 |
sequence-analysis/tapscan-streptophyte-algae |
|
eukrep |
eukrep |
Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets |
2025-07-30 |
https://github.com/patrickwest/EukRep |
0.6.7 |
eukrep |
0.6.7 |
Up-to-date |
Metagenomics |
Nucleic acid sequence analysis |
Nucleic acid sequence analysis |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/eukrep |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/eukrep |
eukrep |
EukRep |
Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
evidencemodeler |
evidencemodeler |
EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. |
2024-07-19 |
https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file |
2.1.0 |
evidencemodeler |
2.1.0 |
Up-to-date |
Genome annotation |
Gene prediction |
Gene prediction |
Gene expression, Gene structure |
Gene expression, Gene structure |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler |
EvidenceModeler |
EvidenceModeler |
The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
27 |
27 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
27 |
27 |
12 |
12 |
|
|
|
exomedepth |
exomedepth |
ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data |
2019-11-08 |
https://cran.r-project.org/package=ExomeDepth |
1.1.0 |
r-exomedepth |
1.1.18 |
To update |
Sequence Analysis, Variant Analysis |
Sequence analysis, Variant calling, Genotyping, Copy number estimation |
Sequence analysis, Variant calling, Genotyping, Copy number estimation |
Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases |
Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases |
crs4 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth |
exomedepth |
ExomeDepth |
Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
61 |
72 |
540 |
607 |
183 |
203 |
2916 |
3164 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3771 |
3456 |
275 |
244 |
|
|
|
exonerate |
exonerate |
Exonerate is a generic tool for pairwise sequence comparison. |
2018-08-02 |
https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate |
2.4.0 |
exonerate |
2.4.0 |
Up-to-date |
Sequence Analysis |
Pairwise sequence alignment, Protein threading, Genome alignment |
Pairwise sequence alignment, Protein threading, Genome alignment |
Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks |
Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate |
exonerate |
Exonerate |
A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
184 |
212 |
829 |
1242 |
191 |
222 |
733 |
1220 |
39 |
39 |
1230 |
1230 |
26 |
27 |
570 |
582 |
4274 |
3362 |
500 |
440 |
|
|
|
export2graphlan |
export2graphlan |
export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn |
2017-03-03 |
https://bitbucket.org/CibioCM/export2graphlan/overview |
0.20 |
export2graphlan |
0.22 |
To update |
Metagenomics |
Conversion |
Conversion |
Taxonomy, Metabolomics, Biomarkers |
Taxonomy, Metabolomics, Biomarkers |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan |
export2graphlan |
export2graphlan |
export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
589 |
710 |
6276 |
7303 |
193 |
213 |
712 |
791 |
122 |
123 |
616 |
632 |
16 |
16 |
43 |
43 |
8769 |
7647 |
1062 |
920 |
https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b5f848dc8e96663c, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=09e8293456ee6d99, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1466?version=2 |
microbiome/metatranscriptomics, microbiome/metatranscriptomics-short |
|
extract_genomic_dna |
Extract genomic DNA 1 |
Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. |
2016-01-14 |
|
3.0.3+galaxy3 |
bx-python |
0.14.0 |
To update |
Genomic Interval Operations |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
930 |
1169 |
9749 |
15264 |
1876 |
12291 |
18355 |
263352 |
0 |
63 |
0 |
611 |
0 |
3 |
0 |
201 |
279428 |
28104 |
13526 |
2806 |
https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=1ee43d90b69829e9, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=2e1feecca56bb0b8, https://usegalaxy.eu/published/workflow?id=4f40ae432d8a4259, https://usegalaxy.eu/published/workflow?id=51cce3b98da3e822, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=6bce1d419a179c50, https://usegalaxy.eu/published/workflow?id=7d343d982f1105bf, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=ad4b347f9b68e127, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06, https://usegalaxy.eu/published/workflow?id=d3a8741131485af2, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c, https://usegalaxy.org/published/workflow?id=0ac68ec25f3534da, https://usegalaxy.org/published/workflow?id=28e86ab943c67417, https://usegalaxy.org/published/workflow?id=30507545aa971637, https://usegalaxy.org/published/workflow?id=468c5a8fe7a40778, https://usegalaxy.org/published/workflow?id=4769befb88f653d6, https://usegalaxy.org/published/workflow?id=56530f4d41413832, https://usegalaxy.org/published/workflow?id=6e75ac640853d0dd, https://usegalaxy.org/published/workflow?id=7643e66a9b4e9c11, https://usegalaxy.org/published/workflow?id=7cae620eea6326af, https://usegalaxy.org/published/workflow?id=94de815260acc3a8, https://usegalaxy.org/published/workflow?id=a666aaaa32f62487, https://usegalaxy.org/published/workflow?id=b8fdf05ec7540510, https://usegalaxy.org/published/workflow?id=ce2619816ce10220, https://usegalaxy.org/published/workflow?id=e75a7802d2941f31, https://usegalaxy.org/published/workflow?id=ecb279a9114140ab, https://workflowhub.eu/workflows/1562?version=1, https://workflowhub.eu/workflows/1706?version=1 |
epigenetics/cut_and_run, transcriptomics/clipseq |
|
fairy |
fairy_cov, fairy_sketch |
Fast approximate contig coverage for metagenomic binning |
2024-12-20 |
https://github.com/bluenote-1577/fairy |
0.5.8 |
fairy |
0.5.8 |
Up-to-date |
Metagenomics |
Read binning, Sequence assembly validation |
Read binning, Sequence assembly validation |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fairy |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fairy |
fairy |
fairy |
fast approximate contig coverage for metagenomic binningFairy computes multi-sample contig coverage for metagenome-assembled genome (MAG) binning.Fairy is used after metagenomic assembly and before binning. It can- Calculate coverage 100x-1000x faster than read alignment (e.g. BWA)- Give comparable bins for multi-sample binning (short read or nanopore reads)- Output formats that are compatible with MetaBAT2, MaxBin2, SemiBin2, and more |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
148 |
148 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
148 |
148 |
5 |
5 |
|
|
|
falco |
falco |
A high throughput sequence QC analysis tool |
2024-04-17 |
https://github.com/smithlabcode/falco/ |
1.2.4 |
falco |
1.2.5 |
To update |
Sequence Analysis |
Sequencing quality control, Visualisation, Read mapping |
Sequencing quality control, Visualisation, Read mapping |
Workflows, Mapping, Imaging |
Workflows, Mapping, Imaging |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco |
falco |
Falco |
A high-speed FastQC emulation for quality control of sequencing data. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
3878 |
3878 |
162045 |
162045 |
965 |
965 |
16492 |
16492 |
274 |
274 |
5029 |
5029 |
24 |
24 |
357 |
357 |
183923 |
183923 |
5141 |
5141 |
https://usegalaxy.eu/published/workflow?id=259f459a45e17e46, https://usegalaxy.eu/published/workflow?id=3d0039098a87642c, https://usegalaxy.eu/published/workflow?id=6368019ffdf6c5ee, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.org.au/published/workflow?id=71bad95f72c9f30d, https://usegalaxy.org.au/published/workflow?id=7cd1acb1da823cdc, https://usegalaxy.org/published/workflow?id=fb789920b057fe8d, https://workflowhub.eu/workflows/1562?version=1, https://workflowhub.eu/workflows/1644?version=1, https://workflowhub.eu/workflows/1715?version=1, https://workflowhub.eu/workflows/1717?version=2, https://workflowhub.eu/workflows/1845?version=1 |
assembly/mrsa-illumina, ecology/ENA_Biodiv_submission, epigenetics/cut_and_run, epigenetics/methylation-seq, galaxy-interface/workflow-fairification, sequence-analysis/quality-contamination-control, transcriptomics/mirna-target-finder, transcriptomics/ref-based, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants |
|
fargene |
fargene |
fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) |
2019-08-30 |
https://github.com/fannyhb/fargene |
0.1 |
fargene |
0.1 |
Up-to-date |
Sequence Analysis |
Antimicrobial resistance prediction |
Antimicrobial resistance prediction |
Metagenomics, Microbiology, Public health and epidemiology, Antimicrobial resistance |
Metagenomics, Microbiology, Public health and epidemiology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene |
fargene |
fARGene |
fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
150 |
159 |
895 |
1011 |
262 |
287 |
1203 |
1346 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
2 |
2359 |
2100 |
448 |
414 |
|
|
|
fasta_clipping_histogram |
cshl_fasta_clipping_histogram |
Length Distribution chart |
2017-07-10 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fasta Manipulation, Graphics, Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
45 |
45 |
306 |
306 |
0 |
0 |
0 |
0 |
96 |
140 |
5703 |
6332 |
1 |
1 |
1 |
1 |
6639 |
6010 |
186 |
142 |
|
|
|
fasta_formatter |
cshl_fasta_formatter |
FASTA Width formatter |
2018-04-24 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fasta Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
363 |
452 |
12086 |
12696 |
479 |
2140 |
4061 |
26449 |
76 |
107 |
733 |
1260 |
8 |
9 |
50 |
60 |
40465 |
16930 |
2708 |
926 |
https://usegalaxy.eu/published/workflow?id=02f240f6cf72080a, https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=44189803f223acd1, https://usegalaxy.eu/published/workflow?id=76e9cd837ea5e7da, https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7, https://usegalaxy.eu/published/workflow?id=90f993a1b245eb68, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=d6ff6be33b8bfe85, https://usegalaxy.eu/published/workflow?id=da19c0eaa757fa39, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.org/published/workflow?id=1d923ce15c17b1fe, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c, https://usegalaxy.org/published/workflow?id=4884918895db9af0, https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c, https://usegalaxy.org/published/workflow?id=63adc811e3ae529d, https://usegalaxy.org/published/workflow?id=63db7f52a280bd2d, https://usegalaxy.org/published/workflow?id=9bea2e9f45f07f32, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://usegalaxy.org/published/workflow?id=a808c139402d7b87, https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1271?version=3, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1738?version=1, https://workflowhub.eu/workflows/1739?version=1, https://workflowhub.eu/workflows/1740?version=1, https://workflowhub.eu/workflows/1741?version=1, https://workflowhub.eu/workflows/1842?version=1, https://workflowhub.eu/workflows/1850?version=1, https://workflowhub.eu/workflows/1854?version=1, https://workflowhub.eu/workflows/517?version=1, https://workflowhub.eu/workflows/518?version=1 |
microbiome/mgnify-amplicon |
|
fasta_nucleotide_changer |
cshl_fasta_nucleotides_changer |
RNA/DNA converter. |
2018-04-24 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fasta Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
74 |
125 |
383 |
882 |
207 |
747 |
1415 |
5767 |
18 |
24 |
427 |
550 |
6 |
8 |
20 |
31 |
7230 |
2245 |
904 |
305 |
https://usegalaxy.org/published/workflow?id=9efb061a87bc9f4d |
|
|
fasta_nucleotide_color_plot |
fasta_nucleotide_color_plot |
Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. |
2016-03-06 |
https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot |
1.0.1 |
openjdk |
|
To update |
Visualization |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
55 |
65 |
392 |
494 |
170 |
230 |
745 |
1074 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1568 |
1137 |
295 |
225 |
|
|
|
fasta_stats |
fasta-stats |
Display summary statistics for a fasta file. |
2018-11-21 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ |
2.0 |
numpy |
|
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3829 |
4225 |
56351 |
58340 |
4298 |
4623 |
34345 |
35598 |
2435 |
3021 |
17734 |
22805 |
147 |
147 |
749 |
749 |
117492 |
109179 |
12016 |
10709 |
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assembly/chloroplast-assembly, assembly/debruijn-graph-assembly, assembly/hifi-assembly, assembly/largegenome, genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short, genome-annotation/braker3 |
|
fastani |
fastani |
Fast alignment-free computation of whole-genome Average Nucleotide Identity |
2020-02-17 |
https://github.com/ParBLiSS/FastANI |
1.3 |
fastani |
1.34 |
To update |
Sequence Analysis |
Genome alignment, Sequence similarity search |
Genome alignment, Sequence similarity search |
Microbiology, Genetic variation |
Microbiology, Genetic variation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani |
fastani |
FastANI |
FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1182 |
1205 |
29436 |
29626 |
1 |
1 |
18 |
18 |
133 |
133 |
1799 |
1799 |
64 |
64 |
949 |
949 |
32392 |
32202 |
1403 |
1380 |
https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75 |
|
|
fastk |
fastk_fastk, fastk_histex, fastk_logex |
FastK: A K-mer counter (for HQ assembly data sets) |
2024-05-03 |
https://github.com/thegenemyers/FASTK |
1.1.0 |
fastk |
1.1.0 |
Up-to-date |
Assembly |
k-mer counting, Sequence analysis |
k-mer counting, Sequence analysis |
Genomics, Sequence analysis |
Genomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk |
fastk |
FASTK |
FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode. |
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
46 |
46 |
742 |
742 |
45 |
45 |
389 |
389 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1131 |
1131 |
91 |
91 |
|
|
|
fastp |
fastp |
Fast all-in-one preprocessing for FASTQ files |
2018-03-07 |
https://github.com/OpenGene/fastp |
1.0.1 |
fastp |
1.0.1 |
Up-to-date |
Sequence Analysis |
Sequencing quality control, Sequence contamination filtering |
Sequence contamination filtering |
Sequence analysis, Probes and primers |
Probes and primers |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp |
fastp |
fastp |
A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
10510 |
10845 |
1229203 |
1372687 |
13972 |
14837 |
495065 |
537410 |
3030 |
3115 |
99990 |
109532 |
303 |
306 |
30703 |
30747 |
2050376 |
1854961 |
29103 |
27815 |
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assembly/assembly-with-preprocessing, assembly/largegenome, assembly/mrsa-illumina, assembly/mrsa-nanopore, ecology/eDNA-taxonomic-analysis, introduction/galaxy-intro-ngs-data-managment, introduction/vsi_qc, microbiome/beer-data-analysis, microbiome/mgnify-amplicon, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, sequence-analysis/quality-contamination-control, transcriptomics/differential-isoform-expression, variant-analysis/aiv-analysis, variant-analysis/pox-tiled-amplicon, variant-analysis/sars-cov-2, variant-analysis/tb-variant-analysis |
|
fastplong |
fastplong |
Fastplong is used for ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.). |
2025-05-06 |
https://github.com/OpenGene/fastplong |
0.4.1 |
fastplong |
0.4.1 |
Up-to-date |
Sequence Analysis, Assembly |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastplong |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastplong |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
40 |
40 |
309 |
309 |
0 |
0 |
0 |
0 |
8 |
8 |
217 |
217 |
0 |
0 |
0 |
0 |
526 |
526 |
48 |
48 |
https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3 |
|
|
fastq_combiner |
fastq_combiner |
Combine FASTA and QUAL into FASTQ |
2019-06-21 |
https://github.com/galaxyproject/sequence_utils |
1.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation, Fasta Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
241 |
306 |
9199 |
9921 |
880 |
3131 |
50082 |
77184 |
83 |
102 |
1967 |
2373 |
16 |
17 |
353 |
354 |
89832 |
61601 |
3556 |
1220 |
https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893, https://usegalaxy.eu/published/workflow?id=e423c80058601e78, https://usegalaxy.org/published/workflow?id=5b2a0da883be03b7, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395 |
|
|
fastq_dl |
fastq_dl |
Download FASTQ files from ENA. |
2024-11-14 |
https://github.com/rpetit3/fastq-dl |
3.0.1 |
fastq-dl |
3.0.1 |
Up-to-date |
Data Source |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
62 |
62 |
303 |
303 |
167 |
167 |
621 |
621 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
924 |
924 |
229 |
229 |
https://usegalaxy.eu/published/workflow?id=32219131f48494bf, https://usegalaxy.eu/published/workflow?id=c8d70d4402852fb5, https://usegalaxy.org/published/workflow?id=77de7101effbff3d, https://usegalaxy.org/published/workflow?id=8e863bbef37cc36b, https://workflowhub.eu/workflows/1274?version=2, https://workflowhub.eu/workflows/1853?version=1 |
microbiome/mgnify-amplicon |
|
fastq_filter |
fastq_filter |
Filter FASTQ reads by quality score and length |
2019-06-21 |
https://github.com/galaxyproject/sequence_utils |
1.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
867 |
1046 |
22450 |
29161 |
2532 |
9682 |
35516 |
127334 |
219 |
331 |
4753 |
6800 |
84 |
84 |
436 |
436 |
163731 |
63155 |
11143 |
3702 |
https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=76e9cd837ea5e7da, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.eu/published/workflow?id=c7f34c67c9054234, https://usegalaxy.eu/published/workflow?id=d6ff6be33b8bfe85, https://usegalaxy.eu/published/workflow?id=da19c0eaa757fa39, https://usegalaxy.eu/published/workflow?id=e271d95a671182ec, https://usegalaxy.eu/published/workflow?id=f39528391f22aab0, https://usegalaxy.org.au/published/workflow?id=8d47811c6154d347, https://usegalaxy.org/published/workflow?id=091896754bcc8ec1, https://usegalaxy.org/published/workflow?id=14f62361a15f8a24, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=344a79d4f12d2cff, https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=3f8e0395007c8e9e, https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4, https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c, https://usegalaxy.org/published/workflow?id=48adcc44fe62a99c, https://usegalaxy.org/published/workflow?id=5004f1087f5e87db, https://usegalaxy.org/published/workflow?id=535484d6482b80f4, https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c, https://usegalaxy.org/published/workflow?id=61d324b1eca6300e, https://usegalaxy.org/published/workflow?id=85c3a1fc1d3d3df8, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9, https://usegalaxy.org/published/workflow?id=d860749fd34809d7, https://usegalaxy.org/published/workflow?id=ea69f4fbdbb88c71, https://workflowhub.eu/workflows/1271?version=3, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1850?version=1, https://workflowhub.eu/workflows/1854?version=1 |
ecology/ENA_Biodiv_submission, microbiome/mgnify-amplicon |
|
fastq_groomer |
fastq_groomer |
Convert between various FASTQ quality formats. |
2019-06-21 |
https://github.com/galaxyproject/sequence_utils |
1.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3066 |
3798 |
107854 |
130022 |
8079 |
45933 |
145592 |
914641 |
656 |
1191 |
15303 |
28714 |
206 |
208 |
7929 |
8019 |
1081396 |
276678 |
51130 |
12007 |
https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=70b1c40b818cc320, https://usegalaxy.eu/published/workflow?id=7117dbcbd5d12de5, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=a52c5dd688def9ba, https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c7e1aee909c9b483, https://usegalaxy.eu/published/workflow?id=cf9dc7ad34c81fa2, https://usegalaxy.eu/published/workflow?id=eb3cfa4d1f05fc0e, https://usegalaxy.eu/published/workflow?id=f39528391f22aab0, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=189c584ea4bde59a, https://usegalaxy.org.au/published/workflow?id=1ac197bae296b2bf, 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https://usegalaxy.org/published/workflow?id=b4bb2c7d8c7b5139, https://usegalaxy.org/published/workflow?id=b5c79535c499bc58, https://usegalaxy.org/published/workflow?id=b72edafe11293d93, https://usegalaxy.org/published/workflow?id=b7e20495b47d5b97, https://usegalaxy.org/published/workflow?id=b9e3676a84b7be5d, https://usegalaxy.org/published/workflow?id=bad9b88a6d5b6759, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9, https://usegalaxy.org/published/workflow?id=c3b3b2ee14bbd374, https://usegalaxy.org/published/workflow?id=c446105e87750aa2, https://usegalaxy.org/published/workflow?id=c4cde7e8d897cd25, https://usegalaxy.org/published/workflow?id=c64719e91e7346a2, https://usegalaxy.org/published/workflow?id=d3e656ab45f40c11, https://usegalaxy.org/published/workflow?id=d3eae9943ce2a62b, https://usegalaxy.org/published/workflow?id=d69ea491b99016f4, https://usegalaxy.org/published/workflow?id=d89e626fa4f9434f, https://usegalaxy.org/published/workflow?id=db8443163482a2e0, https://usegalaxy.org/published/workflow?id=dcc7c5fdef8780fd, https://usegalaxy.org/published/workflow?id=df1fa0b73f741a9c, https://usegalaxy.org/published/workflow?id=df6b9760e071b91b, https://usegalaxy.org/published/workflow?id=df6c398b2d4f1e99, https://usegalaxy.org/published/workflow?id=df7459b7e8acb872, https://usegalaxy.org/published/workflow?id=e2432c4d2b61705a, https://usegalaxy.org/published/workflow?id=e2fa6584853a0dee, https://usegalaxy.org/published/workflow?id=e6838c861b6beaed, https://usegalaxy.org/published/workflow?id=eb20150175a6ab03, https://usegalaxy.org/published/workflow?id=f2465afbdfc8ad46, https://usegalaxy.org/published/workflow?id=f39603063febba82, https://usegalaxy.org/published/workflow?id=f47f0b25c1405128, https://usegalaxy.org/published/workflow?id=f58970e6914a1bba, https://usegalaxy.org/published/workflow?id=f857e8282af234e0, https://usegalaxy.org/published/workflow?id=f895ed9fb68d3379, https://usegalaxy.org/published/workflow?id=fe2d15d352a9919f, https://usegalaxy.org/published/workflow?id=ff137b61d4ef1b86, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1, https://workflowhub.eu/workflows/1702?version=1, https://workflowhub.eu/workflows/655?version=1 |
ecology/ENA_Biodiv_submission, ecology/Obitools-metabarcoding, sequence-analysis/Manage_AB1_Sanger |
|
fastq_manipulation |
fastq_manipulation |
Manipulate FASTQ reads on various attributes. |
2019-06-21 |
https://github.com/galaxyproject/sequence_utils |
1.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
180 |
285 |
5124 |
6437 |
622 |
2173 |
5410 |
15997 |
86 |
164 |
3990 |
5357 |
15 |
15 |
503 |
503 |
28294 |
15027 |
2637 |
903 |
https://usegalaxy.eu/published/workflow?id=7734928ebc0a2654, https://usegalaxy.org.au/published/workflow?id=5926a7669eabb1c6, https://usegalaxy.org/published/workflow?id=41b181f1d763e419, https://workflowhub.eu/workflows/1673?version=1 |
transcriptomics/srna |
|
fastq_masker_by_quality |
fastq_masker_by_quality |
FASTQ Masker by quality score |
2019-06-21 |
https://github.com/galaxyproject/sequence_utils |
1.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
58 |
61 |
675 |
733 |
244 |
1008 |
2111 |
8416 |
13 |
21 |
398 |
577 |
8 |
8 |
34 |
34 |
9760 |
3218 |
1098 |
323 |
https://usegalaxy.org/published/workflow?id=958f78270fc8f55c, https://usegalaxy.org/published/workflow?id=aef91b21e3b72f70 |
sequence-analysis/Manage_AB1_Sanger |
|
fastq_paired_end_deinterlacer |
fastq_paired_end_deinterlacer |
FASTQ de-interlacer on paired end reads. |
2019-06-21 |
https://github.com/galaxyproject/sequence_utils |
1.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
561 |
775 |
8915 |
13227 |
1973 |
2832 |
14532 |
22941 |
202 |
284 |
2045 |
3031 |
57 |
57 |
730 |
730 |
39929 |
26222 |
3948 |
2793 |
https://usegalaxy.org/published/workflow?id=ae81cc0e8263d03e, https://usegalaxy.org/published/workflow?id=b1b75a9323d25085, https://usegalaxy.org/published/workflow?id=c2c6779a8b1821e0 |
|
|
fastq_paired_end_interlacer |
fastq_paired_end_interlacer |
FASTQ interlacer on paired end reads |
2019-06-21 |
https://github.com/galaxyproject/sequence_utils |
1.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2968 |
3318 |
27989 |
31403 |
4447 |
5152 |
25343 |
30506 |
1649 |
1748 |
7253 |
8107 |
135 |
135 |
1103 |
1103 |
71119 |
61688 |
10353 |
9199 |
https://usegalaxy.eu/published/workflow?id=01dc0619e050dc91, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=56edd22d14392691, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=842e0ea7b1eb56af, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=95cb04ffb473623b, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=b7c2440621968526, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=e423c80058601e78, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b, https://usegalaxy.eu/published/workflow?id=f6e8a63283262518, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.fr/published/workflow?id=e6991d64e851b09e, https://usegalaxy.org.au/published/workflow?id=30430b75d05f54eb, https://usegalaxy.org.au/published/workflow?id=408a31694e9c85e6, https://usegalaxy.org.au/published/workflow?id=533dbb3242ee4255, https://usegalaxy.org.au/published/workflow?id=7fa13ccbf044edc5, https://usegalaxy.org.au/published/workflow?id=83e3ceceb1a92493, https://usegalaxy.org.au/published/workflow?id=874492eb776ba813, https://usegalaxy.org.au/published/workflow?id=8b6739a000780d99, https://usegalaxy.org.au/published/workflow?id=9b75924c483b5f6b, https://usegalaxy.org.au/published/workflow?id=aee5b5645c51cac3, https://usegalaxy.org.au/published/workflow?id=ee7a1615f187391d, https://usegalaxy.org.au/published/workflow?id=f25a05070bf97ded, https://usegalaxy.org.au/published/workflow?id=fb0986a952c35e0a, https://usegalaxy.org/published/workflow?id=0a57740c68e85e21, https://usegalaxy.org/published/workflow?id=4e1ae78405034ad3, https://usegalaxy.org/published/workflow?id=51c485af11d90700, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=8d229c0f58a07ebe, https://usegalaxy.org/published/workflow?id=c30f6ca171896908, https://usegalaxy.org/published/workflow?id=c446105e87750aa2, https://usegalaxy.org/published/workflow?id=e745c45651d829b8, https://usegalaxy.org/published/workflow?id=f926e70bee242785, https://workflowhub.eu/workflows/1444?version=2, https://workflowhub.eu/workflows/1466?version=2, https://workflowhub.eu/workflows/1622?version=1, https://workflowhub.eu/workflows/365?version=1 |
assembly/general-introduction, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short |
|
fastq_paired_end_joiner |
fastq_paired_end_joiner |
FASTQ joiner on paired end reads |
2019-06-21 |
https://github.com/galaxyproject/sequence_utils |
1.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
570 |
793 |
12982 |
18847 |
1661 |
5991 |
21263 |
61308 |
152 |
243 |
1664 |
2619 |
25 |
25 |
236 |
236 |
83010 |
36145 |
7052 |
2408 |
https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=bab0322cc0346d81, https://usegalaxy.org/published/workflow?id=5df593510c7d944d, https://usegalaxy.org/published/workflow?id=6c7d320ad951f445, https://usegalaxy.org/published/workflow?id=8d3557a82f49528c, https://usegalaxy.org/published/workflow?id=c337e5265a8079d0, https://usegalaxy.org/published/workflow?id=e4f1cce653812a22, https://usegalaxy.org/published/workflow?id=eeffba361f12a22d |
|
|
fastq_paired_end_splitter |
fastq_paired_end_splitter |
FASTQ splitter on joined paired end reads |
2019-06-21 |
https://github.com/galaxyproject/sequence_utils |
1.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
515 |
636 |
4433 |
4974 |
1317 |
3616 |
27563 |
40409 |
209 |
281 |
865 |
1229 |
17 |
17 |
45 |
45 |
46657 |
32906 |
4550 |
2058 |
https://usegalaxy.org/published/workflow?id=f823b87dd06ba4ac |
|
|
fastq_quality_boxplot |
cshl_fastq_quality_boxplot |
Draw quality score boxplot |
2017-07-10 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fastq Manipulation, Graphics, Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
126 |
192 |
1189 |
1420 |
2021 |
9265 |
12840 |
61870 |
36 |
63 |
207 |
541 |
13 |
13 |
89 |
90 |
63921 |
14325 |
9533 |
2196 |
https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=3c32ad1a07a66843, https://usegalaxy.org/published/workflow?id=4a9b0534b1c88609, https://usegalaxy.org/published/workflow?id=6ad3c2d8a14809ca, https://usegalaxy.org/published/workflow?id=8ea5aaa1cc088077, https://usegalaxy.org/published/workflow?id=b7e20495b47d5b97, https://usegalaxy.org/published/workflow?id=c29b08d56223c274, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a |
|
|
fastq_quality_converter |
cshl_fastq_quality_converter |
Quality format converter (ASCII-Numeric) |
2018-04-24 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
48 |
58 |
279 |
380 |
216 |
2253 |
1115 |
9736 |
14 |
30 |
1232 |
1623 |
4 |
4 |
21 |
21 |
11760 |
2647 |
2345 |
282 |
https://usegalaxy.org/published/workflow?id=3767c9c07462b777 |
|
|
fastq_quality_filter |
cshl_fastq_quality_filter |
Filter by quality |
2017-07-10 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
4665 |
5314 |
37994 |
40749 |
6202 |
14016 |
45014 |
145519 |
1994 |
2474 |
8377 |
11391 |
335 |
340 |
1344 |
1394 |
199053 |
92729 |
22144 |
13196 |
https://usegalaxy.eu/published/workflow?id=01dc0619e050dc91, https://usegalaxy.eu/published/workflow?id=055eae88be2d4dd7, https://usegalaxy.eu/published/workflow?id=13da0b6780007d12, https://usegalaxy.eu/published/workflow?id=1502fd3fa90d32d8, https://usegalaxy.eu/published/workflow?id=1d0f438faa441c4e, https://usegalaxy.eu/published/workflow?id=2a274e0e4ba45c77, https://usegalaxy.eu/published/workflow?id=2aac571c44e6a7c8, https://usegalaxy.eu/published/workflow?id=38c7fa2653c5a2ee, https://usegalaxy.eu/published/workflow?id=39bf638cd7b56fd6, https://usegalaxy.eu/published/workflow?id=4c736e255f4a740f, https://usegalaxy.eu/published/workflow?id=63749bd3045ccd4a, https://usegalaxy.eu/published/workflow?id=71cac07a151f9470, https://usegalaxy.eu/published/workflow?id=76a63b1710da5e60, https://usegalaxy.eu/published/workflow?id=9a1d17c12b139bda, https://usegalaxy.eu/published/workflow?id=a8d814a6d86e9661, https://usegalaxy.eu/published/workflow?id=bd74a116e3f8d5b8, https://usegalaxy.eu/published/workflow?id=c65d98740ca64104, https://usegalaxy.eu/published/workflow?id=ccec1752fcac5e3f, https://usegalaxy.eu/published/workflow?id=d3ae8c51061330f3, https://usegalaxy.eu/published/workflow?id=d5780c37232e3181, https://usegalaxy.eu/published/workflow?id=da3a6d229e422dde, https://usegalaxy.eu/published/workflow?id=db63d53712d2571b, https://usegalaxy.eu/published/workflow?id=dbcf7af09e036754, https://usegalaxy.eu/published/workflow?id=e47351e2edd93a1a, https://usegalaxy.eu/published/workflow?id=e6c5fb1d37d29ec0, https://usegalaxy.eu/published/workflow?id=e85c9385870aadcc, https://usegalaxy.eu/published/workflow?id=f0209559f3686fcc, https://usegalaxy.eu/published/workflow?id=f81534f6cf8733e7, https://usegalaxy.org.au/published/workflow?id=0ed947e76a69028b, https://usegalaxy.org.au/published/workflow?id=5a0fc3b91ae47788, https://usegalaxy.org.au/published/workflow?id=acaca80c4a0c76c8, https://usegalaxy.org.au/published/workflow?id=b46bc04e0418fdfa, https://usegalaxy.org.au/published/workflow?id=c622bd03677314aa, https://usegalaxy.org/published/workflow?id=02d49c5f0d9aa010, https://usegalaxy.org/published/workflow?id=0555313573cd1ee2, https://usegalaxy.org/published/workflow?id=0816aa5461c390d2, https://usegalaxy.org/published/workflow?id=08edef22fa132799, https://usegalaxy.org/published/workflow?id=0d6a4dfbccafd2a2, https://usegalaxy.org/published/workflow?id=0f43fdfe1824e9d7, https://usegalaxy.org/published/workflow?id=24ada8b98b04fedc, https://usegalaxy.org/published/workflow?id=26b2057a8bc0386c, https://usegalaxy.org/published/workflow?id=3e6d4ab34de7918c, https://usegalaxy.org/published/workflow?id=3f8e0395007c8e9e, https://usegalaxy.org/published/workflow?id=58a7a02dade085cf, https://usegalaxy.org/published/workflow?id=58a91a914e381dcf, https://usegalaxy.org/published/workflow?id=58ceaed0a42fe60a, https://usegalaxy.org/published/workflow?id=63adc811e3ae529d, https://usegalaxy.org/published/workflow?id=6c49d9c25ba4ddf5, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=8356ee639055cbca, https://usegalaxy.org/published/workflow?id=947340358dd268ea, https://usegalaxy.org/published/workflow?id=9a1fb6ecff886358, https://usegalaxy.org/published/workflow?id=b6c0208e49cd2271, https://usegalaxy.org/published/workflow?id=cd3bce36b6ef073d, https://usegalaxy.org/published/workflow?id=d8afd017905d6702, https://workflowhub.eu/workflows/1481?version=1 |
introduction/galaxy-intro-short |
|
fastq_stats |
fastq_stats |
FASTQ Summary Statistics by column |
2019-06-21 |
https://github.com/galaxyproject/sequence_utils |
1.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
678 |
941 |
3662 |
5208 |
2614 |
14639 |
13510 |
84786 |
161 |
293 |
3484 |
4398 |
53 |
53 |
296 |
296 |
94688 |
20952 |
15926 |
3506 |
https://usegalaxy.eu/published/workflow?id=6d3ec4203b503810, https://usegalaxy.eu/published/workflow?id=e299721eec23b557, https://usegalaxy.org/published/workflow?id=0017c434354b6f6a, https://usegalaxy.org/published/workflow?id=055eb85c8ecf0ca3, https://usegalaxy.org/published/workflow?id=165c8a58baffe64c, https://usegalaxy.org/published/workflow?id=24adb067c82862fa, https://usegalaxy.org/published/workflow?id=2b3970d9b28810a1, https://usegalaxy.org/published/workflow?id=4339d5625c15ae78, https://usegalaxy.org/published/workflow?id=6f436066dffbc37d, https://usegalaxy.org/published/workflow?id=a57db139837dd24c, https://usegalaxy.org/published/workflow?id=ab23c641cfdefe0c, https://usegalaxy.org/published/workflow?id=b4dda054d2cf15b7, https://usegalaxy.org/published/workflow?id=b72edafe11293d93, https://usegalaxy.org/published/workflow?id=dcb73fce390b36b2, https://usegalaxy.org/published/workflow?id=e2fa6584853a0dee, https://usegalaxy.org/published/workflow?id=e35ac40c58953f74, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a, https://usegalaxy.org/published/workflow?id=f201ce61becf9a80, https://usegalaxy.org/published/workflow?id=f3983646b6df24bf |
|
|
fastq_to_fasta |
cshl_fastq_to_fasta |
FASTQ to FASTA converter |
2017-07-10 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fasta Manipulation, Convert Formats |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2014 |
2152 |
50989 |
55713 |
3019 |
7213 |
46867 |
109930 |
530 |
837 |
10769 |
18067 |
211 |
211 |
3227 |
3227 |
186937 |
111852 |
10413 |
5774 |
https://usegalaxy.eu/published/workflow?id=1b43449ed8481892, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.org/published/workflow?id=9a1fb6ecff886358, https://workflowhub.eu/workflows/1723?version=1 |
ecology/eDNA-taxonomic-analysis, sequence-analysis/Manage_AB1_Sanger |
|
fastq_to_tabular |
fastq_to_tabular |
FASTQ to Tabular converter |
2019-06-21 |
https://github.com/galaxyproject/sequence_utils |
1.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
314 |
388 |
13805 |
20661 |
637 |
1959 |
14158 |
34744 |
78 |
113 |
6297 |
7058 |
27 |
27 |
2036 |
2036 |
64499 |
36296 |
2487 |
1056 |
https://usegalaxy.eu/published/workflow?id=4643edf74f3eaec3, https://usegalaxy.eu/published/workflow?id=5e1b048040ea7535, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=acb9131e84de1ae0, https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab, https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=79ca45e45d76871f, https://usegalaxy.org/published/workflow?id=14f62361a15f8a24, https://usegalaxy.org/published/workflow?id=1e1a299825f27f11, https://usegalaxy.org/published/workflow?id=24ada8b98b04fedc, https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4, https://usegalaxy.org/published/workflow?id=5004f1087f5e87db, https://usegalaxy.org/published/workflow?id=5de035c08af915ea, https://usegalaxy.org/published/workflow?id=b6c0208e49cd2271, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9, https://workflowhub.eu/workflows/1629?version=1, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1 |
contributing/create-new-tutorial, sequence-analysis/Manage_AB1_Sanger, single-cell/scrna-data-ingest |
|
fastq_trimmer |
fastq_trimmer |
FASTQ Trimmer by quality |
2019-06-21 |
https://github.com/galaxyproject/sequence_utils |
1.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
603 |
788 |
10307 |
12822 |
1895 |
9246 |
22836 |
96214 |
118 |
245 |
2064 |
3428 |
16 |
16 |
156 |
156 |
112620 |
35363 |
10295 |
2632 |
https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.org.au/published/workflow?id=79572be1bf642251, https://usegalaxy.org.au/published/workflow?id=a3efc48b5992374e, https://usegalaxy.org.au/published/workflow?id=b518ee5540ed01fd, https://usegalaxy.org.au/published/workflow?id=d0933b5040adf902, https://usegalaxy.org.au/published/workflow?id=d1b604a5441dc4b0, https://usegalaxy.org/published/workflow?id=14410527253c6f40, https://usegalaxy.org/published/workflow?id=1b385fd45ee48614, https://usegalaxy.org/published/workflow?id=462261c5e22635f0, https://usegalaxy.org/published/workflow?id=48dd684196c65735, https://usegalaxy.org/published/workflow?id=61d324b1eca6300e, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=8356ee639055cbca, https://usegalaxy.org/published/workflow?id=9a1fb6ecff886358, https://usegalaxy.org/published/workflow?id=ada910fc3a68757a, https://usegalaxy.org/published/workflow?id=eb20150175a6ab03, https://usegalaxy.org/published/workflow?id=fcce98489c8ca7a3 |
|
|
fastqc |
fastqc |
Read QC reports using FastQC |
2017-01-11 |
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
0.74+galaxy1 |
fastqc |
0.12.1 |
To update |
Fastq Manipulation |
Sequence composition calculation, Sequencing quality control, Statistical calculation |
Sequence composition calculation, Sequencing quality control, Statistical calculation |
Sequencing, Data quality management, Sequence analysis |
Sequencing, Data quality management, Sequence analysis |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc |
fastqc |
FastQC |
This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. |
|
0 |
1 |
1 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
51266 |
57567 |
2264162 |
2546070 |
101879 |
164033 |
2763731 |
4007928 |
16002 |
19516 |
485637 |
571728 |
4458 |
4469 |
201980 |
202663 |
7328389 |
5715510 |
245585 |
173605 |
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assembly/general-introduction, assembly/largegenome, assembly/metagenomics-assembly, assembly/mrsa-illumina, assembly/mrsa-nanopore, assembly/unicycler-assembly, ecology/Obitools-metabarcoding, ecology/de-novo-rad-seq, ecology/ref-based-rad-seq, epigenetics/atac-seq, epigenetics/estrogen-receptor-binding-site-identification, epigenetics/formation_of_super-structures_on_xi, epigenetics/methylation-seq, epigenetics/tal1-binding-site-identification, genome-annotation/crispr-screen, introduction/galaxy-intro-short, microbiome/beer-data-analysis, microbiome/metagenomics-assembly, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/mgnify-amplicon, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, sequence-analysis/mapping, sequence-analysis/quality-control, sequence-analysis/sars-with-galaxy-on-anvil, single-cell/scatac-preprocessing-tenx, single-cell/scrna-umis, transcriptomics/clipseq, transcriptomics/de-novo, transcriptomics/differential-isoform-expression, transcriptomics/full-de-novo, transcriptomics/minerva-pathways, transcriptomics/rna-interactome, transcriptomics/rna-seq-reads-to-counts, transcriptomics/srna, variant-analysis/dunovo, variant-analysis/exome-seq, variant-analysis/non-dip, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants, variant-analysis/tb-variant-analysis |
|
fastqe |
fastqe |
FASTQE |
2020-07-13 |
https://fastqe.com/ |
0.3.1+galaxy0 |
fastqe |
0.3.3 |
To update |
Sequence Analysis |
Sequencing quality control |
Sequencing quality control |
Sequence analysis, Sequencing |
Sequence analysis, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe |
fastqe |
FASTQE |
Compute quality stats for FASTQ files and print those stats as emoji... for some reason. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3154 |
3177 |
6904 |
6978 |
6143 |
6198 |
13534 |
13627 |
1316 |
1323 |
3505 |
3549 |
291 |
291 |
510 |
510 |
24664 |
24453 |
10989 |
10904 |
https://usegalaxy.eu/published/workflow?id=055eae88be2d4dd7, https://usegalaxy.eu/published/workflow?id=2a274e0e4ba45c77, https://usegalaxy.eu/published/workflow?id=340aa3ae5468deb0, https://usegalaxy.eu/published/workflow?id=4c736e255f4a740f, https://usegalaxy.eu/published/workflow?id=519e0ffdfd1790bc, https://usegalaxy.eu/published/workflow?id=76a63b1710da5e60, https://usegalaxy.eu/published/workflow?id=a8d814a6d86e9661, https://usegalaxy.eu/published/workflow?id=c65d98740ca64104, https://usegalaxy.eu/published/workflow?id=d3ae8c51061330f3, https://usegalaxy.eu/published/workflow?id=d5780c37232e3181, https://usegalaxy.org.au/published/workflow?id=115151c2c8998d44, https://usegalaxy.org.au/published/workflow?id=178db14511c8f293, https://usegalaxy.org.au/published/workflow?id=1f63ec596e578b1c, https://usegalaxy.org.au/published/workflow?id=2afeae1ec03c0b57, https://usegalaxy.org.au/published/workflow?id=43f2dabbc1932e30, https://usegalaxy.org.au/published/workflow?id=47cacc06d404a8c6, https://usegalaxy.org.au/published/workflow?id=5d6773ed5b2f41cb, https://usegalaxy.org.au/published/workflow?id=8fe84de499e96485, https://usegalaxy.org.au/published/workflow?id=bd251174d94cde9d, https://usegalaxy.org.au/published/workflow?id=dd6f465ab1eb10b0, https://usegalaxy.org.au/published/workflow?id=e08b04291839e79a, https://usegalaxy.org/published/workflow?id=20da2dcce0ae2ca2, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=cf2dbc29ca20ebee, https://usegalaxy.org/published/workflow?id=fe262214fba1cb8e |
sequence-analysis/quality-control |
|
fastqtofasta |
fastq_to_fasta_python |
FASTQ to FASTA converter |
2019-06-21 |
https://github.com/galaxyproject/sequence_utils |
1.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3845 |
4522 |
249408 |
274687 |
5714 |
14677 |
147702 |
280466 |
876 |
876 |
22007 |
22007 |
3 |
3 |
3 |
3 |
577163 |
419120 |
20078 |
10438 |
https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5, https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=08f41680101a1a45, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=52cb9bacc26b013e, https://usegalaxy.eu/published/workflow?id=6d3ec4203b503810, https://usegalaxy.eu/published/workflow?id=76e9cd837ea5e7da, https://usegalaxy.eu/published/workflow?id=799b924edd3c401b, https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7, https://usegalaxy.eu/published/workflow?id=90f993a1b245eb68, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.eu/published/workflow?id=ab646c6ab6de7061, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=d6ff6be33b8bfe85, https://usegalaxy.eu/published/workflow?id=da19c0eaa757fa39, https://usegalaxy.eu/published/workflow?id=e299721eec23b557, https://usegalaxy.eu/published/workflow?id=e423c80058601e78, https://usegalaxy.org.au/published/workflow?id=5cd804644a34c8fd, https://usegalaxy.org/published/workflow?id=091896754bcc8ec1, https://usegalaxy.org/published/workflow?id=1708fdfd1d485434, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=400c1d170f073279, https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c, https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95, https://usegalaxy.org/published/workflow?id=5c7f3d73543da895, https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c, https://usegalaxy.org/published/workflow?id=63adc811e3ae529d, https://usegalaxy.org/published/workflow?id=6c7d320ad951f445, https://usegalaxy.org/published/workflow?id=81183f40d2f3e395, https://usegalaxy.org/published/workflow?id=8b7e03f09b0183d9, https://usegalaxy.org/published/workflow?id=93810012f2610de4, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d, https://usegalaxy.org/published/workflow?id=cfa9e6e722b086c8, https://usegalaxy.org/published/workflow?id=d860749fd34809d7, https://usegalaxy.org/published/workflow?id=e4f1cce653812a22, https://usegalaxy.org/published/workflow?id=eeffba361f12a22d, https://workflowhub.eu/workflows/1271?version=3, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1850?version=1, https://workflowhub.eu/workflows/1854?version=1, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/794?version=2 |
ecology/ENA_Biodiv_submission, galaxy-interface/ncbi-sarf, microbiome/mgnify-amplicon |
|
fastspar |
fastspar, fastspar_pvalues, fastspar_reduce |
Tool for rapid and scalable correlation estimation for compositional data. |
2025-06-16 |
https://github.com/scwatts/fastspar/ |
1.0.0 |
fastspar |
1.0.0 |
Up-to-date |
Metagenomics, Statistics |
|
|
Metagenomics, Microbial ecology |
Metagenomics, Microbial ecology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastspar |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastspar |
FastSpar |
FastSpar |
FastSpar is a C++ implementation of the SparCC algorithm for fast correlation estimation from compositional count data such as microbiome OTU tables. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
1 |
1 |
|
|
|
fasttree |
fasttree |
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL |
2018-02-02 |
http://www.microbesonline.org/fasttree/ |
2.1.10 |
fasttree |
2.2.0 |
To update |
Phylogenetics |
Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) |
|
Phylogenetics, Sequence analysis |
Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree |
fasttree |
FastTree |
Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1826 |
1923 |
84447 |
85175 |
2879 |
3069 |
29857 |
32881 |
829 |
967 |
8573 |
9437 |
82 |
84 |
411 |
416 |
127909 |
123288 |
6043 |
5616 |
https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=9155ed0e7a6a7b60, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=ce21961260fe4351, https://usegalaxy.eu/published/workflow?id=d07fe8b5a045c176, https://usegalaxy.eu/published/workflow?id=dc57118a95b10a80, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.fr/published/workflow?id=297b71156b297a73, https://usegalaxy.fr/published/workflow?id=c7be6e229a045fad, https://usegalaxy.org.au/published/workflow?id=42137e36791652bc, https://usegalaxy.org.au/published/workflow?id=a01c3004bcef9dd3, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=d62b6717202f42c9, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=2d1ca299c1b058f6, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3d7baebefa7c9b81, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=87685c6247521b54, https://usegalaxy.org/published/workflow?id=b2fb90873471f4e7, https://usegalaxy.org/published/workflow?id=be54e57345ce7ca5, https://usegalaxy.org/published/workflow?id=be9bd7286d38c210, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/1559?version=1 |
evolution/abc_intro_phylo, evolution/bacterial-comparative-genomics, microbiome/pathogen-detection-from-nanopore-foodborne-data |
|
fastx_artifacts_filter |
cshl_fastx_artifacts_filter |
Remove sequencing artifacts |
2017-07-10 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fasta Manipulation, Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
73 |
114 |
1004 |
2340 |
265 |
2463 |
3432 |
26090 |
27 |
55 |
666 |
1270 |
3 |
3 |
4 |
4 |
29704 |
5106 |
2635 |
368 |
https://usegalaxy.org/published/workflow?id=02d49c5f0d9aa010, https://usegalaxy.org/published/workflow?id=8356ee639055cbca, https://usegalaxy.org/published/workflow?id=947340358dd268ea, https://usegalaxy.org/published/workflow?id=9a1fb6ecff886358, https://usegalaxy.org/published/workflow?id=d89e626fa4f9434f |
|
|
fastx_barcode_splitter |
cshl_fastx_barcode_splitter |
Barcode Splitter |
2017-07-10 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fasta Manipulation, Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
259 |
312 |
37602 |
40250 |
977 |
2966 |
52272 |
112642 |
57 |
80 |
868 |
1228 |
16 |
16 |
49 |
49 |
154169 |
90791 |
3374 |
1309 |
https://usegalaxy.org/published/workflow?id=87b6bac79f99c1f8, https://usegalaxy.org/published/workflow?id=cd431e5f912d3616 |
|
|
fastx_clipper |
cshl_fastx_clipper |
Clip adapter sequences |
2017-07-10 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fasta Manipulation, Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
236 |
294 |
3335 |
4086 |
1087 |
6193 |
14946 |
122932 |
41 |
65 |
478 |
882 |
6 |
6 |
27 |
27 |
127927 |
18786 |
6558 |
1370 |
https://usegalaxy.org/published/workflow?id=29a80db9f3208c29, https://usegalaxy.org/published/workflow?id=344a79d4f12d2cff, https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=77e4bb9d6aea0c9a, https://usegalaxy.org/published/workflow?id=85c3a1fc1d3d3df8, https://usegalaxy.org/published/workflow?id=b097fce5358c01e5, https://usegalaxy.org/published/workflow?id=b0a12221ce09c001, https://usegalaxy.org/published/workflow?id=b2176abeb937f026, https://usegalaxy.org/published/workflow?id=c64719e91e7346a2, https://usegalaxy.org/published/workflow?id=d69ea491b99016f4, https://usegalaxy.org/published/workflow?id=d860749fd34809d7, https://usegalaxy.org/published/workflow?id=d89e626fa4f9434f, https://usegalaxy.org/published/workflow?id=d8afd017905d6702, https://usegalaxy.org/published/workflow?id=e6838c861b6beaed |
|
|
fastx_collapser |
cshl_fastx_collapser |
Collapse sequences |
2017-07-10 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fasta Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
401 |
459 |
59500 |
89761 |
876 |
3332 |
82238 |
206527 |
71 |
97 |
23810 |
25032 |
43 |
44 |
223 |
233 |
321553 |
165771 |
3932 |
1391 |
https://usegalaxy.org/published/workflow?id=091896754bcc8ec1, https://usegalaxy.org/published/workflow?id=1708fdfd1d485434, https://usegalaxy.org/published/workflow?id=1a6f552cfe798883, https://usegalaxy.org/published/workflow?id=23bca854e549ad48, https://usegalaxy.org/published/workflow?id=2823322fa85c7ae1, https://usegalaxy.org/published/workflow?id=2d1d69aac67a387a, https://usegalaxy.org/published/workflow?id=2e92cca68b7979f6, https://usegalaxy.org/published/workflow?id=49ca77212cc56ef9, https://usegalaxy.org/published/workflow?id=52cc435f50a6ff29, https://usegalaxy.org/published/workflow?id=52e099f693639115, https://usegalaxy.org/published/workflow?id=5e079a9ac49a5b8c, https://usegalaxy.org/published/workflow?id=66bc5f6d71466b7f, https://usegalaxy.org/published/workflow?id=74fe080f24f7da84, https://usegalaxy.org/published/workflow?id=80afe572b6693ca1, https://usegalaxy.org/published/workflow?id=98286b6154e1b57f, https://usegalaxy.org/published/workflow?id=9efb061a87bc9f4d, https://usegalaxy.org/published/workflow?id=b097fce5358c01e5, https://usegalaxy.org/published/workflow?id=bb8609e8d2d4bd89, https://usegalaxy.org/published/workflow?id=c74a01ba2f2a80d3, https://usegalaxy.org/published/workflow?id=de9c2db125a5ea27, https://usegalaxy.org/published/workflow?id=e4f1cce653812a22 |
|
|
fastx_nucleotides_distribution |
cshl_fastx_nucleotides_distribution |
Draw nucleotides distribution chart |
2017-07-10 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fastq Manipulation, Graphics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
55 |
98 |
140 |
293 |
1246 |
4541 |
5121 |
26678 |
73 |
105 |
1083 |
1309 |
8 |
9 |
11 |
12 |
28292 |
6355 |
4753 |
1382 |
https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=3c32ad1a07a66843, https://usegalaxy.org/published/workflow?id=8ea5aaa1cc088077, https://usegalaxy.org/published/workflow?id=b7e20495b47d5b97, https://usegalaxy.org/published/workflow?id=c29b08d56223c274 |
|
|
fastx_quality_statistics |
cshl_fastx_quality_statistics |
Compute quality statistics |
2018-04-24 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fastq Manipulation, Statistics |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
145 |
219 |
2175 |
2409 |
4427 |
11117 |
34705 |
77345 |
292 |
343 |
3332 |
3945 |
5 |
5 |
65 |
65 |
83764 |
40277 |
11684 |
4869 |
https://usegalaxy.org/published/workflow?id=3767c9c07462b777, https://usegalaxy.org/published/workflow?id=3c32ad1a07a66843, https://usegalaxy.org/published/workflow?id=4a9b0534b1c88609, https://usegalaxy.org/published/workflow?id=6ad3c2d8a14809ca, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4, https://usegalaxy.org/published/workflow?id=8ea5aaa1cc088077, https://usegalaxy.org/published/workflow?id=b7e20495b47d5b97, https://usegalaxy.org/published/workflow?id=c29b08d56223c274 |
|
|
fastx_renamer |
cshl_fastx_renamer |
Rename sequences |
2017-07-10 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fasta Manipulation, Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
224 |
280 |
4631 |
5145 |
276 |
1075 |
9882 |
15505 |
54 |
75 |
498 |
834 |
13 |
13 |
632 |
632 |
22116 |
15643 |
1443 |
567 |
https://usegalaxy.eu/published/workflow?id=08cfb9b21c1ec808, https://usegalaxy.eu/published/workflow?id=d4b3da4cc5a50044, https://usegalaxy.org/published/workflow?id=1a6f552cfe798883, https://usegalaxy.org/published/workflow?id=23bca854e549ad48, https://usegalaxy.org/published/workflow?id=24ada8b98b04fedc, https://usegalaxy.org/published/workflow?id=2823322fa85c7ae1, https://usegalaxy.org/published/workflow?id=2d1d69aac67a387a, https://usegalaxy.org/published/workflow?id=2e92cca68b7979f6, https://usegalaxy.org/published/workflow?id=49ca77212cc56ef9, https://usegalaxy.org/published/workflow?id=52cc435f50a6ff29, https://usegalaxy.org/published/workflow?id=52e099f693639115, https://usegalaxy.org/published/workflow?id=5e079a9ac49a5b8c, https://usegalaxy.org/published/workflow?id=66bc5f6d71466b7f, https://usegalaxy.org/published/workflow?id=74fe080f24f7da84, https://usegalaxy.org/published/workflow?id=80afe572b6693ca1, https://usegalaxy.org/published/workflow?id=b097fce5358c01e5, https://usegalaxy.org/published/workflow?id=bb8609e8d2d4bd89, https://usegalaxy.org/published/workflow?id=c74a01ba2f2a80d3 |
|
|
fastx_reverse_complement |
cshl_fastx_reverse_complement |
Reverse-Complement |
2017-07-10 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fastq Manipulation, Fasta Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
456 |
552 |
11586 |
15931 |
593 |
1664 |
17732 |
70434 |
82 |
105 |
853 |
1100 |
22 |
22 |
3557 |
3557 |
91022 |
33728 |
2343 |
1153 |
https://usegalaxy.eu/published/workflow?id=6d3ec4203b503810, https://usegalaxy.eu/published/workflow?id=e299721eec23b557, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org/published/workflow?id=24ada8b98b04fedc, https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95, https://usegalaxy.org/published/workflow?id=58a7a02dade085cf, https://usegalaxy.org/published/workflow?id=b18a41e364650fee, https://usegalaxy.org/published/workflow?id=e1dcdc125122f561, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1 |
sequence-analysis/Manage_AB1_Sanger |
|
fastx_trimmer |
cshl_fastx_trimmer |
Trim sequences |
2017-07-10 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
0.0.14 |
fastx_toolkit |
0.0.14 |
Up-to-date |
Fasta Manipulation, Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
658 |
834 |
14961 |
18093 |
1662 |
8605 |
113603 |
224353 |
223 |
293 |
3364 |
5948 |
257 |
258 |
1669 |
1672 |
250066 |
133597 |
9990 |
2800 |
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|
|
featurecounts |
featurecounts |
featureCounts counts the number of reads aligned to defined masked regions in a reference genome |
2016-02-09 |
https://subread.sourceforge.net/ |
2.1.1 |
subread |
2.1.1 |
Up-to-date |
RNA, Transcriptomics, Sequence Analysis |
Read summarisation, RNA-Seq quantification |
Read summarisation, RNA-Seq quantification |
RNA-Seq |
RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts |
featurecounts |
FeatureCounts |
featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
14615 |
16504 |
807686 |
914668 |
26510 |
33788 |
760980 |
995817 |
2872 |
3227 |
79521 |
90365 |
1581 |
1583 |
52228 |
52279 |
2053129 |
1700415 |
55102 |
45578 |
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single-cell/scrna-preprocessing, transcriptomics/de-novo, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts |
|
feelnc |
feelnc |
Galaxy wrapper for FEELnc |
2018-03-27 |
https://github.com/tderrien/FEELnc |
0.2.1 |
feelnc |
0.2 |
To update |
Sequence Analysis |
Annotation, Classification |
Annotation, Classification |
RNA-seq, Functional, regulatory and non-coding RNA |
Functional, regulatory and non-coding RNA |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc |
feelnc |
FEELnc |
A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
139 |
151 |
1531 |
1740 |
143 |
156 |
1171 |
1283 |
8 |
8 |
115 |
115 |
15 |
15 |
71 |
71 |
3209 |
2888 |
330 |
305 |
https://workflowhub.eu/workflows/1324?version=1, https://workflowhub.eu/workflows/1484?version=1 |
genome-annotation/lncrna |
|
fermikit |
fermi2, fermikit_variants |
FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. |
2017-01-05 |
https://github.com/lh3/fermikit |
r193 |
fermi2 |
r193 |
Up-to-date |
Assembly, Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
fgsea |
fgsea |
Perform gene set testing using fgsea |
2018-10-19 |
https://bioconductor.org/packages/release/bioc/html/fgsea.html |
1.8.0+galaxy1 |
bioconductor-fgsea |
1.32.2 |
To update |
Visualization, Transcriptomics, Statistics, Single Cell |
Gene-set enrichment analysis |
Gene-set enrichment analysis |
Genetics |
Genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea |
fgsea |
fgsea |
The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
632 |
734 |
7520 |
8942 |
1072 |
1156 |
22759 |
24664 |
121 |
136 |
1144 |
1277 |
9 |
9 |
115 |
115 |
34998 |
31538 |
2035 |
1834 |
https://usegalaxy.eu/published/workflow?id=12bf85cdc8102bb5, https://usegalaxy.eu/published/workflow?id=63c91ea322cd2819, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=73a9ab4f0f0b9907, https://usegalaxy.eu/published/workflow?id=9a83043d5e847318, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=e04be1ab5a16eb9f, https://usegalaxy.eu/published/workflow?id=fa83e26e05418370, https://usegalaxy.org.au/published/workflow?id=9f6e62f465589ca3, https://usegalaxy.org/published/workflow?id=68832752b883c226, https://workflowhub.eu/workflows/1699?version=1 |
transcriptomics/rna-seq-genes-to-pathways |
|
filtlong |
filtlong |
Filtlong - Filtering long reads by quality |
2018-09-14 |
https://github.com/rrwick/Filtlong |
0.3.1 |
filtlong |
0.3.1 |
Up-to-date |
Fastq Manipulation, Sequence Analysis |
Filtering, Sequencing quality control |
Filtering, Sequencing quality control |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong |
filtlong |
Filtlong |
Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2169 |
2318 |
79820 |
82849 |
1410 |
1424 |
72145 |
72255 |
830 |
830 |
17538 |
17538 |
27 |
27 |
150 |
150 |
172792 |
169653 |
4599 |
4436 |
https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df, https://usegalaxy.eu/published/workflow?id=346b46e6316c6950, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=5500de2961f7470c, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://usegalaxy.eu/published/workflow?id=86cf02cc0868d238, https://usegalaxy.eu/published/workflow?id=968f0ac2617aa524, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=ab646c6ab6de7061, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=c3bfedf33bb00069, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org.au/published/workflow?id=b7aa22291322e505, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=d69a765cfc82a399, https://usegalaxy.org.au/published/workflow?id=fc664a96d8099652, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=48dafc35989f13b1, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=7fc8b2398b6f093f, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://usegalaxy.org/published/workflow?id=cc6ee582a6e5cae2, https://usegalaxy.org/published/workflow?id=d5436cee11a34de9, https://usegalaxy.org/published/workflow?id=e1dcdc125122f561, https://workflowhub.eu/workflows/1613?version=1, https://workflowhub.eu/workflows/51?version=1 |
assembly/mrsa-nanopore |
|
flair |
flair_collapse, flair_correct |
FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. |
2020-11-06 |
https://github.com/BrooksLabUCSC/flair |
1.5 |
flair |
2.2.0 |
To update |
Nanopore |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
0 |
29 |
29 |
2028 |
2028 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2028 |
2028 |
29 |
29 |
https://usegalaxy.eu/published/workflow?id=d4a6fb334f5dd10e |
|
|
flash |
flash |
Fast Length Adjustment of SHort reads |
2017-09-25 |
https://ccb.jhu.edu/software/FLASH/ |
1.2.11 |
flash |
1.2.11 |
Up-to-date |
Assembly, Fastq Manipulation |
Read pre-processing, Sequence merging, Sequence assembly |
Read pre-processing, Sequence merging, Sequence assembly |
Sequencing, Sequence assembly |
Sequencing, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash |
flash |
FLASH |
Identifies paired-end reads which overlap in the middle, converting them to single long reads |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
257 |
325 |
36629 |
39853 |
417 |
787 |
10871 |
18175 |
1 |
1 |
4 |
4 |
0 |
0 |
0 |
0 |
58032 |
47504 |
1113 |
675 |
https://usegalaxy.eu/published/workflow?id=4643edf74f3eaec3, https://usegalaxy.eu/published/workflow?id=987a2abb5cd56e57, https://workflowhub.eu/workflows/100?version=1 |
|
|
fraggenescan |
fraggenescan |
Tool for finding (fragmented) genes in short read |
2017-09-04 |
https://sourceforge.net/projects/fraggenescan/ |
|
fraggenescan |
1.32 |
To update |
Sequence Analysis |
Gene prediction |
Gene prediction |
Genetics, Sequence analysis |
Genetics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan |
fraggenescan |
FragGeneScan |
Application for finding (fragmented) genes in short reads |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
160 |
193 |
1267 |
1643 |
0 |
0 |
0 |
0 |
48 |
48 |
1171 |
1208 |
2 |
2 |
12 |
12 |
2863 |
2450 |
243 |
210 |
https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=534f5fc25bc887ca, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893, https://usegalaxy.eu/published/workflow?id=d57d41e306241396 |
|
|
freebayes |
freebayes, bamleftalign |
Galaxy Freebayes Bayesian genetic variant detector tool |
2017-01-11 |
https://github.com/ekg/freebayes |
1.3.10 |
freebayes |
1.3.10 |
Up-to-date |
Variant Analysis |
Variant calling, Statistical calculation |
Variant calling, Statistical calculation |
Genomics, Genetic variation, Rare diseases |
Genomics, Genetic variation, Rare diseases |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes |
freebayes |
FreeBayes |
Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
8440 |
9638 |
175340 |
204865 |
14740 |
26159 |
140150 |
287235 |
1921 |
2607 |
23952 |
29522 |
246 |
246 |
2943 |
2946 |
524568 |
342385 |
38650 |
25347 |
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https://workflowhub.eu/workflows/676?version=1 |
proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation, variant-analysis/dip, variant-analysis/dunovo, variant-analysis/exome-seq, variant-analysis/non-dip, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants |
|
freyja |
freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants |
lineage abundances estimation |
2022-07-05 |
https://github.com/andersen-lab/Freyja |
2.0.0 |
freyja |
2.0.1 |
To update |
Metagenomics, Sequence Analysis |
RNA-Seq quantification |
RNA-Seq quantification |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja |
freyja |
Freyja |
Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset |
|
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
58 |
58 |
24576 |
24576 |
15 |
15 |
327 |
327 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
24903 |
24903 |
73 |
73 |
https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b |
|
|
funannotate |
funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort |
Funannotate is a genome prediction, annotation, and comparison software package. |
2021-08-26 |
https://funannotate.readthedocs.io |
1.8.17 |
|
|
To update |
Genome annotation |
Genome annotation |
Genome annotation |
Genomics |
Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate |
funannotate |
funannotate |
funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). |
|
0 |
5 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
0 |
891 |
891 |
14118 |
14118 |
209 |
209 |
1453 |
1453 |
310 |
310 |
8597 |
8597 |
88 |
88 |
1505 |
1505 |
25673 |
25673 |
1498 |
1498 |
https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.org.au/published/workflow?id=4e161a8f5098cc49, https://usegalaxy.org.au/published/workflow?id=52065a4100b11184, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/1525?version=1, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1, https://workflowhub.eu/workflows/754?version=1 |
ecology/phylogeny-data-prep, genome-annotation/funannotate |
|
gamma |
gamma_s, gamma |
Gene Allele Mutation Microbial Assessment |
2025-08-06 |
https://github.com/rastanton/GAMMA |
2.2 |
GAMMA |
2.2 |
Up-to-date |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gamma/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gamma |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gatk4_mutect2 |
gatk4_mutect2 |
A Galaxy wrapper for Mutect2 from GATK |
2019-10-28 |
https://software.broadinstitute.org/gatk/gatk4 |
4.1.7.0 |
gatk4 |
4.6.2.0 |
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
564 |
611 |
3976 |
4606 |
1831 |
2022 |
10954 |
11924 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16530 |
14930 |
2633 |
2395 |
https://usegalaxy.eu/published/workflow?id=93e32219d412c1f1, https://usegalaxy.eu/published/workflow?id=b02d90c32dc67730, https://usegalaxy.org/published/workflow?id=2f21358621337cf2, https://usegalaxy.org/published/workflow?id=39753cc73284963f, https://usegalaxy.org/published/workflow?id=eb33df15225b8aa0, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a, https://usegalaxy.org/published/workflow?id=eed1aadf2fb83f6c, https://workflowhub.eu/workflows/35?version=1 |
|
|
gdcwebapp |
data_source_gdcwebapp |
GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format |
2017-06-23 |
http://bioinf.iasi.cnr.it/gdcwebapp/ |
1.0.0 |
python |
|
To update |
Data Source, Convert Formats |
|
|
|
|
iuc |
https://github.com/fabio-cumbo/GDCWebApp4Galaxy |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gecko |
gecko |
Ungapped genome comparison |
2020-11-25 |
https://github.com/otorreno/gecko |
1.2 |
gecko |
1.2 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
341 |
341 |
1081 |
1081 |
0 |
0 |
0 |
0 |
124 |
124 |
961 |
961 |
0 |
0 |
0 |
0 |
2042 |
2042 |
465 |
465 |
https://workflowhub.eu/workflows/1541?version=1 |
genome-annotation/hpc-for-lsgc |
|
gem_tools |
gem_check_memote, gem_escher_visualization, gem_extract_exchange, gem_flux_distribution, gem_flux_variability_analysis, gem_knockout, gem_phenotype_phase_plane |
Tools for analyzing genome-scale metabolic models (GEMs) using COBRApy and related libraries. |
2024-12-01 |
https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology |
0.29.1 |
cobra |
0.21.0 |
To update |
Metabolomics, Systems Biology, Synthetic Biology |
|
|
|
|
iuc |
https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gem_tools |
|
|
|
|
0 |
7 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
464 |
464 |
0 |
0 |
0 |
0 |
464 |
464 |
1 |
1 |
|
|
|
gemini |
gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ |
GEMINI: a flexible framework for exploring genome variation |
2014-11-09 |
https://github.com/arq5x/gemini |
0.20.1 |
gemini |
0.30.2 |
To update |
Sequence Analysis, Next Gen Mappers |
Sequence analysis, Genetic variation analysis |
Sequence analysis, Genetic variation analysis |
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini |
gemini |
GEMINI |
GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
1258 |
1488 |
4490 |
6130 |
529 |
529 |
1823 |
1949 |
439 |
453 |
4187 |
4642 |
26 |
26 |
82 |
82 |
12803 |
10582 |
2496 |
2252 |
https://usegalaxy.eu/published/workflow?id=2aede5c6577b28f5, https://usegalaxy.eu/published/workflow?id=3570835f21365be7, https://usegalaxy.eu/published/workflow?id=b3b094f1bdbaa04a, https://usegalaxy.eu/published/workflow?id=b3c0eba755f269b2, https://usegalaxy.eu/published/workflow?id=b82a4065be048ef6, https://usegalaxy.org.au/published/workflow?id=1be22b394f9ec3ab, https://usegalaxy.org.au/published/workflow?id=5442f0437ade82c4, https://usegalaxy.org.au/published/workflow?id=ac89c2d51c32cc9c, https://workflowhub.eu/workflows/1636?version=1, https://workflowhub.eu/workflows/1655?version=1, https://workflowhub.eu/workflows/1668?version=1, https://workflowhub.eu/workflows/1672?version=1, https://workflowhub.eu/workflows/363?version=2 |
variant-analysis/dip, variant-analysis/exome-seq, variant-analysis/trio-analysis |
|
gemini |
glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based |
Glimmer makes gene predictions. |
2017-11-28 |
https://ccb.jhu.edu/software/glimmer/ |
3.02 |
glimmer |
3.02 |
Up-to-date |
Sequence Analysis |
Sequence analysis, Genetic variation analysis |
Sequence analysis, Genetic variation analysis |
Sequence analysis |
Sequence analysis |
bgruening |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer |
gemini |
GEMINI |
GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. |
|
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
0 |
390 |
390 |
6567 |
6567 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6567 |
6567 |
390 |
390 |
https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1 |
ecology/phylogeny-data-prep |
|
genebed_maf_to_fasta |
GeneBed_Maf_Fasta2 |
Stitch gene blocks given a set of coding exon intervals |
2020-08-05 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ |
1.0.1+galaxy0 |
|
|
To update |
Genomic Interval Operations |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
1 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
1 |
2 |
2 |
4 |
4 |
16 |
280 |
152 |
2906 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2910 |
156 |
282 |
18 |
|
|
|
genehunter_modscore |
genehunter_modscore |
Maximised LOD score pedigree analysis utility |
2017-11-27 |
https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1 |
3.0.0 |
ghm |
3.1 |
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
geneiobio |
gene_iobio_display_generation_iframe |
Gene.iobio is an interactive tool for variant and trio analysis. |
2023-06-20 |
https://github.com/iobio/gene.iobio |
4.7.1+galaxy1 |
|
|
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
48 |
48 |
172 |
172 |
0 |
0 |
0 |
0 |
8 |
8 |
158 |
158 |
0 |
0 |
0 |
0 |
330 |
330 |
56 |
56 |
https://usegalaxy.eu/published/workflow?id=b3c0eba755f269b2, https://workflowhub.eu/workflows/1636?version=1 |
variant-analysis/trio-analysis |
|
genetrack |
genetrack |
Contains a tool that separately identifies peaks on the forward "+” (W) and reverse “-” (C) strand. |
2015-12-18 |
|
|
numpy |
|
To update |
ChIP-seq |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
78 |
203 |
228 |
674 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
674 |
228 |
203 |
78 |
|
|
|
genomescope |
genomescope |
Analyze unassembled short reads |
2021-04-30 |
https://github.com/tbenavi1/genomescope2.0 |
2.0.1 |
genomescope2 |
2.0.1 |
Up-to-date |
Statistics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1029 |
1029 |
5878 |
5878 |
641 |
641 |
3149 |
3149 |
261 |
261 |
2337 |
2337 |
37 |
37 |
614 |
614 |
11978 |
11978 |
1968 |
1968 |
https://usegalaxy.eu/published/workflow?id=0ccb3838765a8b84, https://usegalaxy.eu/published/workflow?id=0e642b5407dd595b, https://usegalaxy.eu/published/workflow?id=0fef06a87389eb59, https://usegalaxy.eu/published/workflow?id=10bde4e7f8dbd0c4, https://usegalaxy.eu/published/workflow?id=11ce7a7bf3d075e0, https://usegalaxy.eu/published/workflow?id=238606356787b876, https://usegalaxy.eu/published/workflow?id=29b4710cd24995b2, https://usegalaxy.eu/published/workflow?id=3069c17b52decab4, https://usegalaxy.eu/published/workflow?id=3788bb24b97f7b83, https://usegalaxy.eu/published/workflow?id=41c48e4632684f76, https://usegalaxy.eu/published/workflow?id=7f5da1ebd6673841, https://usegalaxy.eu/published/workflow?id=a85be448600a6789, https://usegalaxy.eu/published/workflow?id=acd29212884f967b, https://usegalaxy.eu/published/workflow?id=acfc7d1b03d5fbd0, https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://usegalaxy.eu/published/workflow?id=c2c7f1815c411bfb, https://usegalaxy.eu/published/workflow?id=c4877de66200667b, https://usegalaxy.eu/published/workflow?id=d1e3d3bb0922d771, https://usegalaxy.eu/published/workflow?id=d67299c34e63f3d9, https://usegalaxy.eu/published/workflow?id=db6640887b5ca0cd, https://usegalaxy.eu/published/workflow?id=dec16871152fac35, https://usegalaxy.eu/published/workflow?id=ff16623a63ff5124, https://usegalaxy.org.au/published/workflow?id=049f61f436ff66df, https://usegalaxy.org.au/published/workflow?id=141ac7a106e49d8f, https://usegalaxy.org.au/published/workflow?id=26b57e0b79ea4559, https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=5364e6ec5b4f48cd, https://usegalaxy.org.au/published/workflow?id=6aaaa084d5339c08, https://usegalaxy.org.au/published/workflow?id=6c54e7f7a4bf17ed, https://usegalaxy.org.au/published/workflow?id=6c5b84bcac127272, https://usegalaxy.org.au/published/workflow?id=8dc05e3ba64e981f, https://usegalaxy.org.au/published/workflow?id=ab9f7a97baaa7fa6, https://usegalaxy.org.au/published/workflow?id=b9d0a39d72b8e5f8, https://usegalaxy.org.au/published/workflow?id=c0aa1f64a89a6115, https://usegalaxy.org.au/published/workflow?id=d7c2d0d49b1a6c86, https://usegalaxy.org.au/published/workflow?id=d9ee934bbae0fa01, https://usegalaxy.org/published/workflow?id=14dc039ee7138b8b, https://usegalaxy.org/published/workflow?id=19e2191687f81c21, https://usegalaxy.org/published/workflow?id=2759eaa8adbd2857, https://usegalaxy.org/published/workflow?id=333c5725006e4154, https://usegalaxy.org/published/workflow?id=49e2570e363fda11, https://usegalaxy.org/published/workflow?id=4b919e575a16d062, https://usegalaxy.org/published/workflow?id=5503f7835226bc04, https://usegalaxy.org/published/workflow?id=6988c29ae84d2788, https://usegalaxy.org/published/workflow?id=7f8d7595cbeebf1d, https://usegalaxy.org/published/workflow?id=815cd221eaaaeb53, https://usegalaxy.org/published/workflow?id=83898f7cbfb7f88e, https://usegalaxy.org/published/workflow?id=9bc46b4d35749b41, https://usegalaxy.org/published/workflow?id=9f1aabc6f5d18d13, https://usegalaxy.org/published/workflow?id=a00f78b74c27b5f3, https://usegalaxy.org/published/workflow?id=ae71399852f34680, https://usegalaxy.org/published/workflow?id=af1f4dba9aaa0b52, https://usegalaxy.org/published/workflow?id=bcf3ff03326c80b7, https://usegalaxy.org/published/workflow?id=c72f94a30ad54327, https://usegalaxy.org/published/workflow?id=faa4f94f070c6213, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1607?version=1, https://workflowhub.eu/workflows/1608?version=1, https://workflowhub.eu/workflows/1641?version=1, https://workflowhub.eu/workflows/223?version=1, https://workflowhub.eu/workflows/365?version=1, https://workflowhub.eu/workflows/366?version=1, https://workflowhub.eu/workflows/603?version=2, https://workflowhub.eu/workflows/631?version=6, https://workflowhub.eu/workflows/632?version=11, https://workflowhub.eu/workflows/698?version=1 |
assembly/ERGA-post-assembly-QC, assembly/largegenome, assembly/vgp_genome_assembly |
|
genomic_super_signature |
genomic_super_signature |
Interpretation of RNAseq experiments through robust, efficient comparison to public databases |
2022-01-12 |
https://github.com/shbrief/GenomicSuperSignature |
1.2.0 |
bioconductor-genomicsupersignature |
1.14.0 |
To update |
Sequence Analysis, RNA, Transcriptomics |
Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction |
Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction |
RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment |
RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature |
genomicsupersignature |
GenomicSuperSignature |
GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
20 |
20 |
58 |
58 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
58 |
58 |
20 |
20 |
|
|
|
genrich |
genrich |
Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). |
2019-07-05 |
https://github.com/jsh58/Genrich |
0.5+galaxy2 |
genrich |
0.6.1 |
To update |
ChIP-seq |
|
|
|
|
iuc |
https://github.com/jsh58/Genrich |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
283 |
435 |
2214 |
3829 |
460 |
460 |
3086 |
3086 |
31 |
31 |
700 |
703 |
0 |
0 |
0 |
0 |
7618 |
6000 |
926 |
774 |
https://usegalaxy.eu/published/workflow?id=02655d0e4af0ee0d, https://usegalaxy.org.au/published/workflow?id=99821674db7682bb |
|
|
geopandas |
geopandas_table2geojson |
GeoPandas is an open source project to make working with geospatial data easier. |
2025-04-20 |
https://geopandas.org |
1.1.1 |
geopandas |
|
To update |
Geo Science |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
41 |
41 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
41 |
41 |
3 |
3 |
|
|
|
get_hrun |
get_hrun |
Annotate indel variants with homopolymer context |
2021-03-02 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun |
0.5.9.2 |
pyfaidx |
0.9.0.3 |
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
5 |
5 |
9 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
9 |
5 |
5 |
|
|
|
getorganelle |
get_annotated_regions_from_gb, get_organelle_from_reads |
GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. |
2022-03-15 |
https://github.com/Kinggerm/GetOrganelle |
1.7.7.1 |
getorganelle |
1.7.7.1 |
Up-to-date |
Assembly |
De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming |
De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming |
Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms |
Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle |
getorganelle |
GetOrganelle |
A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. |
|
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
403 |
403 |
9423 |
9423 |
0 |
0 |
0 |
0 |
108 |
108 |
1588 |
1588 |
0 |
0 |
0 |
0 |
11011 |
11011 |
511 |
511 |
https://usegalaxy.org.au/published/workflow?id=f2541030f6d70b59 |
|
|
gfa_to_fa |
gfa_to_fa |
gfa_to_fa - Converting GFA format to Fasta format |
2019-06-18 |
http://gfa-spec.github.io/GFA-spec/ |
0.1.2 |
|
|
To update |
Convert Formats |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
911 |
1010 |
9926 |
11805 |
621 |
661 |
6768 |
7202 |
186 |
188 |
1778 |
1807 |
52 |
52 |
228 |
228 |
21042 |
18700 |
1911 |
1770 |
https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=d67299c34e63f3d9, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=fba1671d835b6dd3, https://usegalaxy.org.au/published/workflow?id=044b6b475b4db27a, https://usegalaxy.org.au/published/workflow?id=29f0c07c8a24b542, https://usegalaxy.org.au/published/workflow?id=36604d0ab0dee988, https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=98d3def7da131b4c, https://usegalaxy.org.au/published/workflow?id=afab89bc468da8b3, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org.au/published/workflow?id=e07866576cc2f467, https://usegalaxy.org.au/published/workflow?id=f83a3cda33131fb8, https://workflowhub.eu/workflows/1162?version=2, https://workflowhub.eu/workflows/1163?version=2, https://workflowhub.eu/workflows/1164?version=2, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/1607?version=1, https://workflowhub.eu/workflows/221?version=3, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/605?version=1, https://workflowhub.eu/workflows/606?version=2, https://workflowhub.eu/workflows/608?version=1, https://workflowhub.eu/workflows/701?version=1, https://workflowhub.eu/workflows/702?version=1, https://workflowhub.eu/workflows/789?version=1 |
assembly/hifi-assembly, assembly/vgp_genome_assembly, microbiome/plasmid-metagenomics-nanopore |
|
gff3_rebase |
gff3.rebase |
Rebase a GFF against a parent GFF (e.g. an original genome) |
2015-05-25 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase |
1.2 |
bcbiogff |
0.6.6 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
80 |
83 |
1290 |
1337 |
42 |
45 |
179 |
207 |
12 |
12 |
182 |
182 |
1 |
1 |
1 |
1 |
1727 |
1652 |
141 |
135 |
https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=44189803f223acd1, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6 |
|
|
gffcompare |
gffcompare |
Galaxy wrappers for Geo Pertea's GffCompare package. |
2017-03-27 |
https://github.com/gpertea/gffcompare/ |
0.12.10 |
gffcompare |
0.12.10 |
Up-to-date |
Transcriptomics |
Sequence annotation |
Sequence annotation |
Nucleic acids, Sequence analysis |
Nucleic acids, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare |
gffcompare |
gffcompare |
Program for comparing, annotating, merging and tracking transcripts in GFF files. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1157 |
1332 |
4195 |
5221 |
1776 |
2918 |
5168 |
9180 |
179 |
272 |
1521 |
2011 |
29 |
29 |
79 |
79 |
16491 |
10963 |
4551 |
3141 |
https://usegalaxy.eu/published/workflow?id=0de150b19102cb7e, https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=2287afbf248d9c89, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2, https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.eu/published/workflow?id=e8202b7b6338005d, https://usegalaxy.eu/published/workflow?id=f026c4b8341ff94c, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=53010c2f1f207429, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org.au/published/workflow?id=e045a6064ad5fdc4, https://usegalaxy.org/published/workflow?id=31c35b9a93237235, https://usegalaxy.org/published/workflow?id=4061e061f659449b, https://usegalaxy.org/published/workflow?id=454d7310d001a4d0, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=8700f593a3d642f5, https://usegalaxy.org/published/workflow?id=9c022f4028de0bc6, https://usegalaxy.org/published/workflow?id=e336bca259abd474, https://workflowhub.eu/workflows/1407?version=1, https://workflowhub.eu/workflows/1437?version=1, https://workflowhub.eu/workflows/1685?version=1, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/1788?version=1 |
proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation, transcriptomics/de-novo, transcriptomics/differential-isoform-expression |
|
gffread |
gffread |
gffread filters and/or converts GFF3/GTF2 records |
2019-10-29 |
http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ |
0.12.7 |
gffread |
0.12.7 |
Up-to-date |
Sequence Analysis |
Sequence annotation |
Sequence annotation |
Nucleic acids, Sequence analysis |
Nucleic acids, Sequence analysis |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread |
gffread |
gffread |
program for filtering, converting and manipulating GFF files |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2441 |
2656 |
16223 |
18398 |
2944 |
4174 |
18563 |
29048 |
879 |
923 |
5541 |
6033 |
107 |
107 |
998 |
1000 |
54479 |
41325 |
7860 |
6371 |
https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=1590085d315aa80e, https://usegalaxy.eu/published/workflow?id=1d2e17a4f71f2455, https://usegalaxy.eu/published/workflow?id=21dd4bd16579fc12, https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=2a73d658446747de, https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=31bc2a44fb89aa89, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=48fe9c4de045d414, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=6550f72070b24082, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=8976041ef89e4548, https://usegalaxy.eu/published/workflow?id=8bc1c3b9e665ea37, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06, https://usegalaxy.eu/published/workflow?id=dd8b55e7768843b1, https://usegalaxy.eu/published/workflow?id=f28459c5b16549b7, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org.au/published/workflow?id=dd9272826e6dd98d, https://usegalaxy.org.au/published/workflow?id=e263fcb6c98e231b, https://usegalaxy.org.au/published/workflow?id=ec7efff3d3249177, https://usegalaxy.org/published/workflow?id=07fdeadce7a6d5cb, https://usegalaxy.org/published/workflow?id=173ecc0c88090d0e, https://usegalaxy.org/published/workflow?id=228ae7f537a60226, https://usegalaxy.org/published/workflow?id=2a7fbfc1c17e38bc, https://usegalaxy.org/published/workflow?id=427fce51fd9508eb, https://usegalaxy.org/published/workflow?id=4605309321799e9b, https://usegalaxy.org/published/workflow?id=4e6005819e57ed35, https://usegalaxy.org/published/workflow?id=6d0a3f36d2736087, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=7b19452fe35b8b17, https://usegalaxy.org/published/workflow?id=80a7124c40438cc9, https://usegalaxy.org/published/workflow?id=93650de42fb8c015, https://usegalaxy.org/published/workflow?id=a89def2c2462674a, https://usegalaxy.org/published/workflow?id=aac2ae0419f7d515, https://usegalaxy.org/published/workflow?id=b094b6e1e7d48416, https://usegalaxy.org/published/workflow?id=c8653e558a68eb68, https://usegalaxy.org/published/workflow?id=dbe08700353dfc43, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8, https://usegalaxy.org/published/workflow?id=ec3cc032a90c44f1, https://usegalaxy.org/published/workflow?id=f4111a169255535c, https://usegalaxy.org/published/workflow?id=fb789920b057fe8d, https://workflowhub.eu/workflows/1255?version=3, https://workflowhub.eu/workflows/1323?version=1, https://workflowhub.eu/workflows/1324?version=1, https://workflowhub.eu/workflows/1484?version=1, https://workflowhub.eu/workflows/1500?version=1, https://workflowhub.eu/workflows/1504?version=1, https://workflowhub.eu/workflows/1509?version=1, https://workflowhub.eu/workflows/1549?version=1, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/1746?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1 |
genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short, genome-annotation/braker3, genome-annotation/comparison-braker-helixer-annotation, genome-annotation/helixer, genome-annotation/lncrna, transcriptomics/differential-isoform-expression |
|
ggplot2 |
ggplot2_barplot, ggplot2_boxplot, ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin |
ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. |
2017-05-26 |
https://github.com/tidyverse/ggplot2 |
3.5.1 |
r-ggplot2 |
2.2.1 |
To update |
Visualization |
Visualisation |
Visualisation |
Data visualisation |
Data visualisation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 |
ggplot2 |
ggplot2 |
Plotting system for R, based on the grammar of graphics. |
|
0 |
5 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
5 |
1825 |
2030 |
28524 |
31954 |
1894 |
2101 |
31068 |
34254 |
1297 |
1311 |
10678 |
11132 |
220 |
220 |
3884 |
3884 |
81224 |
74154 |
5662 |
5236 |
https://usegalaxy.cz/published/workflow?id=a5241f01bb65bd38, https://usegalaxy.eu/published/workflow?id=069d99391a69baf4, https://usegalaxy.eu/published/workflow?id=075c4126e66def01, https://usegalaxy.eu/published/workflow?id=082bfd9b36e921e8, https://usegalaxy.eu/published/workflow?id=098f43ded1b5fa7f, https://usegalaxy.eu/published/workflow?id=0c3ce9feb83f7920, https://usegalaxy.eu/published/workflow?id=0c6dd9e75d9a2130, https://usegalaxy.eu/published/workflow?id=0cf3c2114ab65858, https://usegalaxy.eu/published/workflow?id=16418e8b023ff226, https://usegalaxy.eu/published/workflow?id=204854b8ec94da85, https://usegalaxy.eu/published/workflow?id=2e6ed783bdf05d16, https://usegalaxy.eu/published/workflow?id=3010ecad1a342331, https://usegalaxy.eu/published/workflow?id=319bc351f7a8e358, https://usegalaxy.eu/published/workflow?id=31c6dcd3a25620df, https://usegalaxy.eu/published/workflow?id=31f8c7c46207432f, https://usegalaxy.eu/published/workflow?id=321ea55011f1248f, 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https://usegalaxy.org.au/published/workflow?id=ae6a03240680712a, https://usegalaxy.org.au/published/workflow?id=b53f82aaf32fbaa9, https://usegalaxy.org.au/published/workflow?id=b5e546197f47f3ec, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=b9e89401313a0cca, https://usegalaxy.org.au/published/workflow?id=bcb0be4f4a0e369f, https://usegalaxy.org.au/published/workflow?id=be35847680078c90, https://usegalaxy.org.au/published/workflow?id=cac0b8a09d59044b, https://usegalaxy.org.au/published/workflow?id=cf775b8ff0745456, https://usegalaxy.org.au/published/workflow?id=d858cfd9303bb99a, https://usegalaxy.org.au/published/workflow?id=e2c49586dc941f38, https://usegalaxy.org.au/published/workflow?id=e6552643a3713b50, https://usegalaxy.org.au/published/workflow?id=ea98be0f99aaceb9, https://usegalaxy.org.au/published/workflow?id=ebf88e79c4f094ba, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org.au/published/workflow?id=edc20b5e70297a7d, https://usegalaxy.org.au/published/workflow?id=f53d8ade897b3f46, https://usegalaxy.org.au/published/workflow?id=fdec6e2fcd5e2cf5, https://usegalaxy.org/published/workflow?id=155839aeb6340f54, https://usegalaxy.org/published/workflow?id=1e264fc06d87899f, https://usegalaxy.org/published/workflow?id=1ea88ca80a7f0038, https://usegalaxy.org/published/workflow?id=23eeee48217654d4, https://usegalaxy.org/published/workflow?id=28dbbfb3d480f4b1, https://usegalaxy.org/published/workflow?id=28ddea356ae57da1, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=325783f21bc5fef6, https://usegalaxy.org/published/workflow?id=349f1bcdbc84045f, https://usegalaxy.org/published/workflow?id=371273ba52f1f5dc, https://usegalaxy.org/published/workflow?id=3b0d42747f598f82, https://usegalaxy.org/published/workflow?id=3d805d7e0f34c727, https://usegalaxy.org/published/workflow?id=3db51822f04f4ff7, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=44bcae0e352563f9, https://usegalaxy.org/published/workflow?id=450c2181f89e6b23, https://usegalaxy.org/published/workflow?id=48dd4a4cb5536670, https://usegalaxy.org/published/workflow?id=49a07807fcea8158, https://usegalaxy.org/published/workflow?id=531d02f7213f9113, https://usegalaxy.org/published/workflow?id=6341c384ceaf47ed, https://usegalaxy.org/published/workflow?id=74049914e4a6c791, https://usegalaxy.org/published/workflow?id=768cee70d9aa8cc6, https://usegalaxy.org/published/workflow?id=79a282b2bf89c6ac, https://usegalaxy.org/published/workflow?id=7b8ee08ba291d231, https://usegalaxy.org/published/workflow?id=85f521f5c7351406, https://usegalaxy.org/published/workflow?id=88327cb2e0fe3c25, https://usegalaxy.org/published/workflow?id=88f8feaad0f615de, https://usegalaxy.org/published/workflow?id=903e35b62946ed76, https://usegalaxy.org/published/workflow?id=91a4daecbb97d03e, https://usegalaxy.org/published/workflow?id=987d5caea37794c8, https://usegalaxy.org/published/workflow?id=9aa6320de30e2675, https://usegalaxy.org/published/workflow?id=9f4c4038d1c519e2, https://usegalaxy.org/published/workflow?id=a253589432a44e5a, https://usegalaxy.org/published/workflow?id=a4a6d6846c1692f9, https://usegalaxy.org/published/workflow?id=afa89bb0e8966753, https://usegalaxy.org/published/workflow?id=b1b4fc510099d592, https://usegalaxy.org/published/workflow?id=b1cfa3c239ef2523, https://usegalaxy.org/published/workflow?id=bf79271a438ffa54, https://usegalaxy.org/published/workflow?id=bff8bc8d0059274f, https://usegalaxy.org/published/workflow?id=c03ada2070e9ca8a, https://usegalaxy.org/published/workflow?id=c95e9116e4b7982b, https://usegalaxy.org/published/workflow?id=ca3f2d9554e9e1c8, https://usegalaxy.org/published/workflow?id=ce4d4397eb8a5298, https://usegalaxy.org/published/workflow?id=d5183b025d0e78dd, https://usegalaxy.org/published/workflow?id=e50e36a25bae863c, https://usegalaxy.org/published/workflow?id=f09033420c6267ab, https://usegalaxy.org/published/workflow?id=f18e6fa5270fcd37, https://usegalaxy.org/published/workflow?id=fa36d9b50e956917, https://usegalaxy.org/published/workflow?id=fb98ef955b3dbd4b, https://workflowhub.eu/workflows/1054?version=1, https://workflowhub.eu/workflows/1057?version=9, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1402?version=1, https://workflowhub.eu/workflows/1405?version=1, https://workflowhub.eu/workflows/1427?version=1, https://workflowhub.eu/workflows/1432?version=1, https://workflowhub.eu/workflows/1441?version=1, https://workflowhub.eu/workflows/1469?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/1489?version=1, https://workflowhub.eu/workflows/1536?version=1, https://workflowhub.eu/workflows/1609?version=1, https://workflowhub.eu/workflows/1628?version=1, https://workflowhub.eu/workflows/1707?version=1, https://workflowhub.eu/workflows/625?version=26, https://workflowhub.eu/workflows/643?version=5 |
climate/climate-101, climate/fates, climate/pangeo, ecology/regionalGAM, galaxy-interface/workflow-reports, introduction/galaxy-intro-101-everyone, introduction/galaxy-reproduce, microbiome/metaplasmidome_query, microbiome/pathogen-detection-from-nanopore-foodborne-data, single-cell/bulk-deconvolution-evaluate, statistics/clustering_machinelearning, variant-analysis/baculovirus-isolate-variation |
|
ggplot2_heatmap2 |
ggplot2_heatmap2 |
heatmap.2 function from the R gplots package |
2019-02-10 |
https://github.com/cran/gplots |
3.2.0 |
r-gplots |
2.17.0 |
To update |
Visualization |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
5453 |
6454 |
52101 |
62236 |
6555 |
8257 |
69586 |
84002 |
840 |
946 |
8530 |
9871 |
281 |
285 |
2996 |
3046 |
159155 |
133213 |
15942 |
13129 |
https://usegalaxy.eu/published/workflow?id=17ad465d9515cd25, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=21dd4bd16579fc12, https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=511b023121b7c488, https://usegalaxy.eu/published/workflow?id=63964ba7d9edce74, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=68e8042f11d5a3fd, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=7d44ea091d437edf, https://usegalaxy.eu/published/workflow?id=81f1927bfe3ffea1, https://usegalaxy.eu/published/workflow?id=82ef590b5821805d, https://usegalaxy.eu/published/workflow?id=95c4d5549e820d88, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.eu/published/workflow?id=a65a17122d2234a8, https://usegalaxy.eu/published/workflow?id=a7dc6e0c43cb6d6d, https://usegalaxy.eu/published/workflow?id=a9469155eee12ff1, https://usegalaxy.eu/published/workflow?id=ca286c2fdc71e960, https://usegalaxy.eu/published/workflow?id=ccef778cfd9024d1, https://usegalaxy.eu/published/workflow?id=d6f7e86d52d43555, https://usegalaxy.eu/published/workflow?id=dfee2bd4e4600ad9, https://usegalaxy.eu/published/workflow?id=e7e26967cf6cb8d8, https://usegalaxy.eu/published/workflow?id=f58526da1fd68108, https://usegalaxy.eu/published/workflow?id=f78e16c669481efd, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.org.au/published/workflow?id=04ab43fb3e7840ef, https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c, https://usegalaxy.org.au/published/workflow?id=28705b86e0595ded, https://usegalaxy.org.au/published/workflow?id=2cef9a1633e0a067, https://usegalaxy.org.au/published/workflow?id=42305ed876d19d08, https://usegalaxy.org.au/published/workflow?id=5490661d0153962b, https://usegalaxy.org.au/published/workflow?id=71bad95f72c9f30d, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=7ef245f5ae3b916d, https://usegalaxy.org.au/published/workflow?id=84a8eb379440656e, https://usegalaxy.org.au/published/workflow?id=85aede91db0122e4, https://usegalaxy.org.au/published/workflow?id=8eab5e2b2c683076, https://usegalaxy.org.au/published/workflow?id=8fb691706f47527a, https://usegalaxy.org.au/published/workflow?id=a9e59d38c6c710bc, https://usegalaxy.org.au/published/workflow?id=ae773dfaa074cb72, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org.au/published/workflow?id=e4ddf33ee5b5e259, https://usegalaxy.org.au/published/workflow?id=f7fd24318c4bf949, https://usegalaxy.org/published/workflow?id=19fcce20ecaf2ef6, https://usegalaxy.org/published/workflow?id=25cdc47baba556c5, https://usegalaxy.org/published/workflow?id=40a65b5bc1dcc0b4, https://usegalaxy.org/published/workflow?id=4c840284d2984fa0, https://usegalaxy.org/published/workflow?id=667493d318b86b7d, https://usegalaxy.org/published/workflow?id=68832752b883c226, https://usegalaxy.org/published/workflow?id=abf1aec0f3d48d03, https://usegalaxy.org/published/workflow?id=dcc7c5fdef8780fd, https://workflowhub.eu/workflows/1201?version=4, https://workflowhub.eu/workflows/1426?version=1, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1713?version=1, https://workflowhub.eu/workflows/1718?version=1 |
proteomics/maxquant-msstats-dda-lfq, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-viz-with-heatmap2 |
|
ggupset |
emc-ggupset |
Create Upset Plots with ggupset |
2022-12-17 |
https://github.com/const-ae/ggupset |
1.0 |
r-ggupset |
|
To update |
Graphics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
goenrichment |
goenrichment, goslimmer |
Performs GO Enrichment analysis. |
2018-12-28 |
https://github.com/DanFaria/GOEnrichment |
2.0.1 |
goenrichment |
2.0.1 |
Up-to-date |
Genome annotation |
Gene-set enrichment analysis |
Gene-set enrichment analysis |
Transcriptomics |
Transcriptomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment |
goenrichment |
GOEnrichment |
GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de CiĂŞncia. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
799 |
928 |
6000 |
7557 |
1081 |
1196 |
8060 |
9309 |
230 |
233 |
1602 |
1647 |
5 |
6 |
39 |
44 |
18557 |
15701 |
2363 |
2115 |
https://usegalaxy.eu/published/workflow?id=5f053303601cc630, https://usegalaxy.eu/published/workflow?id=7136ce9f18c74853, https://usegalaxy.org.au/published/workflow?id=d04b26372b28e8ed, https://workflowhub.eu/workflows/1515?version=1, https://workflowhub.eu/workflows/1667?version=1 |
single-cell/GO-enrichment, transcriptomics/goenrichment |
|
goseq |
goseq |
goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data |
2016-11-12 |
https://bioconductor.org/packages/release/bioc/html/goseq.html |
1.50.0 |
bioconductor-goseq |
1.58.0 |
To update |
Statistics, RNA, Micro-array Analysis |
Gene functional annotation |
Gene functional annotation |
RNA-Seq |
RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq |
goseq |
GOseq |
Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3196 |
3921 |
23708 |
28273 |
3528 |
4089 |
26762 |
31254 |
640 |
680 |
4461 |
5015 |
103 |
104 |
751 |
784 |
65326 |
55682 |
8794 |
7467 |
https://usegalaxy.eu/published/workflow?id=032ad839dab7ae70, https://usegalaxy.eu/published/workflow?id=12bf85cdc8102bb5, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=63c91ea322cd2819, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.eu/published/workflow?id=c1a6d11e1eab6a42, https://usegalaxy.eu/published/workflow?id=e7e26967cf6cb8d8, https://usegalaxy.eu/published/workflow?id=fa83e26e05418370, https://usegalaxy.org.au/published/workflow?id=4f0814ec9f9f8425, https://usegalaxy.org.au/published/workflow?id=5490661d0153962b, https://usegalaxy.org.au/published/workflow?id=71bad95f72c9f30d, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=9f6e62f465589ca3, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=420a332da24fb9e9, https://usegalaxy.org/published/workflow?id=742120336d5ff997, https://workflowhub.eu/workflows/1194?version=1, https://workflowhub.eu/workflows/1684?version=1, https://workflowhub.eu/workflows/1699?version=1, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1713?version=1, https://workflowhub.eu/workflows/689?version=1 |
transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-genes-to-pathways |
|
gprofiler |
gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense |
functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more |
2019-10-30 |
https://biit.cs.ut.ee/gprofiler |
@TOOL_VERSION@+galaxy11 |
r-gprofiler2 |
|
To update |
Statistics, Web Services |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler |
|
|
|
|
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
5 |
550 |
584 |
4378 |
4901 |
792 |
850 |
8647 |
9196 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
14097 |
13025 |
1434 |
1342 |
https://usegalaxy.eu/published/workflow?id=1590085d315aa80e, https://usegalaxy.eu/published/workflow?id=1d2e17a4f71f2455, https://usegalaxy.eu/published/workflow?id=21dd4bd16579fc12, https://usegalaxy.eu/published/workflow?id=2a73d658446747de, https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=48fe9c4de045d414, https://usegalaxy.eu/published/workflow?id=5f053303601cc630, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=8bc1c3b9e665ea37, https://usegalaxy.eu/published/workflow?id=f28459c5b16549b7, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.org/published/workflow?id=092be3cf6e40282c, https://usegalaxy.org/published/workflow?id=173ecc0c88090d0e, https://usegalaxy.org/published/workflow?id=68832752b883c226, https://usegalaxy.org/published/workflow?id=6d0a3f36d2736087, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=b094b6e1e7d48416, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8, https://usegalaxy.org/published/workflow?id=dec0cf06fa059e65, https://workflowhub.eu/workflows/1515?version=1 |
single-cell/GO-enrichment |
|
graphembed |
graphembed |
Compute a 2D embedding of a data matrix given supervised class information |
2019-12-10 |
https://github.com/fabriziocosta/GraphEmbed |
2.4 |
graph_embed |
2.4 |
Up-to-date |
Statistics, Graphics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
5 |
7 |
18 |
79 |
44 |
49 |
71 |
134 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
213 |
89 |
56 |
49 |
|
|
|
graphlan |
graphlan, graphlan_annotate |
GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees |
2017-03-03 |
https://github.com/biobakery/graphlan |
|
graphlan |
1.1.3 |
To update |
Metagenomics, Graphics, Phylogenetics |
Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification |
Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification |
Metagenomics, Phylogenetics, Phylogenomics, Cladistics |
Metagenomics, Phylogenetics, Phylogenomics, Cladistics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphlan/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan |
graphlan |
GraPhlAn |
GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
799 |
940 |
11872 |
13928 |
325 |
325 |
1773 |
1773 |
202 |
207 |
1432 |
1470 |
21 |
21 |
90 |
90 |
17261 |
15167 |
1493 |
1347 |
https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=7ab70660e6235cf0, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=994e5ff1df7d6c9e, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b5f848dc8e96663c, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=dfc2c53ac3103eff, https://usegalaxy.eu/published/workflow?id=ec50dd6d56f50db1, https://usegalaxy.eu/published/workflow?id=ed0ad728cf21702b, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=09e8293456ee6d99, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1466?version=2 |
microbiome/metatranscriptomics, microbiome/metatranscriptomics-short |
|
groot |
groot |
GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples |
2024-05-14 |
https://github.com/will-rowe/groot |
1.1.2 |
groot |
1.1.2 |
Up-to-date |
Metagenomics |
Antimicrobial resistance prediction |
Antimicrobial resistance prediction |
Metagenomics, Microbiology, Genomics |
Metagenomics, Microbiology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot |
groot |
GROOT |
Indexed variation graphs for efficient and accurate resistome profiling. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
7 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
37 |
37 |
44 |
44 |
8 |
8 |
|
|
|
gtdb_to_taxdump |
gtdb_to_taxdump |
Convert GTDB taxonomy to NCBI taxdump format |
2024-08-25 |
https://github.com/nick-youngblut/gtdb_to_taxdump |
0.1.9 |
gtdb_to_taxdump |
0.1.9 |
Up-to-date |
Metagenomics |
Data handling, Mapping, Generation |
Data handling, Mapping, Generation |
Computational biology |
Computational biology |
iuc |
https://github.com/nick-youngblut/gtdb_to_taxdump |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump |
gtdb_to_taxdump |
gtdb_to_taxdump |
Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
27 |
27 |
1127 |
1127 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1127 |
1127 |
27 |
27 |
https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1 |
|
|
gtdbtk |
gtdbtk_classify_wf |
GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. |
2022-12-13 |
https://github.com/Ecogenomics/GTDBTk |
2.5.2 |
gtdbtk |
2.5.2 |
Up-to-date |
Metagenomics |
Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval |
Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval |
Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins |
Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk |
GTDB-Tk |
GTDB-Tk |
a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
462 |
462 |
3982 |
3982 |
305 |
305 |
1566 |
1566 |
177 |
177 |
1095 |
1095 |
15 |
15 |
1439 |
1439 |
8082 |
8082 |
959 |
959 |
https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=17d2e76147fc940c, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=8d229c0f58a07ebe, https://workflowhub.eu/workflows/1352?version=3 |
|
|
gtftobed12 |
gtftobed12 |
Convert GTF files to BED12 format |
2018-05-17 |
http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README |
357 |
ucsc-gtftogenepred |
482 |
To update |
Convert Formats |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3876 |
4805 |
9565 |
11802 |
3850 |
4091 |
9783 |
10498 |
436 |
457 |
2010 |
2130 |
213 |
214 |
432 |
460 |
24890 |
21790 |
9567 |
8375 |
https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=985044b4b2c51425, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.eu/published/workflow?id=a28c207730e7e13d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.eu/published/workflow?id=cc37667c2d1f9056, https://usegalaxy.eu/published/workflow?id=ccef778cfd9024d1, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=85aede91db0122e4, https://usegalaxy.org.au/published/workflow?id=a1b97364f84022cf, https://usegalaxy.org.au/published/workflow?id=a763e53653b10ce0, https://usegalaxy.org.au/published/workflow?id=ce7f6a1c824920e2, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=044c5ce43f2e1829, https://usegalaxy.org/published/workflow?id=2049d38325423cfe, https://usegalaxy.org/published/workflow?id=582f3de3971fc38c, https://usegalaxy.org/published/workflow?id=7022c4d9af725e5c, https://usegalaxy.org/published/workflow?id=8c4fcd4bd9d5a72d, https://usegalaxy.org/published/workflow?id=e33f6a058c5f57e5, https://usegalaxy.org/published/workflow?id=fb789920b057fe8d, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/1715?version=1, https://workflowhub.eu/workflows/878?version=1 |
transcriptomics/differential-isoform-expression, transcriptomics/ref-based |
|
gubbins |
gubbins |
Gubbins - bacterial recombination detection |
2017-06-22 |
|
3.2.1 |
gubbins |
3.4.3 |
To update |
Sequence Analysis |
Genotyping, Phylogenetic inference, Ancestral reconstruction |
Genotyping, Phylogenetic inference, Ancestral reconstruction |
Phylogeny, Genotype and phenotype, Whole genome sequencing |
Phylogeny, Genotype and phenotype, Whole genome sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins |
gubbins |
Gubbins |
Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
402 |
428 |
4731 |
5118 |
268 |
288 |
3847 |
4061 |
250 |
317 |
1977 |
2858 |
0 |
0 |
0 |
0 |
12037 |
10555 |
1033 |
920 |
|
|
|
gvcftools |
gvcftools_extract_variants |
gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf. |
2016-12-29 |
https://github.com/sequencing/gvcftools |
0.1 |
gvcftools |
0.17.0 |
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gwastools |
gwastools_manhattan_plot |
|
2019-10-07 |
https://bioconductor.org/packages/release/bioc/html/GWASTools.html |
0.1.0 |
bioconductor-gwastools |
1.52.0 |
To update |
Visualization, Variant Analysis |
Deposition, Analysis, Annotation |
Deposition, Analysis, Annotation |
GWAS study |
GWAS study |
iuc |
|
https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools |
gwastools |
GWASTools |
Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. |
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
26 |
26 |
26 |
26 |
6 |
6 |
https://usegalaxy.fr/published/workflow?id=1ad87b99f0cb828c |
|
|
halfdeep |
halfdeep |
HalfDeep: Automated detection of intervals covered at half depth by sequenced reads. |
2024-11-27 |
https://github.com/makovalab-psu/HalfDeep |
0.1.0 |
halfdeep |
0.1.0 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/halfdeep |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/halfdeep |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
52 |
52 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
52 |
52 |
5 |
5 |
|
|
|
hamronization |
hamronize_summarize, hamronize_tool |
Convert AMR gene detection tool output to hAMRonization specification format. |
2021-02-02 |
https://github.com/pha4ge/hAMRonization |
1.1.4 |
hamronization |
1.1.9 |
To update |
Sequence Analysis |
Data handling, Antimicrobial resistance prediction, Parsing |
Antimicrobial resistance prediction, Parsing |
Public health and epidemiology, Microbiology, Bioinformatics |
Public health and epidemiology, Microbiology, Bioinformatics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization |
hamronization |
hAMRonization |
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure |
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
254 |
254 |
18459 |
18459 |
1 |
1 |
20 |
20 |
1 |
1 |
21 |
21 |
6 |
6 |
191 |
191 |
18691 |
18691 |
262 |
262 |
https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/470?version=1 |
|
|
hapcut2 |
hapcut2 |
Robust and accurate haplotype assembly for diverse sequencing technologies |
2022-10-19 |
https://github.com/vibansal/HapCUT2 |
1.3.4 |
hapcut2 |
1.3.4 |
Up-to-date |
Assembly |
Haplotype mapping, Variant classification |
Haplotype mapping, Variant classification |
|
|
galaxy-australia |
https://github.com/galaxyproject/tools-iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 |
hapcut2 |
HapCUT2 |
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md |
|
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
131 |
131 |
0 |
0 |
0 |
0 |
131 |
131 |
6 |
6 |
|
|
|
hapog |
hapog |
Hapo-G - Haplotype-Aware Polishing of Genomes |
2022-09-16 |
https://github.com/institut-de-genomique/HAPO-G |
1.3.8 |
hapog |
1.3.8 |
Up-to-date |
Assembly |
Genome assembly, Optimisation and refinement |
Genome assembly, Optimisation and refinement |
Sequence assembly, Genomics |
Sequence assembly, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog |
hapog |
Hapo-G |
Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
94 |
94 |
677 |
677 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
36 |
36 |
392 |
392 |
1069 |
1069 |
130 |
130 |
|
|
|
happy |
som.py |
A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. |
2022-01-25 |
https://github.com/Illumina/hap.py |
0.3.14 |
hap.py |
0.3.15 |
To update |
Variant Analysis |
Variant calling, Sequence analysis, Genotyping |
Variant calling, Sequence analysis, Genotyping |
Genomics, DNA polymorphism |
Genomics, DNA polymorphism |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy |
hap.py |
hap.py |
This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
heinz |
heinz_bum, heinz, heinz_scoring, heinz_visualization |
An algorithm for identification of the optimal scoring subnetwork. |
2018-06-11 |
https://github.com/ls-cwi/heinz |
1.0 |
bioconductor-bionet |
1.66.0 |
To update |
Transcriptomics, Visualization, Statistics, Single Cell |
Pathway or network analysis |
Pathway or network analysis |
Genetics, Gene expression, Molecular interactions, pathways and networks |
Genetics, Gene expression, Molecular interactions, pathways and networks |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz |
heinz |
Heinz |
Tool for single-species active module discovery. |
|
0 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
4 |
123 |
160 |
823 |
1460 |
318 |
345 |
1490 |
1678 |
36 |
36 |
847 |
913 |
0 |
0 |
0 |
0 |
4051 |
3160 |
541 |
477 |
https://usegalaxy.eu/published/workflow?id=12c80c5b5e2305d8, https://usegalaxy.org.au/published/workflow?id=6a161c87d19a543c, https://workflowhub.eu/workflows/1677?version=1 |
transcriptomics/network-analysis-with-heinz |
|
hgvsparser |
hgvsparser |
Parsing and building variant descriptor strings compliant with the HGVS standard |
2024-06-07 |
https://github.com/VariantEffect/hgvsParseR/tree/master |
0.1.0 |
r-base |
|
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
6353 |
6353 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6353 |
6353 |
2 |
2 |
|
|
|
hicexplorer |
hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hicbuildmatrixmicroc, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations |
HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. |
2017-08-24 |
https://github.com/deeptools/HiCExplorer |
3.7.6 |
hicexplorer |
3.7.6 |
Up-to-date |
Sequence Analysis, Visualization |
|
|
|
|
bgruening |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer |
|
|
|
|
0 |
38 |
39 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
13 |
0 |
0 |
0 |
0 |
0 |
0 |
33 |
35 |
33 |
354 |
633 |
40441 |
75024 |
55 |
55 |
2146 |
2146 |
27 |
27 |
5559 |
5584 |
1 |
1 |
2 |
2 |
82756 |
48148 |
716 |
437 |
https://usegalaxy.eu/published/workflow?id=2f053b615d9788bf, https://usegalaxy.eu/published/workflow?id=5cb54278075696ca, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1610?version=1, https://workflowhub.eu/workflows/1847?version=1 |
epigenetics/hicexplorer |
|
hicstuff |
hicstuff_pipeline |
A toolkit to generate and manipulate Hi-C matrices |
2022-11-25 |
https://github.com/koszullab/hicstuff |
3.2.4 |
hicstuff |
3.2.4 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
hifiasm |
hifiasm |
A fast haplotype-resolved de novo assembler |
2024-07-11 |
https://github.com/chhylp123/hifiasm |
0.25.0 |
hifiasm |
0.25.0 |
Up-to-date |
Assembly |
|
|
|
|
bgruening |
https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
803 |
803 |
2713 |
2713 |
585 |
585 |
2136 |
2136 |
187 |
187 |
3817 |
3817 |
51 |
51 |
183 |
183 |
8849 |
8849 |
1626 |
1626 |
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assembly/hifi-assembly, assembly/vgp_genome_assembly |
|
hifiasm_meta |
hifiasm_meta |
A hifiasm fork for metagenome assembly using Hifi reads. |
2023-01-18 |
https://github.com/xfengnefx/hifiasm-meta |
0.3.1 |
hifiasm_meta |
hamtv0.3.1 |
To update |
Metagenomics |
Sequence assembly |
Sequence assembly |
Sequence assembly, Metagenomics |
Sequence assembly, Metagenomics |
galaxy-australia |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta |
hifiasm-meta |
Hifiasm-meta |
Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
40 |
40 |
229 |
229 |
0 |
0 |
0 |
0 |
16 |
16 |
368 |
368 |
0 |
0 |
0 |
0 |
597 |
597 |
56 |
56 |
|
|
|
hisat2 |
hisat2 |
HISAT2 is a fast and sensitive spliced alignment program. |
2015-09-29 |
http://ccb.jhu.edu/software/hisat2/ |
2.2.1 |
hisat2 |
2.2.1 |
Up-to-date |
Assembly |
Sequence alignment |
Sequence alignment |
RNA-seq |
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 |
hisat2 |
HISAT2 |
Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
12585 |
14119 |
420921 |
467443 |
28716 |
40390 |
729970 |
1057729 |
5266 |
6509 |
88398 |
111027 |
1273 |
1277 |
52049 |
52136 |
1688335 |
1291338 |
62295 |
47840 |
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proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation, transcriptomics/de-novo, transcriptomics/minerva-pathways, transcriptomics/rna-seq-reads-to-counts, transcriptomics/srna |
|
hivclustering |
hivclustering |
Infers transmission networks from pairwise distances inferred by tn93 |
2018-06-06 |
https://pypi.org/project/hivclustering/ |
1.3.1 |
python-hivclustering |
1.8.0 |
To update |
Next Gen Mappers |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
hmmer3 |
hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer |
HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). |
2015-02-16 |
http://hmmer.org/ |
3.4 |
hmmer |
3.4 |
Up-to-date |
Sequence Analysis |
Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search |
Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search |
Sequence analysis, Sequence sites, features and motifs, Gene and protein families |
Sequence analysis, Sequence sites, features and motifs, Gene and protein families |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 |
hmmer3 |
HMMER3 |
This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. |
|
0 |
12 |
12 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
12 |
380 |
403 |
36302 |
43262 |
0 |
0 |
0 |
0 |
83 |
84 |
4731 |
4887 |
97 |
97 |
540 |
543 |
48692 |
41573 |
584 |
560 |
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|
|
htseq_count |
htseq_count |
Count aligned reads (SAM/BAM) that overlap genomic features (GFF) |
2016-09-15 |
https://readthedocs.org/projects/htseq/ |
2.0.9 |
htseq |
2.0.9 |
Up-to-date |
Genomic Interval Operations, SAM, Sequence Analysis, RNA |
Nucleic acid sequence analysis |
Nucleic acid sequence analysis |
Sequence analysis |
Sequence analysis |
lparsons |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count |
htseq |
HTSeq |
Python framework to process and analyse high-throughput sequencing (HTS) data |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3989 |
5200 |
135497 |
191189 |
11193 |
18984 |
254054 |
434409 |
2158 |
3031 |
21954 |
36591 |
552 |
555 |
16740 |
16789 |
678978 |
428245 |
27770 |
17892 |
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|
|
humann |
humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways |
HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution |
2021-05-12 |
http://huttenhower.sph.harvard.edu/humann |
3.9 |
humann |
3.9 |
Up-to-date |
Metagenomics |
Species frequency estimation, Taxonomic classification, Phylogenetic analysis |
Species frequency estimation, Taxonomic classification, Phylogenetic analysis |
Metagenomics, Phylogenomics |
Metagenomics, Phylogenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann |
humann |
humann |
HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” |
|
0 |
10 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
0 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
10 |
10 |
795 |
795 |
52483 |
52483 |
123 |
123 |
3171 |
3171 |
122 |
122 |
4812 |
4812 |
17 |
17 |
987 |
987 |
61453 |
61453 |
1057 |
1057 |
https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0, https://usegalaxy.eu/published/workflow?id=23dd2253da51e22e, https://usegalaxy.eu/published/workflow?id=3118d383c81cf805, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=5ce8a472e6e95c60, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=a7a6d8ecc2795f58, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.fr/published/workflow?id=fd733565098d76c9, https://workflowhub.eu/workflows/1447?version=2, https://workflowhub.eu/workflows/1456?version=2, https://workflowhub.eu/workflows/1466?version=2 |
microbiome/metatranscriptomics, microbiome/metatranscriptomics-short |
|
hybpiper |
hybpiper |
Analyse targeted sequence capture data |
2023-08-30 |
https://github.com/mossmatters/HybPiper |
2.1.6 |
hybpiper |
2.3.3 |
To update |
Sequence Analysis, Phylogenetics |
Sequence trimming, Sequence assembly, Read mapping |
Sequence trimming, Sequence assembly, Read mapping |
Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics |
Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper |
HybPiper |
HybPiper |
Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
9 |
1679 |
1679 |
0 |
0 |
0 |
0 |
6 |
6 |
258 |
258 |
0 |
0 |
0 |
0 |
1937 |
1937 |
15 |
15 |
|
|
|
hyphy |
hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary |
Hypothesis Testing using Phylogenies |
2018-06-08 |
http://www.hyphy.org |
2.5.47 |
hyphy |
2.5.81 |
To update |
Phylogenetics |
Statistical calculation |
Statistical calculation |
Phylogeny, Small molecules, Molecular interactions, pathways and networks |
Phylogeny, Small molecules, Molecular interactions, pathways and networks |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy |
HyPhy |
HyPhy |
Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. |
|
0 |
2 |
17 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
17 |
12 |
88 |
94 |
11584 |
12537 |
78 |
108 |
4798 |
8431 |
33 |
42 |
815 |
909 |
3 |
5 |
22 |
27 |
21904 |
17219 |
249 |
202 |
https://usegalaxy.eu/published/workflow?id=1d40d6deb2da04cc, https://usegalaxy.eu/published/workflow?id=e7f03b4bd9b3d6fd, https://usegalaxy.fr/published/workflow?id=297b71156b297a73, https://usegalaxy.org.au/published/workflow?id=42137e36791652bc, https://usegalaxy.org/published/workflow?id=2d1ca299c1b058f6, https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e |
|
|
hypo |
hypo |
Super Fast & Accurate Polisher for Long Read Genome Assemblies |
2021-11-15 |
https://github.com/kensung-lab/hypo |
1.0.3 |
hypo |
1.0.3 |
Up-to-date |
Assembly |
Optimisation and refinement, Genome assembly |
Optimisation and refinement, Genome assembly |
Sequence assembly, Genomics |
Sequence assembly, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo |
HyPo |
HyPo |
HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
107 |
107 |
575 |
575 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
575 |
575 |
107 |
107 |
https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://workflowhub.eu/workflows/788?version=1, https://workflowhub.eu/workflows/789?version=1 |
|
|
icescreen |
icescreen |
identification of ICEs and IMEs in Bacillota genomes. |
2022-01-04 |
https://forgemia.inra.fr/ices_imes_analysis/icescreen |
1.3.3 |
icescreen |
1.3.3 |
Up-to-date |
Genome annotation |
Database search, Protein feature detection |
Database search, Protein feature detection |
Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation |
Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen |
icescreen |
ICEscreen |
A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
153 |
153 |
4 |
4 |
15 |
15 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
168 |
168 |
7 |
7 |
|
|
|
idba |
idba_hybrid, idba_tran, idba_ud |
Wrappers for the idba assembler variants. |
2018-04-26 |
https://i.cs.hku.hk/~alse/hkubrg/projects/index.html |
|
idba |
1.1.3 |
To update |
Assembly |
Sequence assembly |
Sequence assembly |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud |
idba |
IDBA |
A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. |
|
0 |
0 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
106 |
126 |
944 |
1353 |
146 |
169 |
1199 |
1700 |
0 |
0 |
0 |
0 |
1 |
1 |
3 |
3 |
3056 |
2146 |
296 |
253 |
|
|
|
idr |
idr |
Galaxy wrappers for the IDR package from Nathan Boleu |
2017-08-21 |
https://github.com/nboley/idr |
2.0.3 |
idr |
2.0.4.2 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
124 |
147 |
2665 |
3214 |
209 |
231 |
1828 |
2058 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5272 |
4493 |
378 |
333 |
https://usegalaxy.eu/published/workflow?id=3817cfbab7b39ee1, https://usegalaxy.org/published/workflow?id=59d34b4f0178120b |
epigenetics/cut_and_run |
|
idr_download_by_ids |
idr_download_by_ids |
Image Data Resource downloading tool |
2020-02-04 |
https://idr.openmicroscopy.org |
0.45 |
omero-py |
5.11.1 |
To update |
Data Source |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
37 |
46 |
232 |
457 |
0 |
0 |
0 |
0 |
1 |
1 |
445 |
445 |
0 |
0 |
0 |
0 |
902 |
677 |
47 |
38 |
https://usegalaxy.eu/published/workflow?id=7d7550ce7004d71e, https://workflowhub.eu/workflows/1505?version=1, https://workflowhub.eu/workflows/1528?version=1, https://workflowhub.eu/workflows/41?version=2 |
imaging/2D-spot-detection, imaging/tutorial-CP |
|
iedb_api |
iedb_api |
Get epitope binding predictions from IEDB-API |
2020-02-26 |
http://tools.immuneepitope.org/main/tools-api/ |
2.15.2 |
python |
|
To update |
Data Source, Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
38 |
43 |
3543 |
4425 |
6 |
6 |
33 |
33 |
3 |
3 |
234 |
234 |
0 |
0 |
0 |
0 |
4692 |
3810 |
52 |
47 |
https://usegalaxy.eu/published/workflow?id=9b4e6c5f2c1babce, https://usegalaxy.eu/published/workflow?id=c3f2350f0be2d9c9, https://usegalaxy.org.au/published/workflow?id=832a30759469d3fe, https://usegalaxy.org/published/workflow?id=d0847ce8261eb922, https://workflowhub.eu/workflows/1406?version=1, https://workflowhub.eu/workflows/1789?version=1 |
proteomics/neoantigen-hla-binding-novel-peptides |
|
infercnv |
infercnv |
Infer Copy Number Variation from Single-Cell RNA-Seq Data |
2024-07-23 |
https://github.com/broadinstitute/infercnv |
1.22.0 |
bioconductor-infercnv |
1.22.0 |
Up-to-date |
Transcriptomics, Variant Analysis, Single Cell |
Heat map generation, Expression analysis, RNA-Seq analysis, Copy number variation detection, Clustering |
Heat map generation, RNA-Seq analysis, Copy number variation detection, Clustering |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv |
infercnv |
InferCNV |
Inferring copy number alterations from tumor single cell RNA-Seq data |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
31 |
31 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
31 |
31 |
7 |
7 |
|
|
|
instrain |
instrain_compare, instrain_profile |
InStrain is a tool for analysis of co-occurring genome populations from metagenomes |
2021-08-11 |
https://instrain.readthedocs.io/en/latest/# |
1.5.3 |
instrain |
1.10.0 |
To update |
Metagenomics |
SNP detection, Genome comparison |
SNP detection, Genome comparison |
Mapping, Metagenomics |
Mapping, Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain |
instrain |
InStrain |
InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
22 |
22 |
208 |
208 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
208 |
208 |
22 |
22 |
|
|
|
integronfinder |
integron_finder |
"IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching" |
2022-09-22 |
https://github.com/gem-pasteur/Integron_Finder |
2.0.5 |
integron_finder |
2.0.6 |
To update |
Sequence Analysis |
Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation |
Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation |
Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis |
Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder |
integron_finder |
Integron Finder |
A tool to detect Integron in DNA sequences. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
390 |
390 |
64428 |
64428 |
252 |
252 |
7167 |
7167 |
132 |
132 |
12061 |
12061 |
34 |
34 |
2504 |
2504 |
86160 |
86160 |
808 |
808 |
https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=b1afc8d1e81fc904, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.eu/published/workflow?id=fd63b9884fda75b6, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=3940186d02245b1d, https://usegalaxy.org/published/workflow?id=49da012e2839c046, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=649cdc14757e5755, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=12, https://workflowhub.eu/workflows/1513?version=1 |
genome-annotation/bacterial-genome-annotation |
|
intermine_galaxy_exchange |
galaxy_intermine_exchange |
InterMine Exporter |
2018-07-01 |
https://github.com/intermine |
0.0.1 |
coreutils |
8.25 |
To update |
Convert Formats |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
7 |
14 |
15 |
53 |
10 |
17 |
21 |
90 |
1 |
1 |
159 |
159 |
0 |
0 |
0 |
0 |
302 |
195 |
32 |
18 |
https://workflowhub.eu/workflows/1398?version=1 |
galaxy-interface/intermine |
|
interproscan |
interproscan |
Interproscan queries the interpro database and provides annotations. |
2021-11-15 |
http://www.ebi.ac.uk/Tools/pfa/iprscan5/ |
5.59-91.0 |
interproscan |
5.59_91.0 |
To update |
Sequence Analysis |
Sequence motif recognition, Protein feature detection |
Sequence motif recognition, Protein feature detection |
Gene and protein families, Sequence analysis |
Gene and protein families, Sequence analysis |
bgruening |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan |
interproscan_ebi |
InterProScan (EBI) |
Scan sequences against the InterPro protein signature databases. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2350 |
2550 |
44154 |
69658 |
486 |
486 |
3914 |
3914 |
799 |
804 |
13188 |
13204 |
144 |
144 |
9435 |
9435 |
96211 |
70691 |
3984 |
3779 |
https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0b9071d5dfa38559, https://usegalaxy.eu/published/workflow?id=2d2862b48918b22f, https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a95556ec171d405, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.eu/published/workflow?id=df7d9943423549df, https://usegalaxy.eu/published/workflow?id=f62d7c0c7cc57eb6, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=876163677f1cccc4, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org/published/workflow?id=92613e1e0b13aa0a, https://usegalaxy.org/published/workflow?id=c451e4dca9981ed0, https://workflowhub.eu/workflows/1262?version=1, https://workflowhub.eu/workflows/1521?version=1, https://workflowhub.eu/workflows/1525?version=1, https://workflowhub.eu/workflows/1663?version=1, https://workflowhub.eu/workflows/754?version=1, https://workflowhub.eu/workflows/755?version=1 |
ecology/marine_omics_bgc, genome-annotation/funannotate, genome-annotation/functional |
|
interval2maf |
Interval2Maf1 |
Extract MAF blocks given a set of intervals |
2020-07-14 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ |
1.0.1+galaxy1 |
bx-python |
0.14.0 |
To update |
Genomic Interval Operations |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf |
bx-python |
bx-python |
Tools for manipulating biological data, particularly multiple sequence alignments. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
6 |
10 |
21 |
107 |
82 |
1259 |
711 |
19652 |
2 |
2 |
23 |
31 |
1 |
1 |
7 |
7 |
19797 |
762 |
1272 |
91 |
https://usegalaxy.org/published/workflow?id=7cae620eea6326af, https://usegalaxy.org/published/workflow?id=d3a69b0b826331ef |
|
|
intervene |
intervene_pairwise, intervene_upset |
Create pairwise and upset plots |
2018-09-11 |
https://intervene.readthedocs.io |
0.6.5 |
intervene |
0.6.5 |
Up-to-date |
Statistics |
Sequence comparison, Sequence visualisation |
Sequence comparison, Sequence visualisation |
Computational biology |
Computational biology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene |
intervene |
Intervene |
Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
270 |
284 |
1959 |
2152 |
274 |
295 |
4435 |
4873 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7025 |
6394 |
579 |
544 |
|
|
|
ipfp_normalisation |
ipfp_norm |
Normalisation algorithm used to adjust matrices iteratively to satisfy specific row and column sum constraints while preserving the data structure. |
2025-01-28 |
https://isoquac.net/ |
0.1.0+galaxy0 |
numpy |
|
To update |
Statistics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ipfp_normalisation |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ipfp_normalisation |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
iqtree |
iqtree |
Efficient phylogenomic software by maximum likelihood |
2017-09-26 |
http://www.iqtree.org/ |
2.4.0 |
iqtree |
3.0.1 |
To update |
Phylogenetics |
Phylogenetic analysis, Sequence analysis |
Phylogenetic analysis, Sequence analysis |
Phylogenetics |
Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree |
iqtree |
iqtree |
A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2588 |
2695 |
44137 |
45132 |
2814 |
3035 |
34112 |
35898 |
1165 |
1337 |
16490 |
18756 |
17 |
17 |
229 |
229 |
100015 |
94968 |
7084 |
6584 |
https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.eu/published/workflow?id=d5cf994c03a60fa4, https://usegalaxy.eu/published/workflow?id=e97b938ca4723827, https://usegalaxy.org.au/published/workflow?id=3242ec69dec6e13f, https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=23212ae74fc2d2b5, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=78d8b738f5715a8a, https://usegalaxy.org/published/workflow?id=952b83e52f7d7cff, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://usegalaxy.org/published/workflow?id=9c4038fa15af6995, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/1559?version=1, https://workflowhub.eu/workflows/1839?version=1, https://workflowhub.eu/workflows/359?version=1 |
evolution/abc_intro_phylo, sequence-analysis/tapscan-streptophyte-algae, variant-analysis/aiv-analysis |
|
irissv |
irissv |
Refine insertion sequences |
2021-01-17 |
https://github.com/mkirsche/Iris |
1.0.5 |
samtools |
1.22.1 |
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tools/irissv/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
8 |
8 |
30 |
30 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
30 |
30 |
8 |
8 |
|
|
|
irma |
irma |
Iterative Refinement Meta-Assembler (IRMA) is a tool to construct assembly of highly variable RNA viruses. |
2024-11-09 |
https://wonder.cdc.gov/amd/flu/irma/irma.html |
1.2.0 |
irma |
1.2.0 |
Up-to-date |
Sequence Analysis |
Mapping assembly |
Mapping assembly |
|
|
iuc |
https://github.com/aaronKol/tools-iuc/tree/main/tools/irma |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/irma |
irma-virus |
IRMA |
Iterative Refinement Meta-Assembler for robust assembly, variant calling, and phasing of highly variable RNA virus sequencing data |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
16450 |
16450 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16450 |
16450 |
12 |
12 |
|
|
|
isoformswitchanalyzer |
isoformswitchanalyzer |
Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. |
2022-12-17 |
https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html |
1.20.0 |
bioconductor-isoformswitchanalyzer |
2.6.0 |
To update |
Transcriptomics, RNA, Statistics |
Sequence comparison, Sequence analysis |
Sequence comparison, Sequence analysis |
Computational biology, Gene transcripts |
Computational biology, Gene transcripts |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer |
IsoformSwitchAnalyzeR |
IsoformSwitchAnalyzeR |
Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
107 |
107 |
2460 |
2460 |
126 |
126 |
2434 |
2434 |
21 |
21 |
1287 |
1287 |
2 |
2 |
12 |
12 |
6193 |
6193 |
256 |
256 |
https://usegalaxy.eu/published/workflow?id=11eba1b28ec87963, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://workflowhub.eu/workflows/1688?version=1 |
transcriptomics/differential-isoform-expression |
|
ivar |
ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants |
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing |
2020-03-21 |
https://github.com/andersen-lab/ivar |
1.4.4 |
ivar |
1.4.4 |
Up-to-date |
Sequence Analysis |
Primer removal |
Primer removal |
Virology |
Virology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar |
andersen-lab_ivar |
iVar |
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. |
|
0 |
5 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
5 |
1081 |
1087 |
1414011 |
1417441 |
1310 |
1330 |
147224 |
148408 |
374 |
379 |
43473 |
54915 |
19 |
19 |
7502 |
7502 |
1628266 |
1612210 |
2815 |
2784 |
https://usegalaxy.eu/published/workflow?id=0189bab68f828d86, https://usegalaxy.eu/published/workflow?id=0be293debca8fb9b, https://usegalaxy.eu/published/workflow?id=0f6a7bd5362e4a2b, https://usegalaxy.eu/published/workflow?id=2573209308aaad23, https://usegalaxy.eu/published/workflow?id=2d9d4445a1871230, https://usegalaxy.eu/published/workflow?id=3f046b416b10b871, https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a, https://usegalaxy.eu/published/workflow?id=40d2c7ac42bd5302, https://usegalaxy.eu/published/workflow?id=429ae28a178cd07c, https://usegalaxy.eu/published/workflow?id=45fc2dada84d251e, https://usegalaxy.eu/published/workflow?id=476db04368d5e90c, https://usegalaxy.eu/published/workflow?id=4b4bfc79205d83f1, https://usegalaxy.eu/published/workflow?id=4c75ab0be3c56494, https://usegalaxy.eu/published/workflow?id=4d97068a725c975c, https://usegalaxy.eu/published/workflow?id=4f40ae432d8a4259, https://usegalaxy.eu/published/workflow?id=529f30e894beacc2, 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variant-analysis/aiv-analysis, variant-analysis/pox-tiled-amplicon |
|
iwtomics |
iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot |
Interval-Wise Testing for Omics Data |
2017-06-08 |
https://bioconductor.org/packages/release/bioc/html/IWTomics.html |
1.0.0 |
bioconductor-iwtomics |
1.30.0 |
To update |
Statistics |
Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison |
Differential gene expression analysis, Peak calling, Genome annotation, Comparison |
Statistics and probability |
Statistics and probability |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics |
iwtomics |
IWTomics |
Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset. |
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0 |
3 |
3 |
0 |
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0 |
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0 |
0 |
0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
9 |
13 |
644 |
760 |
14 |
34 |
32 |
252 |
5 |
5 |
478 |
518 |
0 |
0 |
0 |
0 |
1530 |
1154 |
52 |
28 |
https://workflowhub.eu/workflows/1719?version=1 |
statistics/iwtomics |
|
jasminesv |
jasminesv |
Merge structural variants across samples |
2021-01-17 |
https://github.com/mkirsche/Jasmine/ |
1.0.11 |
jasminesv |
1.1.5 |
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/jasminesv/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
15 |
15 |
94 |
94 |
25 |
25 |
62 |
62 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
156 |
156 |
40 |
40 |
|
|
|
jbrowse |
jbrowse_to_standalone, jbrowse |
JBrowse Genome Browser integrated as a Galaxy Tool |
2015-05-01 |
https://jbrowse.org |
1.16.11 |
jbrowse |
1.16.11 |
Up-to-date |
Sequence Analysis |
Genome visualisation |
Genome visualisation |
Genomics |
Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse |
jbrowse |
JBrowse |
Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
6793 |
7423 |
26043 |
28614 |
7372 |
7751 |
22125 |
23288 |
3208 |
4288 |
18197 |
22221 |
299 |
300 |
1697 |
1712 |
75835 |
68062 |
19762 |
17672 |
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assembly/chloroplast-assembly, assembly/ecoli_comparison, genome-annotation/amr-gene-detection, genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short, genome-annotation/annotation-with-prokka, genome-annotation/apollo, genome-annotation/apollo-euk, genome-annotation/bacterial-genome-annotation, genome-annotation/braker3, genome-annotation/comparison-braker-helixer-annotation, genome-annotation/funannotate, genome-annotation/helixer, sequence-analysis/mapping, sequence-analysis/sars-with-galaxy-on-anvil, variant-analysis/microbial-variants, variant-analysis/tb-variant-analysis, visualisation/jbrowse |
|
jcvi_gff_stats |
jcvi_gff_stats |
Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) |
2018-07-31 |
https://github.com/tanghaibao/jcvi |
0.8.4 |
jcvi |
1.5.7 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats |
|
|
|
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0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
761 |
859 |
3063 |
3622 |
833 |
902 |
2694 |
2899 |
611 |
616 |
1558 |
1578 |
49 |
49 |
439 |
439 |
8538 |
7754 |
2426 |
2254 |
https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=31bc2a44fb89aa89, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=6550f72070b24082, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.eu/published/workflow?id=8976041ef89e4548, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=49b253f75ab6f38f, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org.au/published/workflow?id=dd9272826e6dd98d, https://usegalaxy.org.au/published/workflow?id=e263fcb6c98e231b, https://usegalaxy.org.au/published/workflow?id=ec7efff3d3249177, https://usegalaxy.org/published/workflow?id=4605309321799e9b, https://usegalaxy.org/published/workflow?id=65b4051e722228b8, https://usegalaxy.org/published/workflow?id=7fc8b2398b6f093f, https://usegalaxy.org/published/workflow?id=80a7124c40438cc9, https://usegalaxy.org/published/workflow?id=dbe08700353dfc43, https://usegalaxy.org/published/workflow?id=f4111a169255535c, https://workflowhub.eu/workflows/1255?version=3, https://workflowhub.eu/workflows/1323?version=1, https://workflowhub.eu/workflows/1500?version=1, https://workflowhub.eu/workflows/1504?version=1, https://workflowhub.eu/workflows/1549?version=1, https://workflowhub.eu/workflows/881?version=5 |
genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short, genome-annotation/helixer |
|
jellyfish |
jellyfish |
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA |
2021-04-07 |
https://github.com/gmarcais/Jellyfish |
|
kmer-jellyfish |
2.3.1 |
To update |
Assembly |
k-mer counting |
k-mer counting |
Sequence analysis, Genomics |
Sequence analysis, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish |
Jellyfish |
Jellyfish |
A command-line algorithm for counting k-mers in DNA sequence. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
369 |
369 |
4901 |
4901 |
0 |
0 |
0 |
0 |
87 |
87 |
1492 |
1492 |
35 |
35 |
1519 |
1519 |
7912 |
7912 |
491 |
491 |
https://usegalaxy.eu/published/workflow?id=bc32937d505135ab |
|
|
join_files_by_id |
join_files_by_id |
This tool will join datasets according to a column with identifier |
2017-05-31 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id |
1.0 |
r-data.table |
1.11.6 |
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
jq |
jq |
JQ is a lightweight and flexible command-line JSON processor |
2017-06-22 |
https://stedolan.github.io/jq/ |
1.0 |
jq |
1.5 |
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
65 |
72 |
510 |
2396 |
87 |
95 |
659 |
722 |
14 |
14 |
388 |
388 |
3 |
3 |
8 |
8 |
3514 |
1565 |
184 |
169 |
https://workflowhub.eu/workflows/245?version=1, https://workflowhub.eu/workflows/373?version=2, https://workflowhub.eu/workflows/374?version=1, https://workflowhub.eu/workflows/375?version=1 |
galaxy-interface/ncbi-sarf |
|
jvarkit |
jvarkit_wgscoverageplotter |
Jvarkit : Java utilities for Bioinformatics |
2021-02-11 |
https://lindenb.github.io/jvarkit/ |
20201223 |
jvarkit-wgscoverageplotter |
20201223 |
Up-to-date |
SAM |
|
|
|
|
iuc |
https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
748 |
748 |
10984 |
10984 |
1487 |
1487 |
15150 |
15150 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
26134 |
26134 |
2235 |
2235 |
https://usegalaxy.eu/published/workflow?id=cd3398e29f375d97, https://usegalaxy.org/published/workflow?id=3dbe754882a263cd |
variant-analysis/tb-variant-analysis |
|
kaiju |
kaiju_addtaxonnames, kaiju_mergeoutputs, kaiju_kaiju, kaiju_kaiju2krona, kaiju_kaiju2table |
taxonomic classification of high-throughput sequencing reads |
2025-04-22 |
https://github.com/bioinformatics-centre/kaiju |
1.10.1 |
kaiju |
1.10.1 |
Up-to-date |
Metagenomics |
Taxonomic classification |
Taxonomic classification |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju |
kaiju |
Kaiju |
Program for the taxonomic assignment of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from Bacteria, Archaea, Fungi, microbial eukaryotes and viruses. |
|
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
2 |
|
|
|
kallisto |
kallisto_pseudo, kallisto_quant |
kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. |
2017-08-04 |
https://pachterlab.github.io/kallisto/ |
0.48.0 |
kallisto |
0.51.1 |
To update |
Transcriptomics |
Gene expression profiling |
Gene expression profiling |
Transcriptomics, RNA-Seq, Gene expression |
Transcriptomics, RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto |
kallisto |
kallisto |
A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
892 |
996 |
31647 |
35827 |
2181 |
2848 |
76773 |
93407 |
210 |
242 |
6155 |
7133 |
17 |
17 |
564 |
564 |
136931 |
115139 |
4103 |
3300 |
https://usegalaxy.eu/published/workflow?id=385cc7df70d7916b, https://usegalaxy.eu/published/workflow?id=fd90652d475ed739, https://usegalaxy.org/published/workflow?id=08bdcecd1cb0bda3, https://usegalaxy.org/published/workflow?id=526b05cbffecbc85, https://usegalaxy.org/published/workflow?id=7d9bf3437e0a3d27, https://usegalaxy.org/published/workflow?id=c2c6779a8b1821e0 |
|
|
kc_align |
kc-align |
Kc-Align custom tool |
2020-02-20 |
https://github.com/davebx/kc-align |
1.0.2 |
kcalign |
1.0.2 |
Up-to-date |
Sequence Analysis |
Multiple sequence alignment |
Multiple sequence alignment |
Mapping |
Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align |
kc-align |
kc-align |
A fast and accurate tool for performing codon-aware multiple sequence alignments. Kc-Align is a codon-aware multiple aligner that uses Kalgin2 to produce in-frame gapped codon alignments for selection analysis of small genomes (mostly viral and some smaller bacterial genomes). Takes nucleotide seqeunces as inputs, converts them to their in-frame amino acid sequences, performs multiple alignment with Kalign, and then converts the alignments back to their original codon sequence while preserving the gaps. Produces three outputs: the gapped nucleotide alignments in FASTA format and in CLUSTAL format and the amino acid level alignment.Kc-Align will also attempt to detect any frameshift mutations in the input reads. If a frameshift is detected, that sequence will not be included in the multiple alignment and its ID will be printed to stdout. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
51 |
57 |
243 |
385 |
263 |
295 |
7653 |
8360 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8745 |
7896 |
352 |
314 |
https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e |
|
|
khmer |
khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median |
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more |
2015-03-24 |
https://khmer.readthedocs.org/ |
3.0.0a3 |
khmer |
3.0.0a3 |
Up-to-date |
Assembly, Next Gen Mappers |
Standardisation and normalisation, De-novo assembly |
Standardisation and normalisation, De-novo assembly |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer |
khmer |
khmer |
khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. |
|
0 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
8 |
98 |
116 |
1572 |
2262 |
169 |
185 |
1179 |
1564 |
25 |
25 |
2179 |
2179 |
0 |
0 |
0 |
0 |
6005 |
4930 |
326 |
292 |
|
|
|
king |
king |
Kinship-based INference for Gwas |
2021-11-16 |
http://people.virginia.edu/~wc9c/KING/ |
2.2.7 |
king |
2.2.7 |
Up-to-date |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/king |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
8 |
8 |
16 |
16 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
16 |
8 |
8 |
|
|
|
kleborate |
kleborate |
Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) |
2022-09-09 |
https://github.com/katholt/Kleborate/wiki |
2.3.2 |
kleborate |
3.2.4 |
To update |
Metagenomics |
Multilocus sequence typing, Genome assembly, Virulence prediction |
Multilocus sequence typing, Genome assembly, Virulence prediction |
Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing |
Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing |
iuc |
https://github.com/katholt/Kleborate |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate |
kleborate |
Kleborate |
Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
123 |
123 |
1479 |
1479 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1479 |
1479 |
123 |
123 |
|
|
|
kma |
kma_map |
Map with KMA |
2019-10-30 |
https://bitbucket.org/genomicepidemiology/kma |
1.5.1 |
kma |
1.6.6 |
To update |
Next Gen Mappers |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2 |
2 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
2 |
2 |
https://workflowhub.eu/workflows/407?version=1 |
|
|
kmer2stats |
kmer2stats |
A tool for creating data files for statistics based on kmers |
2025-04-16 |
https://github.com/SantaMcCloud/kmer2stats |
1.0.1 |
kmer2stats |
1.0.1 |
Up-to-date |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/kmer2stats/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
310 |
310 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
310 |
310 |
8 |
8 |
|
|
|
kofamscan |
kofamscan |
Gene function annotation tool based on KEGG Orthology and hidden Markov model |
2020-11-12 |
https://github.com/takaram/kofam_scan |
1.3.0 |
kofamscan |
1.3.0 |
Up-to-date |
Sequence Analysis |
Sequence analysis, Gene functional annotation |
Sequence analysis, Gene functional annotation |
Genomics, Structure analysis |
Genomics, Structure analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan |
kofamscan |
kofamscan |
KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
94 |
94 |
2904 |
2904 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
3 |
3 |
2907 |
2907 |
96 |
96 |
https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=d57d41e306241396 |
|
|
kraken |
kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken |
Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. |
2017-01-24 |
http://ccb.jhu.edu/software/kraken/ |
|
kraken |
1.1.1 |
To update |
Metagenomics |
Taxonomic classification |
Taxonomic classification |
Taxonomy, Metagenomics |
Taxonomy, Metagenomics |
devteam |
https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken |
kraken |
Kraken |
System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. |
|
0 |
5 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
5 |
5 |
5 |
1452 |
1453 |
75318 |
75385 |
2535 |
4229 |
59050 |
144905 |
904 |
1133 |
38078 |
44609 |
114 |
114 |
3720 |
3720 |
268619 |
176166 |
6929 |
5005 |
https://usegalaxy.org.au/published/workflow?id=b6bad1f167257248, https://usegalaxy.org/published/workflow?id=2ec3e326c51d3147, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=7321c6ad5425d347, https://usegalaxy.org/published/workflow?id=a89e1018a00b883c, https://usegalaxy.org/published/workflow?id=e0c33057ac2670ba, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be |
|
|
kraken2 |
kraken2 |
Kraken2 for taxonomic designation. |
2019-03-05 |
http://ccb.jhu.edu/software/kraken/ |
2.1.3 |
kraken2 |
2.14 |
To update |
Metagenomics |
Taxonomic classification |
Taxonomic classification |
Taxonomy, Metagenomics, Microbial ecology, Microbiology |
Taxonomy, Metagenomics, Microbial ecology |
iuc |
https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 |
kraken2 |
kraken2 |
Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.Any assumption that Kraken’s raw read assignments can be directly translated into species or strain-level abundance estimates is flawed. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN), estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree. (Lu, Jennifer et al. “Bracken: estimating species abundance in metagenomics data.”) |
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assembly/assembly-decontamination, ecology/bacterial-isolate-species-contamination-checking, microbiome/beer-data-analysis, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/taxonomic-profiling, sequence-analysis/quality-contamination-control, variant-analysis/tb-variant-analysis |
|
kraken_biom |
kraken_biom |
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) |
2022-09-03 |
https://github.com/smdabdoub/kraken-biom |
1.2.0 |
kraken-biom |
1.2.0 |
Up-to-date |
Metagenomics |
Genome annotation, Taxonomic classification |
Genome annotation, Taxonomic classification |
Metagenomics, Taxonomy |
Metagenomics, Taxonomy |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken-biom |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom |
kraken-biom |
kraken-biom |
Create BIOM-format tables from Kraken output |
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0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
857 |
857 |
4747 |
4747 |
47 |
47 |
150 |
150 |
95 |
95 |
963 |
963 |
9 |
9 |
17 |
17 |
5877 |
5877 |
1008 |
1008 |
https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=a0ea6fc756dd17ea, https://usegalaxy.eu/published/workflow?id=b67b5ecd3305f830, https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962, https://workflowhub.eu/workflows/1470?version=1 |
microbiome/taxonomic-profiling |
|
kraken_taxonomy_report |
kraken_taxonomy_report |
Kraken taxonomy report |
2016-06-01 |
https://github.com/blankenberg/Kraken-Taxonomy-Report |
0.0.3 |
biopython |
1.70 |
To update |
Metagenomics |
Visualisation, Classification |
Visualisation, Classification |
Metagenomics, Taxonomy |
Metagenomics, Taxonomy |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report |
Kraken-Taxonomy-Report |
Kraken-Taxonomy-Report |
view report of classification for multiple samples |
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1 |
1 |
1 |
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0 |
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0 |
0 |
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0 |
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0 |
0 |
0 |
0 |
1 |
1 |
1 |
1148 |
1155 |
5719 |
5735 |
1291 |
1717 |
5613 |
7684 |
148 |
148 |
587 |
587 |
10 |
10 |
25 |
25 |
14031 |
11944 |
3030 |
2597 |
https://usegalaxy.eu/published/workflow?id=2e5e6291cd112225, https://usegalaxy.eu/published/workflow?id=b659069edd9b1d4e |
|
|
krakentools |
krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa |
KrakenTools is a suite of scripts to be used alongside the Kraken |
2023-01-13 |
https://github.com/jenniferlu717/KrakenTools |
1.2.1 |
krakentools |
1.2.1 |
Up-to-date |
Metagenomics |
Visualisation, Aggregation |
Visualisation, Aggregation |
Taxonomy, Metagenomics |
Taxonomy, Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools |
krakentools |
KrakenTools |
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files |
|
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6 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
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6 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
1 |
2603 |
2603 |
161915 |
161915 |
1861 |
1861 |
40010 |
40010 |
488 |
488 |
18602 |
18602 |
64 |
64 |
5824 |
5824 |
226351 |
226351 |
5016 |
5016 |
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microbiome/beer-data-analysis, microbiome/diversity, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/taxonomic-profiling |
|
krocus |
krocus |
Predict MLST directly from uncorrected long reads |
2019-09-03 |
https://github.com/quadram-institute-bioscience/krocus |
1.0.1 |
krocus |
1.0.3 |
To update |
Sequence Analysis |
Multilocus sequence typing, k-mer counting |
Multilocus sequence typing, k-mer counting |
Public health and epidemiology |
Public health and epidemiology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus |
krocus |
krocus |
Predict MLST directly from uncorrected long reads |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
last |
last_al, last_db, last_split, last_train, last_maf_convert |
LAST finds similar regions between sequences. |
2020-06-17 |
http://last.cbrc.jp/ |
1205 |
last |
1642 |
To update |
Sequence Analysis |
Sequence alignment |
Sequence alignment |
Genomics, Comparative genomics |
Comparative genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/last |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/last |
last |
LAST |
Short read alignment program incorporating quality scores |
|
0 |
0 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
5 |
40 |
43 |
316 |
384 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
22 |
22 |
406 |
338 |
46 |
43 |
|
|
|
lastz |
lastz_wrapper_2, lastz_d_wrapper |
Galaxy wrappers for the Lastz and Lastz_d |
2018-02-12 |
https://github.com/lastz/lastz |
1.04.22 |
lastz |
1.04.52 |
To update |
Next Gen Mappers |
Sequence alignment, Read mapping |
Sequence alignment, Read mapping |
Genomics |
Genomics |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz |
lastz |
LASTZ |
A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
493 |
570 |
57942 |
85720 |
758 |
3548 |
154432 |
208919 |
149 |
206 |
14671 |
39255 |
13 |
14 |
4663 |
4664 |
338558 |
231708 |
4338 |
1413 |
https://usegalaxy.eu/published/workflow?id=0e492839192d26e0, https://usegalaxy.org.au/published/workflow?id=b808cd1c0090b068, https://usegalaxy.org/published/workflow?id=23212ae74fc2d2b5, https://workflowhub.eu/workflows/1638?version=1 |
assembly/ecoli_comparison |
|
lcrgenie |
lcrgenie |
Ligase Chain Reaction Genie |
2022-12-02 |
https://github.com/neilswainston/LCRGenie |
1.0.2 |
lcr_genie |
|
To update |
Synthetic Biology |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
legsta |
legsta |
Performs in silico Legionella pneumophila sequence based typing. |
2022-02-21 |
https://github.com/tseemann/legsta |
0.5.1 |
legsta |
0.5.1 |
Up-to-date |
Sequence Analysis |
Sequence analysis |
Sequence analysis |
Public health and epidemiology |
Public health and epidemiology |
iuc |
https://github.com/tseemann/legsta |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta |
legsta |
legsta |
Performs in silico Legionella pneumophila sequence based typing |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
13 |
13 |
134 |
134 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
134 |
134 |
13 |
13 |
|
|
|
length_and_gc_content |
length_and_gc_content |
Gets gene length and gc content from a fasta and a GTF file |
2016-11-13 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content |
0.1.2 |
r-optparse |
1.3.2 |
To update |
Fasta Manipulation, Statistics, RNA, Micro-array Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
973 |
1056 |
4962 |
5219 |
1265 |
1410 |
2651 |
3077 |
123 |
123 |
317 |
317 |
8 |
8 |
14 |
14 |
8627 |
7944 |
2597 |
2369 |
https://usegalaxy.eu/published/workflow?id=985044b4b2c51425, https://usegalaxy.eu/published/workflow?id=a28c207730e7e13d, https://usegalaxy.eu/published/workflow?id=e7e26967cf6cb8d8, https://usegalaxy.org.au/published/workflow?id=2cef9a1633e0a067, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1713?version=1, https://workflowhub.eu/workflows/1715?version=1 |
transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz |
|
lexicmap |
lexicmap_index, lexicmap_search |
LexicMap is a nucleotide sequence alignment tool for efficiently querying genomes. |
2025-06-16 |
https://github.com/shenwei356/LexicMap |
0.8.0 |
lexicmap |
0.8.0 |
Up-to-date |
Next Gen Mappers |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap |
lexicmap |
LexicMap |
LexicMap is a nucleotide sequence alignment tool for efficiently querying gene, plasmid, viral, or long-read sequences (>100 bp) against up to millions of prokaryotic genomes. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
limma_voom |
limma_voom |
Perform RNA-Seq differential expression analysis using limma voom pipeline |
2017-05-24 |
http://bioconductor.org/packages/release/bioc/html/limma.html |
3.58.1 |
bioconductor-limma |
3.62.1 |
To update |
Transcriptomics, RNA, Statistics |
RNA-Seq analysis |
RNA-Seq analysis |
Molecular biology, Genetics |
Molecular biology, Genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom |
limma |
limma |
Data analysis, linear models and differential expression for microarray data. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2902 |
3166 |
27013 |
30001 |
5247 |
6265 |
50381 |
59995 |
921 |
1003 |
10130 |
11326 |
26 |
26 |
329 |
329 |
101651 |
87853 |
10460 |
9096 |
https://usegalaxy.eu/published/workflow?id=09c77b6fc5add851, https://usegalaxy.eu/published/workflow?id=14226641bba951f3, https://usegalaxy.eu/published/workflow?id=1590085d315aa80e, https://usegalaxy.eu/published/workflow?id=1c1083b159e5bfb2, https://usegalaxy.eu/published/workflow?id=1d2e17a4f71f2455, https://usegalaxy.eu/published/workflow?id=21dd4bd16579fc12, https://usegalaxy.eu/published/workflow?id=227d97974573aaf2, https://usegalaxy.eu/published/workflow?id=263eed267aa3e76b, https://usegalaxy.eu/published/workflow?id=2a73d658446747de, https://usegalaxy.eu/published/workflow?id=2ecf737b53f77cf8, https://usegalaxy.eu/published/workflow?id=2f37c35ade97aa8d, https://usegalaxy.eu/published/workflow?id=2f7c04ad219a9d2d, https://usegalaxy.eu/published/workflow?id=3386856a60b35897, https://usegalaxy.eu/published/workflow?id=47f2c44d79896f08, https://usegalaxy.eu/published/workflow?id=48fe9c4de045d414, https://usegalaxy.eu/published/workflow?id=67e20e3082d24fbd, https://usegalaxy.eu/published/workflow?id=6d47a24218d08930, https://usegalaxy.eu/published/workflow?id=6fc2b9bea5b75a49, https://usegalaxy.eu/published/workflow?id=7036a6cf67d53bc7, https://usegalaxy.eu/published/workflow?id=732fa536cdc70c96, https://usegalaxy.eu/published/workflow?id=8ab363878cd34ef0, https://usegalaxy.eu/published/workflow?id=8bc1c3b9e665ea37, https://usegalaxy.eu/published/workflow?id=8f095e5b9594b098, https://usegalaxy.eu/published/workflow?id=9a83043d5e847318, https://usegalaxy.eu/published/workflow?id=ad3be77eb2e8c10e, https://usegalaxy.eu/published/workflow?id=bb4ecac751a94c79, https://usegalaxy.eu/published/workflow?id=c8deb8952abce1ec, https://usegalaxy.eu/published/workflow?id=d6eb0562d0036940, https://usegalaxy.eu/published/workflow?id=dd8b55e7768843b1, https://usegalaxy.eu/published/workflow?id=f28459c5b16549b7, https://usegalaxy.eu/published/workflow?id=f9ddc4dd9140b293, https://usegalaxy.eu/published/workflow?id=fa83e26e05418370, https://usegalaxy.eu/published/workflow?id=fe64d430d50faf0b, https://usegalaxy.eu/published/workflow?id=fe6c64676be56ee9, https://usegalaxy.org.au/published/workflow?id=bdb498b1f0e8944f, https://usegalaxy.org/published/workflow?id=07fdeadce7a6d5cb, https://usegalaxy.org/published/workflow?id=092be3cf6e40282c, https://usegalaxy.org/published/workflow?id=0a009cf9e88171f1, https://usegalaxy.org/published/workflow?id=0c052e50594f6d2d, https://usegalaxy.org/published/workflow?id=173ecc0c88090d0e, https://usegalaxy.org/published/workflow?id=204d0da8a023d7da, https://usegalaxy.org/published/workflow?id=228ae7f537a60226, https://usegalaxy.org/published/workflow?id=3f8e0395007c8e9e, https://usegalaxy.org/published/workflow?id=427fce51fd9508eb, https://usegalaxy.org/published/workflow?id=43c39bc86399188f, https://usegalaxy.org/published/workflow?id=5203bc68df3cf819, https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6, https://usegalaxy.org/published/workflow?id=6d0a3f36d2736087, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=93650de42fb8c015, https://usegalaxy.org/published/workflow?id=a89def2c2462674a, https://usegalaxy.org/published/workflow?id=aac2ae0419f7d515, https://usegalaxy.org/published/workflow?id=b094b6e1e7d48416, https://usegalaxy.org/published/workflow?id=b3823d276917baf0, https://usegalaxy.org/published/workflow?id=d5514e327878b531, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8, https://usegalaxy.org/published/workflow?id=dec0cf06fa059e65, https://workflowhub.eu/workflows/1684?version=1, https://workflowhub.eu/workflows/1703?version=1, https://workflowhub.eu/workflows/689?version=1 |
transcriptomics/minerva-pathways, transcriptomics/rna-seq-counts-to-genes |
|
lineagespot |
lineagespot |
Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) |
2023-07-04 |
https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html |
1.6.0 |
r-base |
|
To update |
Metagenomics, Sequence Analysis |
Variant calling |
Variant calling |
Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation |
Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot |
lineagespot |
lineagespot |
Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
4 |
4 |
39 |
39 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
39 |
39 |
4 |
4 |
|
|
|
links |
links |
Scaffold genome assemblies with long reads. |
2022-02-23 |
https://github.com/bcgsc/LINKS |
2.0.1 |
links |
2.0.1 |
Up-to-date |
Assembly |
Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming |
Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming |
Sequence assembly, Mapping, Sequencing |
Sequence assembly, Mapping, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/links |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/links |
links |
LINKS |
LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
181 |
181 |
940 |
940 |
0 |
0 |
0 |
0 |
87 |
87 |
778 |
778 |
0 |
0 |
0 |
0 |
1718 |
1718 |
268 |
268 |
|
|
|
lofreq |
lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi |
LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. |
2019-11-25 |
https://csb5.github.io/lofreq/ |
2.1.5 |
lofreq |
2.1.5 |
Up-to-date |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq |
|
|
|
|
0 |
5 |
5 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
4 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
5 |
2011 |
2074 |
3863858 |
4206633 |
4705 |
5024 |
450169 |
545066 |
673 |
701 |
127920 |
138242 |
52 |
54 |
8858 |
8924 |
4898865 |
4450805 |
7853 |
7441 |
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galaxy-interface/collections, introduction/galaxy-intro-ngs-data-managment, variant-analysis/sars-cov-2 |
|
lorikeet_spoligotype |
lorikeet_spoligotype |
Tools for M. tuberculosis DNA fingerprinting (spoligotyping) |
2018-05-07 |
https://github.com/AbeelLab/lorikeet |
20 |
lorikeet |
20 |
Up-to-date |
Sequence Analysis |
Sequence analysis, Genotyping |
Sequence analysis, Genotyping |
Genotype and phenotype |
Genotype and phenotype |
iuc |
https://github.com/AbeelLab/lorikeet |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet |
lorikeet |
lorikeet |
Tools for M. tuberculosis DNA fingerprinting (spoligotyping) |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
18 |
18 |
930 |
930 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
930 |
930 |
18 |
18 |
|
|
|
lumpy_sv |
lumpy_prep, lumpy_sv |
LUMPY - a general probabilistic framework for structural variant discovery |
2020-11-12 |
http://layerlab.org/software/ |
0.3.1 |
lumpy-sv |
0.3.1 |
Up-to-date |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/arq5x/lumpy-sv |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
0 |
139 |
139 |
2586 |
2586 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2586 |
2586 |
139 |
139 |
https://usegalaxy.eu/published/workflow?id=3d8aa05129e44fdf |
|
|
m6anet |
m6anet |
m6anet to detect m6A RNA modifications from nanopore data |
2023-10-25 |
https://m6anet.readthedocs.io/en/latest |
2.1.0 |
m6anet |
2.1.0 |
Up-to-date |
Sequence Analysis |
Quantification, Imputation, Gene expression profiling |
Quantification, Imputation, Gene expression profiling |
RNA-Seq, Transcriptomics, RNA, Machine learning |
RNA-Seq, Transcriptomics, RNA, Machine learning |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet |
m6Anet |
m6Anet |
Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
12 |
12 |
47 |
47 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
47 |
47 |
12 |
12 |
|
|
|
maaslin2 |
maaslin2 |
MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. |
2021-11-05 |
http://huttenhower.sph.harvard.edu/maaslin |
1.18.0 |
bioconductor-maaslin2 |
1.18.0 |
Up-to-date |
Metagenomics |
Filtering, Statistical calculation, Standardisation and normalisation, Visualisation |
Filtering, Standardisation and normalisation, Visualisation |
Metagenomics, Statistics and probability |
Metagenomics, Statistics and probability |
iuc |
https://github.com/biobakery/Maaslin2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 |
maaslin2 |
MaAsLin2 |
MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
100 |
100 |
3676 |
3676 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
4 |
4 |
3680 |
3680 |
102 |
102 |
https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=4ddf2ec5c460d622, https://usegalaxy.eu/published/workflow?id=e1296dbcf34499b0, https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962 |
|
|
macs2 |
macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak |
MACS - Model-based Analysis of ChIP-Seq |
2014-11-12 |
https://github.com/taoliu/MACS |
2.2.9.1 |
macs2 |
2.2.9.1 |
Up-to-date |
Sequence Analysis, Statistics |
Peak calling, Enrichment analysis, Gene regulatory network analysis |
Peak calling, Enrichment analysis, Gene regulatory network analysis |
ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites |
ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 |
macs |
MACS |
Model-based Analysis of ChIP-seq data. |
|
0 |
9 |
9 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
9 |
9 |
4539 |
5553 |
101779 |
121444 |
9434 |
15168 |
156715 |
260074 |
584 |
718 |
11876 |
14828 |
423 |
423 |
5024 |
5066 |
401412 |
275394 |
21862 |
14980 |
https://usegalaxy.eu/published/workflow?id=020f877513f2d0d1, https://usegalaxy.eu/published/workflow?id=0229f3f3835c2d53, https://usegalaxy.eu/published/workflow?id=02655d0e4af0ee0d, https://usegalaxy.eu/published/workflow?id=079e2a968d8e6176, https://usegalaxy.eu/published/workflow?id=07aefca769095616, https://usegalaxy.eu/published/workflow?id=0ae360bfbb3b2494, https://usegalaxy.eu/published/workflow?id=0fb12e3a127fc4be, https://usegalaxy.eu/published/workflow?id=1089e5c66dbcc1a3, https://usegalaxy.eu/published/workflow?id=111527fe542846af, https://usegalaxy.eu/published/workflow?id=117177b0c231dc55, https://usegalaxy.eu/published/workflow?id=133b299125ff9905, https://usegalaxy.eu/published/workflow?id=146cef3acb2eba75, https://usegalaxy.eu/published/workflow?id=14b9753269cd368f, https://usegalaxy.eu/published/workflow?id=16080c3c1488a8b5, https://usegalaxy.eu/published/workflow?id=166eb3f14feffa1b, https://usegalaxy.eu/published/workflow?id=1aa1344d6145ade3, 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epigenetics/atac-seq, epigenetics/cut_and_run, epigenetics/estrogen-receptor-binding-site-identification, epigenetics/formation_of_super-structures_on_xi, epigenetics/tal1-binding-site-identification, single-cell/scatac-preprocessing-tenx |
|
maf_stats |
maf_stats1 |
MAF Coverage statistics |
2020-08-12 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ |
1.0.2+galaxy0 |
|
|
To update |
Genomic Interval Operations |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
1 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
1 |
5 |
9 |
9 |
21 |
47 |
469 |
176 |
2482 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
2504 |
186 |
479 |
53 |
|
|
|
maf_tools |
ucsc_mafaddirows, ucsc_mafcoverage, ucsc_maffetch, ucsc_mafFilter, ucsc_maffrag, ucsc_maffrags |
Utilities for working with MAF (Multiple Alignment Format) files from UCSC |
2025-06-03 |
http://genome.ucsc.edu |
482 |
ucsc-mafaddirows |
482 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
mageck |
mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test |
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. |
2017-11-08 |
https://sourceforge.net/projects/mageck/ |
0.5.9.2 |
mageck |
0.5.9.5 |
To update |
Genome editing |
Genetic variation analysis |
Genetic variation analysis |
Genetics, Genetic variation, Genomics |
Genetics, Genetic variation, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck |
mageck |
MAGeCK |
Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. |
|
0 |
5 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
5 |
407 |
423 |
13575 |
15010 |
433 |
433 |
13443 |
13443 |
137 |
139 |
6643 |
7099 |
5 |
5 |
41 |
41 |
35593 |
33702 |
1000 |
982 |
https://workflowhub.eu/workflows/1534?version=1 |
genome-annotation/crispr-screen |
|
magicblast |
magicblast |
Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome |
2022-04-05 |
https://ncbi.github.io/magicblast/ |
1.7.0 |
magicblast |
1.7.0 |
Up-to-date |
Next Gen Mappers |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
230 |
230 |
8803 |
8803 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
8805 |
8805 |
231 |
231 |
|
|
|
maker |
maker, maker_map_ids |
MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. |
2017-10-04 |
http://www.yandell-lab.org/software/maker.html |
2.31.11 |
maker |
3.01.04 |
To update |
Sequence Analysis |
Genome annotation |
Genome annotation |
Genomics, DNA, Sequence analysis |
Genomics, DNA, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker |
maker |
MAKER |
Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
1323 |
1455 |
7332 |
8835 |
1701 |
1808 |
9536 |
10359 |
904 |
904 |
4968 |
4989 |
33 |
33 |
211 |
211 |
24394 |
22047 |
4200 |
3961 |
https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://usegalaxy.org/published/workflow?id=65b4051e722228b8, https://usegalaxy.org/published/workflow?id=dbe08700353dfc43, https://workflowhub.eu/workflows/1323?version=1, https://workflowhub.eu/workflows/1504?version=1, https://workflowhub.eu/workflows/1549?version=1 |
genome-annotation/annotation-with-maker, genome-annotation/annotation-with-maker-short |
|
malt_run |
malt_run |
Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. |
2021-11-12 |
https://github.com/husonlab/malt |
0.5.3 |
malt |
0.62 |
To update |
Next Gen Mappers |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
9 |
9 |
27 |
27 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
27 |
27 |
9 |
9 |
|
|
|
map_damage |
map_damage |
Tracks and quantifies specific ancient DNA damage patterns for authentication. |
2025-06-27 |
https://ginolhac.github.io/mapDamage/ |
2.2.3 |
mapdamage2 |
2.2.3 |
Up-to-date |
Sequence Analysis, Statistics, Visualization |
Sequencing quality control, Statistical calculation |
Sequencing quality control, Statistical calculation |
DNA, Sequencing |
DNA, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage |
mapdamage |
MapDamage |
Identify and quantify DNA damage patterns in ancient DNA. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
36 |
36 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
3 |
3 |
39 |
39 |
5 |
5 |
|
|
|
map_param_value |
map_param_value |
Map a parameter value to another value |
2022-10-13 |
|
0.2.0 |
|
|
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
163 |
163 |
6460 |
6460 |
216 |
216 |
5530 |
5530 |
10 |
10 |
321 |
321 |
4 |
4 |
30 |
30 |
12341 |
12341 |
393 |
393 |
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https://workflowhub.eu/workflows/625?version=26 |
|
|
maplot |
maplot |
Generate MA plots for visualizing data distributions using Plotly or Matplotlib. |
2025-04-17 |
https://github.com/galaxyproject/tools-iuc |
1.0.0 |
plotly |
|
To update |
Visualization, Statistics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/maplot |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
mapseq |
mapseq |
fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. |
2023-08-02 |
https://github.com/jfmrod/MAPseq |
2.1.1b |
perl |
|
To update |
Metagenomics |
k-mer counting |
k-mer counting |
Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs |
Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq |
mapseq |
MAPseq |
Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
64 |
64 |
9612 |
9612 |
24 |
24 |
434 |
434 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10046 |
10046 |
88 |
88 |
https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=fb806b88850f3427, https://usegalaxy.org/published/workflow?id=45f959d5bf505b15, https://usegalaxy.org/published/workflow?id=8151be18aab3a3c6, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1273?version=2, https://workflowhub.eu/workflows/1842?version=1, https://workflowhub.eu/workflows/1856?version=1 |
microbiome/mgnify-amplicon |
|
mash |
mash_dist, mash_paste, mash_screen, mash_sketch |
Fast genome and metagenome distance estimation using MinHash |
2018-12-07 |
https://github.com/marbl/Mash |
2.3 |
mash |
2.3 |
Up-to-date |
Metagenomics |
Sequence distance matrix generation |
Sequence distance matrix generation |
Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation |
Metagenomics, Statistics and probability, Sequence analysis, DNA mutation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash |
mash |
Mash |
Fast genome and metagenome distance estimation using MinHash. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
49 |
57 |
10768 |
10867 |
18 |
18 |
922 |
922 |
18 |
18 |
3187 |
3187 |
3 |
3 |
29 |
29 |
15005 |
14906 |
96 |
88 |
|
|
|
mashmap |
mashmap |
Fast local alignment boundaries |
2024-02-26 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap |
3.1.3 |
mashmap |
3.1.3 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
33 |
33 |
1329 |
1329 |
35 |
35 |
1094 |
1094 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2423 |
2423 |
68 |
68 |
https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=5aaa64ecdf9f7d6e, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=f9a73b39b2051af1 |
|
|
masigpro |
masigpro |
Identify significantly differential expression profiles in time-course microarray experiments |
2017-05-09 |
https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html |
1.49.3 |
coreutils |
8.25 |
To update |
Transcriptomics, RNA, Statistics |
Regression analysis |
Regression analysis |
Gene expression, Molecular genetics, Microarray experiment, RNA-Seq |
Gene expression, Microarray experiment, RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro |
masigpro |
maSigPro |
Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
35 |
44 |
200 |
628 |
75 |
88 |
522 |
630 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1258 |
722 |
132 |
110 |
|
|
|
maxbin2 |
maxbin2 |
clusters metagenomic contigs into bins |
2019-10-24 |
https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html |
|
maxbin2 |
2.2.7 |
To update |
Metagenomics |
Sequence assembly |
Sequence assembly |
Metagenomics, Sequence assembly, Microbiology |
Metagenomics, Sequence assembly, Microbiology |
mbernt |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 |
maxbin |
MaxBin |
Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
1 |
1 |
408 |
433 |
5244 |
5537 |
634 |
675 |
2694 |
2993 |
106 |
108 |
1135 |
1198 |
6 |
6 |
648 |
648 |
10376 |
9721 |
1222 |
1154 |
https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://workflowhub.eu/workflows/1352?version=3 |
|
|
mcl |
mcl |
The Markov Cluster Algorithm, a cluster algorithm for graphs |
2022-05-12 |
https://micans.org/mcl/man/mcl.html |
22.282 |
mcl |
22.282 |
Up-to-date |
Sequence Analysis |
Clustering, Network analysis, Gene regulatory network analysis |
Clustering, Gene regulatory network analysis |
Molecular interactions, pathways and networks |
Molecular interactions, pathways and networks |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/mcl |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl |
mcl |
MCL |
MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
18 |
18 |
153 |
153 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
153 |
153 |
18 |
18 |
|
|
|
medaka |
medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant |
Sequence correction provided by ONT Research |
2020-02-23 |
https://github.com/nanoporetech/medaka |
1.7.2 |
medaka |
2.1.1 |
To update |
Sequence Analysis |
Base-calling, Variant calling, Sequence assembly |
Base-calling, Variant calling, Sequence assembly |
Sequence assembly, Machine learning |
Sequence assembly, Machine learning |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka |
medaka |
Medaka |
medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. |
|
0 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
1728 |
1734 |
155538 |
156220 |
735 |
735 |
76698 |
76698 |
421 |
421 |
11622 |
11622 |
17 |
17 |
2659 |
2659 |
247199 |
246517 |
2907 |
2901 |
https://usegalaxy.eu/published/workflow?id=0f6a7bd5362e4a2b, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=2d9d4445a1871230, https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df, https://usegalaxy.eu/published/workflow?id=34a07bf6407510ef, https://usegalaxy.eu/published/workflow?id=429ae28a178cd07c, https://usegalaxy.eu/published/workflow?id=476db04368d5e90c, https://usegalaxy.eu/published/workflow?id=4d97068a725c975c, https://usegalaxy.eu/published/workflow?id=529f30e894beacc2, https://usegalaxy.eu/published/workflow?id=585c21b7b1d864fc, https://usegalaxy.eu/published/workflow?id=70d3ebf31940bfb3, https://usegalaxy.eu/published/workflow?id=77e5bbd317750915, https://usegalaxy.eu/published/workflow?id=7bdd9ad918edab0b, https://usegalaxy.eu/published/workflow?id=86cf02cc0868d238, https://usegalaxy.eu/published/workflow?id=b97532c398b821a2, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=cf8591391a17a914, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.fr/published/workflow?id=61235264d5d2f666, https://usegalaxy.fr/published/workflow?id=727cfdb7c79287d1, https://usegalaxy.fr/published/workflow?id=e3c04a30258421aa, https://usegalaxy.org.au/published/workflow?id=084bb76cf47d7060, https://usegalaxy.org.au/published/workflow?id=0c6f7bfc826433c4, https://usegalaxy.org.au/published/workflow?id=47ce6a2d30887637, https://usegalaxy.org.au/published/workflow?id=48a60965b6b3ff54, https://usegalaxy.org.au/published/workflow?id=4bc8ac41ecff7daf, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=705658f68ae73930, https://usegalaxy.org.au/published/workflow?id=888f8377eb6eabf2, https://usegalaxy.org.au/published/workflow?id=932bad88f8dc8d33, https://usegalaxy.org.au/published/workflow?id=ba7a9d4c857d26b7, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=ef8c22c2525063a2, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=3f252e077e0bcce5, https://usegalaxy.org/published/workflow?id=4357180d40560019, https://usegalaxy.org/published/workflow?id=48dafc35989f13b1, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://usegalaxy.org/published/workflow?id=88d0b64011c3148c, https://usegalaxy.org/published/workflow?id=953d9cbe05e632a8, https://usegalaxy.org/published/workflow?id=9adf8691809326e5, https://usegalaxy.org/published/workflow?id=c12e6b7896f8e114, https://usegalaxy.org/published/workflow?id=c7b2d2ccc4b0dec5, https://usegalaxy.org/published/workflow?id=cce88bc57b180d09, https://usegalaxy.org/published/workflow?id=d3428dd172a78102, https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/1062?version=1, https://workflowhub.eu/workflows/111?version=5, https://workflowhub.eu/workflows/1495?version=1, https://workflowhub.eu/workflows/1578?version=1, https://workflowhub.eu/workflows/226?version=1 |
assembly/largegenome, microbiome/pathogen-detection-from-nanopore-foodborne-data |
|
megahit |
megahit |
An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. |
2017-09-22 |
https://github.com/voutcn/megahit |
1.2.9 |
megahit |
1.2.9 |
Up-to-date |
Sequence Analysis, Assembly, Metagenomics |
Genome assembly |
Genome assembly |
Metagenomics, Sequencing, Ecology, Sequence assembly |
Metagenomics, Sequencing, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit |
megahit |
MEGAHIT |
Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
1 |
1 |
2052 |
2197 |
22340 |
24371 |
2823 |
2929 |
23973 |
24874 |
615 |
632 |
9338 |
9643 |
54 |
54 |
1387 |
1387 |
60275 |
57038 |
5812 |
5544 |
https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1524b189069b42a5, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=534f5fc25bc887ca, https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3, https://usegalaxy.eu/published/workflow?id=7d84b0419296857d, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=b37800d990cceb83, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://usegalaxy.eu/published/workflow?id=d4a95588e6e50893, https://usegalaxy.eu/published/workflow?id=f141db5179ea8422, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://workflowhub.eu/workflows/1352?version=3, https://workflowhub.eu/workflows/1390?version=2, https://workflowhub.eu/workflows/1480?version=1, https://workflowhub.eu/workflows/1631?version=1, https://workflowhub.eu/workflows/1634?version=1 |
assembly/metagenomics-assembly, microbiome/metagenomics-assembly, microbiome/metagenomics-binning |
|
megahit_contig2fastg |
megahit_contig2fastg |
A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) |
2018-11-09 |
https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp |
1.1.3 |
megahit |
1.2.9 |
To update |
Sequence Analysis, Assembly, Metagenomics |
Genome assembly |
Genome assembly |
Metagenomics, Sequencing, Ecology, Sequence assembly |
Metagenomics, Sequencing, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg |
megahit |
MEGAHIT |
Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
200 |
212 |
763 |
862 |
113 |
113 |
338 |
338 |
33 |
33 |
150 |
150 |
6 |
6 |
80 |
80 |
1430 |
1331 |
364 |
352 |
https://usegalaxy.eu/published/workflow?id=62c47e3c9d4f3aa3, https://workflowhub.eu/workflows/1390?version=2, https://workflowhub.eu/workflows/1634?version=1 |
assembly/metagenomics-assembly, microbiome/metagenomics-assembly |
|
megan |
megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma |
MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). |
2021-11-24 |
https://github.com/husonlab/megan-ce |
6.21.7 |
megan |
6.25.10 |
To update |
Sequence Analysis |
Sequence analysis, Taxonomic classification |
Sequence analysis, Taxonomic classification |
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan |
megan |
MEGAN |
Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzerÂť) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. |
|
0 |
1 |
7 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
0 |
250 |
250 |
5164 |
5164 |
0 |
0 |
0 |
0 |
5 |
5 |
72 |
72 |
3 |
3 |
4 |
4 |
5240 |
5240 |
258 |
258 |
|
|
|
meme |
meme_dreme, meme_fimo, meme_meme, meme_psp_gen, meme_streme |
The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. |
2015-12-13 |
http://meme-suite.org/ |
5.5.8 |
meme |
5.5.8 |
Up-to-date |
ChIP-seq |
Sequence motif discovery, Sequence motif recognition, Sequence motif comparison, Transcriptional regulatory element prediction |
Sequence motif discovery, Sequence motif recognition, Sequence motif comparison, Transcriptional regulatory element prediction |
Sequence sites, features and motifs, ChIP-seq, RNA immunoprecipitation, Epigenetics, Small molecules |
Sequence sites, features and motifs, ChIP-seq, RNA immunoprecipitation, Epigenetics, Small molecules |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme |
streme |
STREME |
STREME is accurate and versatile sequence motif discovery tool. The MEME Suite allows you to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses. It provides motif discovery algorithms using both probabilistic (MEME) and discrete models (STREME), which have complementary strengths. It also allows discovery of motifs with arbitrary insertions and deletions (GLAM2). MEME-ChIP performs a comprehensive motif-based analysis of ChIP-seq and other large sequence datasets. |
|
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
4 |
4 |
476 |
632 |
6756 |
24611 |
1135 |
2866 |
9050 |
27707 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
150 |
52468 |
15806 |
3500 |
1611 |
https://usegalaxy.org/published/workflow?id=2049d38325423cfe, https://usegalaxy.org/published/workflow?id=ecb279a9114140ab |
|
|
meme_chip |
meme_chip |
Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. |
2018-03-15 |
http://meme-suite.org/ |
4.11.2 |
graphicsmagick |
1.3.26 |
To update |
ChIP-seq |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip |
|
|
|
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0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
724 |
899 |
6897 |
8466 |
1240 |
1394 |
7722 |
8507 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16973 |
14619 |
2293 |
1964 |
https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=ad4b347f9b68e127, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c, https://usegalaxy.org/published/workflow?id=59d34b4f0178120b, https://workflowhub.eu/workflows/1562?version=1, https://workflowhub.eu/workflows/1706?version=1 |
epigenetics/cut_and_run, transcriptomics/clipseq |
|
meningotype |
meningotype |
Assign sequence type to N. meningitidis genome assemblies |
2023-06-06 |
https://github.com/MDU-PHL/meningotype |
0.8.5 |
meningotype |
0.8.5 |
Up-to-date |
Sequence Analysis |
Genotyping, Multilocus sequence typing |
Multilocus sequence typing |
Microbiology, Genotype and phenotype |
Microbiology, Genotype and phenotype |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype |
meningotype |
meningotype |
In silico typing of Neisseria meningitidis contigs. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
merlin |
merlin |
Pedigree Analysis package |
2020-04-15 |
http://csg.sph.umich.edu/abecasis/Merlin/ |
1.1.2 |
merlin |
1.1.2 |
Up-to-date |
Variant Analysis |
Haplotype mapping, Genetic mapping |
Haplotype mapping |
GWAS study, Mapping |
GWAS study, Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin |
merlin |
Merlin |
Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
merqury |
merqury, merquryplot |
Merqury is a tool for evaluating genomes assemblies based of k-mer operations. |
2021-04-18 |
https://github.com/marbl/merqury |
1.3 |
merqury |
1.3 |
Up-to-date |
Assembly |
Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly |
Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly |
Sequence assembly, Whole genome sequencing, Plant biology |
Sequence assembly, Whole genome sequencing, Plant biology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury |
merqury |
Merqury |
Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
661 |
661 |
4657 |
4657 |
264 |
264 |
1645 |
1645 |
243 |
243 |
1945 |
1945 |
77 |
77 |
440 |
440 |
8687 |
8687 |
1245 |
1245 |
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assembly/ERGA-post-assembly-QC, assembly/assembly-quality-control, assembly/vgp_genome_assembly |
|
merquryfk |
merquryfk_asmplot, merquryfk_cnplot, merquryfk_hapmaker, merquryfk_happlot, merquryfk_merquryfk |
FastK based version of Merqury |
2025-02-11 |
https://github.com/thegenemyers/MERQURY.FK |
1.1.1 |
merquryfk |
1.1.3 |
To update |
Sequence Analysis, Assembly |
|
|
|
|
iuc |
https://github.com/thegenemyers/MERQURY.FK |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/merquryfk |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
meryl |
meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode |
Meryl a k-mer counter. |
2021-04-05 |
https://github.com/marbl/meryl |
1.3 |
merqury |
1.3 |
Up-to-date |
Assembly |
k-mer counting |
k-mer counting |
Whole genome sequencing, Genomics, Sequence analysis, Sequencing |
Whole genome sequencing, Genomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl |
meryl |
Meryl |
Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. |
|
0 |
0 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
55 |
55 |
1850 |
1850 |
77 |
77 |
1478 |
1478 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3328 |
3328 |
132 |
132 |
https://usegalaxy.eu/published/workflow?id=0ccb3838765a8b84, https://usegalaxy.eu/published/workflow?id=10bde4e7f8dbd0c4, https://usegalaxy.eu/published/workflow?id=41c48e4632684f76, https://usegalaxy.org/published/workflow?id=4b919e575a16d062, https://usegalaxy.org/published/workflow?id=5503f7835226bc04, https://usegalaxy.org/published/workflow?id=6988c29ae84d2788, https://usegalaxy.org/published/workflow?id=83898f7cbfb7f88e, https://usegalaxy.org/published/workflow?id=9f1aabc6f5d18d13, https://usegalaxy.org/published/workflow?id=af1f4dba9aaa0b52, https://workflowhub.eu/workflows/631?version=6, https://workflowhub.eu/workflows/632?version=11 |
|
|
metabat2 |
metabat2_jgi_summarize_bam_contig_depths, metabat2 |
MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. |
2022-01-28 |
https://bitbucket.org/berkeleylab/metabat/src/master/ |
2.17 |
metabat2 |
2.18 |
To update |
Metagenomics |
Read binning, Sequence assembly, Genome annotation |
Read binning, Sequence assembly, Genome annotation |
Metagenomics, Sequence assembly, Metagenomic sequencing |
Metagenomics, Sequence assembly, Metagenomic sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 |
MetaBAT_2 |
MetaBAT 2 |
an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning |
|
0 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
2 |
0 |
670 |
670 |
14194 |
14194 |
375 |
375 |
2591 |
2591 |
167 |
167 |
1738 |
1738 |
18 |
18 |
1359 |
1359 |
19882 |
19882 |
1230 |
1230 |
https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://workflowhub.eu/workflows/1352?version=3 |
|
|
metabuli |
metabuli_classify |
Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences |
2024-06-04 |
https://github.com/steineggerlab/Metabuli |
1.0.5 |
metabuli |
1.1.0 |
To update |
Sequence Analysis, Metagenomics |
Taxonomic classification |
Taxonomic classification |
Taxonomy |
Taxonomy |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli |
metabuli |
metabuli |
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
metaeuk |
metaeuk_easy_predict |
MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. |
2020-08-04 |
https://github.com/soedinglab/metaeuk |
7.bba0d80 |
metaeuk |
6.a5d39d9 |
To update |
Sequence Analysis, Genome annotation |
Homology-based gene prediction |
Homology-based gene prediction |
Metagenomics, Gene and protein families |
Metagenomics, Gene and protein families |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk |
MetaEuk |
MetaEuk |
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
57 |
58 |
507 |
509 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
509 |
507 |
58 |
57 |
https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92 |
|
|
metagenomeseq_normalization |
metagenomeseq_normalizaton |
metagenomeSeq Normalization |
2017-03-27 |
https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html |
1.16.0-0.0.1 |
bioconductor-metagenomeseq |
1.43.0 |
To update |
Metagenomics |
Sequence visualisation, Statistical calculation |
Sequence visualisation, Statistical calculation |
Metagenomics, Sequencing |
Metagenomics, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq |
metagenomeseq |
metagenomeSeq |
Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
15 |
23 |
521 |
763 |
28 |
56 |
261 |
530 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1293 |
782 |
79 |
43 |
|
|
|
metaphlan |
customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan |
MetaPhlAn for Metagenomic Phylogenetic Analysis |
2021-03-11 |
https://github.com/biobakery/MetaPhlAn |
4.1.1 |
metaphlan |
4.2.2 |
To update |
Metagenomics |
Taxonomic classification, Taxonomic classification |
Taxonomic classification, Taxonomic classification |
Metagenomics, Phylogenomics |
Metagenomics, Phylogenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan |
metaphlan |
MetaPhlAn |
Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. |
|
0 |
2 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
4 |
4 |
1552 |
1552 |
30934 |
31014 |
1122 |
1122 |
20021 |
20021 |
314 |
314 |
6347 |
6347 |
28 |
28 |
211 |
211 |
57593 |
57513 |
3016 |
3016 |
https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=21a17d6c473a88c0, https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=4f0daf8e9dd54127, https://usegalaxy.eu/published/workflow?id=4f21205e71cabd37, https://usegalaxy.eu/published/workflow?id=5f0faac42b0a5062, https://usegalaxy.eu/published/workflow?id=713a5485e2007f90, https://usegalaxy.eu/published/workflow?id=79b4ae4403772098, https://usegalaxy.eu/published/workflow?id=87cc0cd143a12c41, https://usegalaxy.eu/published/workflow?id=9472be79da012999, https://usegalaxy.eu/published/workflow?id=a8f829deb69b30ab, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7, https://usegalaxy.eu/published/workflow?id=fdca6c9d394986bf, https://usegalaxy.fr/published/workflow?id=09e8293456ee6d99, https://usegalaxy.fr/published/workflow?id=c4f6062e51d0f45e, https://usegalaxy.org.au/published/workflow?id=6b7e565258a9da2a, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1466?version=2, https://workflowhub.eu/workflows/1470?version=1, https://workflowhub.eu/workflows/624?version=1 |
microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/taxonomic-profiling |
|
metasbt |
metasbt_index, metasbt_profile |
Microbial genomes characterization with Sequence Bloom Trees |
2025-08-22 |
https://github.com/cumbof/MetaSBT |
0.1.5 |
sed |
|
To update |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
metawrapmg_binning |
metawrapmg_binning |
A flexible pipeline for genome-resolved metagenomic data analysis |
2024-04-11 |
https://github.com/bxlab/metaWRAP |
1.3.0 |
metawrap-mg |
1.3.0 |
Up-to-date |
Metagenomics |
Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing |
Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing |
Whole genome sequencing, Metagenomic sequencing, Metagenomics |
Whole genome sequencing, Metagenomic sequencing, Metagenomics |
galaxy-australia |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg |
metawrap |
MetaWRAP |
MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
100 |
100 |
1596 |
1596 |
0 |
0 |
0 |
0 |
67 |
67 |
587 |
587 |
0 |
0 |
0 |
0 |
2183 |
2183 |
167 |
167 |
|
|
|
mg_toolkit |
mg_toolkit_bulk_download, mg_toolkit_original_metadata |
Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. |
2024-07-12 |
https://github.com/EBI-Metagenomics/emg-toolkit |
0.10.4 |
mg-toolkit |
0.10.4 |
Up-to-date |
Metagenomics |
Data retrieval |
Data retrieval |
Metagenomics |
Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit |
mg-toolkit |
mg-toolkit |
Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
21 |
21 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
21 |
21 |
10 |
10 |
|
|
|
micro_decon |
micro_decon |
An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing |
2025-08-05 |
https://github.com/donaldtmcknight/microdecon |
1.0.2 |
|
|
To update |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
microsatbed |
microsatbed |
Select microsatellites for a bed file |
2024-07-21 |
https://github.com/lmdu/pytrf |
1.3.3 |
python |
|
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
16 |
949 |
949 |
20 |
20 |
740 |
740 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1689 |
1689 |
36 |
36 |
https://usegalaxy.eu/published/workflow?id=3b94f511c52da835 |
|
|
migmap |
migmap |
mapper for full-length T- and B-cell repertoire sequencing |
2017-09-29 |
https://github.com/mikessh/migmap |
1.0.3 |
migmap |
1.0.3 |
Up-to-date |
RNA, Sequence Analysis |
Sequence analysis, Read mapping |
Sequence analysis, Read mapping |
Immunoproteins, genes and antigens, Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap |
MiGMAP |
MiGMAP |
Mapper for full-length T- and B-cell repertoire sequencing. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
24 |
39 |
931 |
1301 |
73 |
101 |
1138 |
1564 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2865 |
2069 |
140 |
97 |
|
|
|
minia |
minia |
Short-read assembler based on a de Bruijn graph |
2020-04-08 |
https://gatb.inria.fr/software/minia/ |
3.2.6 |
minia |
3.2.6 |
Up-to-date |
Assembly |
Genome assembly |
Genome assembly |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia |
minia |
Minia |
Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
272 |
287 |
6758 |
7224 |
0 |
0 |
0 |
0 |
77 |
77 |
357 |
357 |
0 |
0 |
0 |
0 |
7581 |
7115 |
364 |
349 |
https://usegalaxy.eu/published/workflow?id=9ba580ba8b01db40 |
|
|
miniasm |
miniasm |
Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) |
2019-06-18 |
https://github.com/lh3/miniasm |
0.3_r179 |
miniasm |
0.3 |
To update |
Assembly |
De-novo assembly |
De-novo assembly |
Genomics, Sequence assembly |
Genomics, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm |
miniasm |
miniasm |
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
571 |
687 |
11506 |
14702 |
474 |
538 |
9124 |
10016 |
88 |
96 |
1235 |
1277 |
16 |
16 |
166 |
166 |
26161 |
22031 |
1337 |
1149 |
https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/406?version=1 |
microbiome/plasmid-metagenomics-nanopore |
|
minimap2 |
minimap2 |
A fast pairwise aligner for genomic and spliced nucleotide sequences |
2017-11-03 |
https://github.com/lh3/minimap2 |
2.28 |
minimap2 |
2.30 |
To update |
Next Gen Mappers |
Pairwise sequence alignment |
Pairwise sequence alignment |
Mapping |
Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 |
minimap2 |
Minimap2 |
Pairwise aligner for genomic and spliced nucleotide sequences |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
5844 |
6182 |
414670 |
442793 |
5535 |
5834 |
153408 |
159247 |
1454 |
1492 |
29827 |
30676 |
169 |
170 |
4829 |
4841 |
637557 |
602734 |
13678 |
13002 |
https://usegalaxy.eu/published/workflow?id=032a7281a86eba0d, https://usegalaxy.eu/published/workflow?id=03bb4c20a1f4b4de, https://usegalaxy.eu/published/workflow?id=0444c98a3ca2a3ca, https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, https://usegalaxy.eu/published/workflow?id=0a3ebee985c26060, https://usegalaxy.eu/published/workflow?id=0c92c3c322c3effe, https://usegalaxy.eu/published/workflow?id=0f207a15b6f7fa10, https://usegalaxy.eu/published/workflow?id=0f6a7bd5362e4a2b, https://usegalaxy.eu/published/workflow?id=122da0054fd40adf, https://usegalaxy.eu/published/workflow?id=12b0bd336c76a874, https://usegalaxy.eu/published/workflow?id=14714876dda7186d, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1af73dc855d0a5ed, https://usegalaxy.eu/published/workflow?id=1b38e0d69e366be1, https://usegalaxy.eu/published/workflow?id=1cc3b4f1b50ba427, https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, 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assembly/ERGA-post-assembly-QC, assembly/assembly-with-preprocessing, assembly/largegenome, assembly/vgp_genome_assembly, microbiome/metaplasmidome_query, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/plasmid-metagenomics-nanopore |
|
miniprot |
miniprot, miniprot_index |
Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. |
2022-09-19 |
https://github.com/lh3/miniprot |
0.18 |
miniprot |
0.18 |
Up-to-date |
Sequence Analysis |
Sequence alignment, Protein sequence analysis |
Sequence alignment, Protein sequence analysis |
Sequence sites, features and motifs, Sequence analysis |
Sequence sites, features and motifs, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot |
miniprot |
miniprot |
Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. |
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
100 |
100 |
5038 |
5038 |
42 |
42 |
364 |
364 |
0 |
0 |
0 |
0 |
25 |
25 |
283 |
283 |
5685 |
5685 |
167 |
167 |
https://usegalaxy.eu/published/workflow?id=0c92c3c322c3effe |
|
|
mirmachine |
mirmachine |
Tool to detect miRNA in genome sequences |
2024-03-15 |
https://github.com/sinanugur/MirMachine |
0.3.0.1 |
mirmachine |
0.3.0.1 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
13 |
13 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
13 |
13 |
10 |
10 |
|
|
|
mirnature |
mirnature |
Computational detection of canonical microRNAs |
2022-12-11 |
https://github.com/Bierinformatik/miRNAture |
1.1 |
mirnature |
1.1 |
Up-to-date |
RNA, Sequence Analysis |
|
|
|
|
iuc |
https://github.com/Bierinformatik/miRNAture |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
11 |
11 |
23 |
23 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
23 |
23 |
11 |
11 |
|
|
|
mitobim |
mitobim |
assemble mitochondrial genomes |
2020-12-29 |
https://github.com/chrishah/MITObim |
1.9.1 |
mitobim |
1.9.1 |
Up-to-date |
Assembly |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
168 |
168 |
1463 |
1463 |
0 |
0 |
0 |
0 |
39 |
39 |
533 |
533 |
0 |
0 |
0 |
0 |
1996 |
1996 |
207 |
207 |
|
|
|
mitos |
mitos, mitos2 |
de-novo annotation of metazoan mitochondrial genomes |
2020-02-18 |
http://mitos.bioinf.uni-leipzig.de/ |
1.1.7 |
mitos |
2.1.9 |
To update |
Sequence Analysis |
Genome annotation |
Genome annotation |
Zoology, Whole genome sequencing |
Zoology, Whole genome sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos |
mitos |
MITOS |
De novo metazoan mitochondrial genome annotation. |
|
0 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
1 |
1326 |
1336 |
267673 |
268177 |
772 |
772 |
84561 |
84561 |
151 |
151 |
15492 |
15492 |
6 |
6 |
109 |
109 |
368339 |
367835 |
2265 |
2255 |
https://usegalaxy.eu/published/workflow?id=0de5fcc38ef1501d, https://usegalaxy.eu/published/workflow?id=2d0400b5d05c6c10 |
|
|
mlst |
mlst, mlst_list |
Scan contig files against PubMLST typing schemes |
2016-12-12 |
https://github.com/tseemann/mlst |
2.22.0 |
mlst |
2.23.0 |
To update |
Sequence Analysis |
Multilocus sequence typing |
Multilocus sequence typing |
Immunoproteins and antigens |
Immunoproteins and antigens |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst |
mlst |
MLST |
Multi Locus Sequence Typing from an assembled genome or from a set of reads. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
1786 |
1918 |
24365 |
26341 |
1356 |
1420 |
12903 |
13604 |
1137 |
1439 |
12595 |
15564 |
22 |
22 |
99 |
99 |
55608 |
49962 |
4799 |
4301 |
https://usegalaxy.eu/published/workflow?id=2b888e200dfd91bc, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=49c46d7653d6c349, https://usegalaxy.eu/published/workflow?id=5826e573b6f93762, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=a337bfb2eb1e583f, https://usegalaxy.eu/published/workflow?id=a84bac86ec183d46, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://usegalaxy.org.au/published/workflow?id=914330feb75ea9ab, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org.au/published/workflow?id=e20172eb0f30d6cd, https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be |
microbiome/pathogen-detection-from-nanopore-foodborne-data |
|
mmseqs2 |
mmseqs2_easy_linclust_clustering, mmseqs2_taxonomy_assignment |
MMseqs2 is an ultra fast and sensitive sequence search and clustering suite |
2025-03-27 |
https://github.com/soedinglab/MMseqs2 |
17-b804f |
mmseqs2 |
17.b804f |
To update |
Sequence Analysis, Metagenomics |
Sequence similarity search, Sequence alignment, Sequence clustering, Taxonomic classification |
Sequence similarity search, Sequence alignment, Sequence clustering, Taxonomic classification |
Metagenomics, Sequence analysis, Proteins, Nucleic acids, Gene and protein families, Taxonomy |
Metagenomics, Sequence analysis, Nucleic acids, Gene and protein families, Taxonomy |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmseqs2 |
MMseqs2 |
MMseqs2 |
MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.MMseqs2 includes Linclust, the first clustering algorithm whose runtime scales linearly With Linclust we clustered 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity. |
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
42 |
42 |
260 |
260 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
29 |
29 |
289 |
289 |
45 |
45 |
|
|
|
mmuphin |
mmuphin |
MMUPHin is an R package implementing meta-analysis methods for microbial community profiles |
2024-11-22 |
https://huttenhower.sph.harvard.edu/mmuphin |
1.16.0 |
bioconductor-mmuphin |
1.16.0 |
Up-to-date |
Metagenomics |
|
|
|
|
iuc |
https://github.com/biobakery/MMUPHin |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmuphin |
mmuphin |
mmuphin |
MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: a) covariate-controlled batch- and cohort effect adjustment, b) meta-analysis differential abundance testing, c) meta-analysis unsupervised discrete structure (clustering) discovery, and d) meta-analysis unsupervised continuous structure discovery. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
14 |
14 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
14 |
14 |
3 |
3 |
https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 |
|
|
moabs |
moabs |
MOABS for differential methylation analysis on Bisulfite sequencing data. |
2019-07-28 |
https://github.com/sunnyisgalaxy/moabs |
1.3.4.6 |
moabs |
1.3.9.6 |
To update |
Epigenetics |
|
|
|
|
iuc |
https://github.com/sunnyisgalaxy/moabs |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
46 |
59 |
185 |
351 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
351 |
185 |
59 |
46 |
|
|
|
mosdepth |
mosdepth |
fast and flexible BAM/CRAM depth calculation |
2022-12-04 |
https://github.com/brentp/mosdepth |
0.3.11 |
mosdepth |
0.3.11 |
Up-to-date |
SAM |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
201 |
201 |
14592 |
14592 |
173 |
173 |
13590 |
13590 |
73 |
73 |
3292 |
3292 |
1 |
1 |
1500 |
1500 |
32974 |
32974 |
448 |
448 |
https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df, https://usegalaxy.org.au/published/workflow?id=aa1d123c0a0929f3, https://usegalaxy.org/published/workflow?id=0c6dbb2ef5eee5b9, https://usegalaxy.org/published/workflow?id=695d20ef3ee4cf1e, https://usegalaxy.org/published/workflow?id=779ea0b19d07a1bd, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1647?version=1 |
variant-analysis/tb-variant-analysis |
|
mothur |
mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn |
Mothur wrappers |
2016-06-24 |
https://www.mothur.org |
1.0 |
mothur |
1.48.3 |
To update |
Metagenomics |
DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis |
DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis |
Microbial ecology, Taxonomy, Sequence analysis, Phylogeny |
Microbial ecology, Taxonomy, Sequence analysis, Phylogeny |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur |
mothur |
mothur |
Open-source, platform-independent, community-supported software for describing and comparing microbial communities |
|
0 |
129 |
129 |
129 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
129 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
126 |
129 |
129 |
2291 |
2805 |
265024 |
361038 |
4027 |
5455 |
423935 |
750968 |
1447 |
1742 |
164152 |
213607 |
147 |
149 |
14583 |
14948 |
1340561 |
867694 |
10151 |
7912 |
https://usegalaxy.eu/published/workflow?id=565c989730f68362, https://usegalaxy.eu/published/workflow?id=6d06bd22f206e176, https://usegalaxy.eu/published/workflow?id=6efd80daabf518bf, https://usegalaxy.eu/published/workflow?id=7783eeebfa264bf5, https://usegalaxy.eu/published/workflow?id=83a0c1ba280785e6, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=b66e1d8171e6dac2, https://usegalaxy.eu/published/workflow?id=b86f24473a282ef9, https://usegalaxy.eu/published/workflow?id=b91a380ceaa0342b, https://usegalaxy.eu/published/workflow?id=c1e26abe61c69688, https://usegalaxy.eu/published/workflow?id=c55388a8fbfd7381, https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19, https://usegalaxy.eu/published/workflow?id=ce21961260fe4351, https://usegalaxy.eu/published/workflow?id=dadca1020f586338, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.eu/published/workflow?id=f21d6a40a10a8ae8, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=177579096e009178, https://usegalaxy.org.au/published/workflow?id=1954437da1e0c4de, https://usegalaxy.org.au/published/workflow?id=2717e90438c7fb8c, https://usegalaxy.org.au/published/workflow?id=2a6324600f159061, https://usegalaxy.org.au/published/workflow?id=57fe85f947217994, https://usegalaxy.org.au/published/workflow?id=5877e2d5eba79f36, https://usegalaxy.org.au/published/workflow?id=58bd08b1530e7cae, https://usegalaxy.org.au/published/workflow?id=670e100ed3c039e2, https://usegalaxy.org.au/published/workflow?id=74bd939615090c2c, https://usegalaxy.org.au/published/workflow?id=7e381c150820e506, https://usegalaxy.org.au/published/workflow?id=832fe9dfc67fd8ed, https://usegalaxy.org.au/published/workflow?id=a52609119b30e64d, https://usegalaxy.org.au/published/workflow?id=fa8d1de86aa944a2, https://usegalaxy.org/published/workflow?id=2d149545a4920326, https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=64fa13bb48fcd7df, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=6f090b2c259847d2, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=775335812a6b7a61, https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4, https://usegalaxy.org/published/workflow?id=a383ce2e2bc3c7b9, https://usegalaxy.org/published/workflow?id=b2f3d7e4cd4d0f11, https://usegalaxy.org/published/workflow?id=bc01b8b203ecc754, https://usegalaxy.org/published/workflow?id=cade0c5c11978323, https://usegalaxy.org/published/workflow?id=d653eaefcf6b4697, https://usegalaxy.org/published/workflow?id=d7a11a4dfda3dab4, https://workflowhub.eu/workflows/1400?version=1, https://workflowhub.eu/workflows/1404?version=1, https://workflowhub.eu/workflows/1408?version=1, https://workflowhub.eu/workflows/1412?version=1, https://workflowhub.eu/workflows/1418?version=1, https://workflowhub.eu/workflows/1422?version=1, https://workflowhub.eu/workflows/1428?version=1, https://workflowhub.eu/workflows/1465?version=1, https://workflowhub.eu/workflows/1476?version=1, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1, https://workflowhub.eu/workflows/648?version=1, https://workflowhub.eu/workflows/649?version=1, https://workflowhub.eu/workflows/650?version=1, https://workflowhub.eu/workflows/651?version=1, https://workflowhub.eu/workflows/652?version=1, https://workflowhub.eu/workflows/653?version=1 |
microbiome/general-tutorial, microbiome/mothur-miseq-sop, microbiome/mothur-miseq-sop-short, sequence-analysis/Manage_AB1_Sanger |
|
msaboot |
msaboot |
A multiple sequences alignment bootstrapping tool. |
2018-02-12 |
https://github.com/phac-nml/msaboot |
0.1.2 |
msaboot |
0.1.2 |
Up-to-date |
Fasta Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
109 |
131 |
1009 |
1133 |
199 |
228 |
1049 |
1320 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2453 |
2058 |
359 |
308 |
|
|
|
multigps |
multigps |
Analyzes collections of multi-condition ChIP-seq data. |
2017-03-06 |
http://mahonylab.org/software/multigps/ |
0.74.0 |
fonts-conda-ecosystem |
|
To update |
ChIP-seq |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
121 |
304 |
317 |
891 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
892 |
318 |
305 |
122 |
|
|
|
multigsea |
multigsea |
GSEA-based pathway enrichment analysis for multi-omics data |
2023-06-07 |
https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html |
1.12.0 |
bioconductor-multigsea |
1.16.0 |
To update |
Transcriptomics, Proteomics, Statistics, Single Cell |
Gene-set enrichment analysis, Aggregation, Pathway analysis |
Gene-set enrichment analysis, Aggregation, Pathway analysis |
Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules |
Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea |
multiGSEA |
multiGSEA |
A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
65 |
65 |
212 |
212 |
0 |
0 |
0 |
0 |
5 |
5 |
46 |
46 |
0 |
0 |
0 |
0 |
258 |
258 |
70 |
70 |
https://workflowhub.eu/workflows/1388?version=1 |
proteomics/multiGSEA-tutorial |
|
multiqc |
multiqc |
MultiQC aggregates results from bioinformatics analyses across many samples into a single report |
2017-09-21 |
http://multiqc.info/ |
1.27 |
multiqc |
1.31 |
To update |
Fastq Manipulation, Statistics, Visualization |
Validation, Sequencing quality control |
Sequencing quality control |
Sequencing, Bioinformatics, Sequence analysis, Genomics |
Sequencing, Bioinformatics, Sequence analysis, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc |
multiqc |
MultiQC |
MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
24162 |
26916 |
223019 |
248625 |
32289 |
38522 |
203104 |
241071 |
7040 |
7764 |
49577 |
54957 |
2276 |
2280 |
43768 |
43966 |
588619 |
519468 |
75482 |
65767 |
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assembly/assembly-with-preprocessing, assembly/general-introduction, assembly/largegenome, assembly/unicycler-assembly, contributing/create-new-tutorial-content, ecology/ENA_Biodiv_submission, ecology/ref-based-rad-seq, epigenetics/cut_and_run, galaxy-interface/workflow-fairification, genome-annotation/crispr-screen, introduction/galaxy-intro-ngs-data-managment, introduction/vsi_qc, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/mgnify-amplicon, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, sequence-analysis/mapping, sequence-analysis/quality-control, single-cell/scrna-preprocessing, single-cell/scrna-preprocessing-tenx, transcriptomics/differential-isoform-expression, transcriptomics/full-de-novo, transcriptomics/minerva-pathways, transcriptomics/mirna-target-finder, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts, variant-analysis/exome-seq, variant-analysis/sars-cov-2, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants, variant-analysis/tb-variant-analysis |
|
mummer4 |
mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords |
Mummer4 Tools |
2018-06-28 |
https://github.com/mummer4/mummer |
4.0.0 |
mummer4 |
4.0.1 |
To update |
Sequence Analysis |
Multiple sequence alignment |
Multiple sequence alignment |
Sequence analysis, Human genetics |
Sequence analysis, Human genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 |
mummer4 |
MUMmer4 |
System for rapidly aligning large DNA sequences to one another. |
|
0 |
6 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
6 |
842 |
940 |
30656 |
33196 |
1586 |
1727 |
32334 |
36481 |
295 |
295 |
12782 |
12782 |
21 |
21 |
595 |
595 |
83054 |
76367 |
2983 |
2744 |
https://usegalaxy.eu/published/workflow?id=1f88311a8e365c17, https://usegalaxy.eu/published/workflow?id=35629b113a6f23ab, https://usegalaxy.fr/published/workflow?id=ce4acd38084ee9ef, https://usegalaxy.org/published/workflow?id=8b4b62a55a93a258 |
|
|
muon |
cluster_analyze_embed_muon, mudata_import_export, plot_muon, preprocess_muon |
muon is a Python framework for multimodal omics analysis |
2024-03-15 |
https://muon.readthedocs.io |
0.1.6 |
muon |
|
To update |
Single Cell, Sequence Analysis, Transcriptomics, Epigenetics |
|
|
Cell biology, Single-cell sequencing, Gene expression, Epigenetics, Multiomics |
Cell biology, Gene expression, Epigenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/muon/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/muon |
muon |
muon |
muon is a Python framework for multimodal omics analysis. |
|
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
mykrobe |
mykrobe_predict |
Antibiotic resistance predictions |
2017-12-18 |
https://github.com/Mykrobe-tools/mykrobe |
0.10.0 |
mykrobe |
0.13.0 |
To update |
Sequence Analysis |
Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming |
Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming |
Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics |
Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe |
Mykrobe |
Mykrobe |
Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
mzmine_batch |
mzmine_batch |
mass-spectrometry data processing, with the main focus on LC-MS data |
2023-10-21 |
http://mzmine.github.io/ |
3.9.0 |
mzmine |
4.7.29 |
To update |
Metabolomics |
Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation |
Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation |
Proteomics, Metabolomics, Proteomics experiment, Small molecules |
Proteomics, Metabolomics, Proteomics experiment, Small molecules |
iuc |
https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine |
mzmine |
MZmine |
Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
21 |
21 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
21 |
21 |
8 |
8 |
|
|
|
naltorfs |
bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs |
nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) |
2022-04-11 |
https://github.com/BlankenbergLab/nAltORFs |
0.1.2 |
naltorfs |
0.1.2 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
60 |
60 |
271 |
271 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
271 |
271 |
60 |
60 |
|
|
|
nanocomp |
nanocomp |
Compare multiple runs of long read sequencing data and alignments |
2025-05-21 |
https://github.com/wdecoster/NanoComp |
1.25.3 |
nanocomp |
1.25.4 |
To update |
Visualization, Statistics, Fastq Manipulation |
Box-Whisker plot plotting, Visualisation, Multiple sample visualisation |
Box-Whisker plot plotting, Multiple sample visualisation |
Nucleic acids, Bioinformatics |
Nucleic acids, Bioinformatics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp |
nanocomp |
nanocomp |
Compare multiple runs of long read sequencing data and alignments. Creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
2 |
2 |
|
|
|
nanocompore |
nanocompore_db, nanocompore_sampcomp |
Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. |
2020-04-27 |
https://nanocompore.rna.rocks/ |
1.0.0rc3.post2 |
nanocompore |
1.0.4 |
To update |
Sequence Analysis |
Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting |
PolyA signal detection, Genotyping, k-mer counting |
Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites |
Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore |
Nanocompore |
Nanocompore |
RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro |
|
0 |
1 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
5 |
7 |
27 |
839 |
0 |
0 |
0 |
0 |
5 |
5 |
365 |
371 |
0 |
0 |
0 |
0 |
1210 |
392 |
12 |
10 |
https://usegalaxy.eu/published/workflow?id=778923dd04996e07, https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d |
|
|
nanoplot |
nanoplot |
Plotting tool for long read sequencing data and alignments |
2018-09-24 |
https://github.com/wdecoster/NanoPlot |
1.46.1 |
nanoplot |
1.46.1 |
Up-to-date |
Visualization |
Scatter plot plotting, Box-Whisker plot plotting |
Scatter plot plotting, Box-Whisker plot plotting |
Genomics |
Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot |
nanoplot |
NanoPlot |
NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
7663 |
7942 |
168514 |
173861 |
4903 |
5029 |
72856 |
74900 |
2940 |
2983 |
25741 |
26566 |
295 |
297 |
3814 |
3828 |
279155 |
270925 |
16251 |
15801 |
https://usegalaxy.eu/published/workflow?id=0bafeb17c21ebc9c, https://usegalaxy.eu/published/workflow?id=14714876dda7186d, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=181e751be8dd9abc, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302, https://usegalaxy.eu/published/workflow?id=34a07bf6407510ef, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=49ce9e738fadef4a, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=57cfe5062c8e01bf, https://usegalaxy.eu/published/workflow?id=57d3109f32defa3b, 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https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=dd3193aaaf08e798, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=eb5ab8bc82569eee, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.fr/published/workflow?id=776ef2fa51094ba6, https://usegalaxy.org.au/published/workflow?id=03b090e75c61c1c3, https://usegalaxy.org.au/published/workflow?id=143d4cc586aff5a0, https://usegalaxy.org.au/published/workflow?id=22bd45f60c60a338, https://usegalaxy.org.au/published/workflow?id=24f0d1f7a28756b5, https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b, https://usegalaxy.org.au/published/workflow?id=2cb16d321a804b1a, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, 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https://workflowhub.eu/workflows/1616?version=1, https://workflowhub.eu/workflows/1617?version=1, https://workflowhub.eu/workflows/222?version=1, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/521?version=1, https://workflowhub.eu/workflows/697?version=1 |
assembly/assembly-with-preprocessing, assembly/chloroplast-assembly, assembly/largegenome, assembly/mrsa-nanopore, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/plasmid-metagenomics-nanopore, sequence-analysis/quality-control |
|
nanopolishcomp |
nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate |
NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. |
2020-04-27 |
https://a-slide.github.io/NanopolishComp |
0.6.11 |
nanopolishcomp |
0.6.12 |
To update |
Sequence Analysis |
Methylation analysis, Collapsing methods |
Methylation analysis, Collapsing methods |
Sequence analysis, Sequencing, Genetic variation |
Sequence analysis, Sequencing, Genetic variation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp |
nanopolishcomp |
NanopolishComp |
NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. |
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
36 |
38 |
709 |
1129 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
1130 |
710 |
39 |
37 |
https://usegalaxy.eu/published/workflow?id=77db45ad90b4033d |
|
|
ncbi_acc_download |
ncbi_acc_download |
Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API |
2019-11-06 |
https://github.com/kblin/ncbi-acc-download |
0.2.8 |
ncbi-acc-download |
0.2.8 |
Up-to-date |
Data Source |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2027 |
2167 |
9533 |
10236 |
4656 |
5221 |
17731 |
19952 |
1153 |
1204 |
6985 |
7379 |
47 |
49 |
329 |
345 |
37912 |
34578 |
8641 |
7883 |
https://usegalaxy.eu/published/workflow?id=08f41680101a1a45, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=4d80a87510b2a54e, https://usegalaxy.eu/published/workflow?id=52cb9bacc26b013e, https://usegalaxy.eu/published/workflow?id=9155ed0e7a6a7b60, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=a018307be3563f28, https://usegalaxy.eu/published/workflow?id=d07fe8b5a045c176, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.fr/published/workflow?id=c7be6e229a045fad, https://usegalaxy.org.au/published/workflow?id=0f71c97671bb401f, https://usegalaxy.org.au/published/workflow?id=cb6f49d4ebfa0891, https://usegalaxy.org.au/published/workflow?id=d62b6717202f42c9, https://usegalaxy.org/published/workflow?id=005924662f68a480, https://usegalaxy.org/published/workflow?id=0596162a499b4074, https://usegalaxy.org/published/workflow?id=23212ae74fc2d2b5, https://usegalaxy.org/published/workflow?id=2cbcfeb772f348c9, https://usegalaxy.org/published/workflow?id=be54e57345ce7ca5, https://workflowhub.eu/workflows/1558?version=1, https://workflowhub.eu/workflows/1628?version=1 |
genome-annotation/secondary-metabolite-discovery, variant-analysis/baculovirus-isolate-variation |
|
ncbi_datasets |
datasets_download_gene, datasets_download_genome |
NCBI datasets downloads biological sequence data across all domains of life from NCBI. |
2022-01-27 |
https://github.com/ncbi/datasets |
18.5.1 |
ncbi-datasets-cli |
|
To update |
Data Source |
Data handling, Sequence database search, Data retrieval |
Data handling, Sequence database search, Data retrieval |
Biological databases |
Biological databases |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets |
ncbi_datasets |
NCBI Datasets |
NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. |
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
2 |
2 |
1310 |
1310 |
6574 |
6574 |
3022 |
3022 |
17889 |
17889 |
2 |
2 |
3 |
3 |
88 |
88 |
425 |
425 |
24891 |
24891 |
4422 |
4422 |
https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 |
genome-annotation/bacterial-comparative-genomics-dataset-construction |
|
ncbi_entrez_direct |
ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch |
NCBI Entrez Direct allow fetching data from NCBI Databases |
2022-03-22 |
http://www.ncbi.nlm.nih.gov/books/NBK179288/ |
22.4 |
entrez-direct |
24.0 |
To update |
Data Source |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
1 |
0 |
|
|
|
ncbi_entrez_eutils |
ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary |
NCBI Entrez E-Utilties allow fetching data from NCBI Databases |
2015-04-14 |
https://www.ncbi.nlm.nih.gov/books/NBK25501/ |
1.70 |
python |
|
To update |
Data Source |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils |
|
|
|
|
0 |
0 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
242 |
422 |
2452 |
3350 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3350 |
2452 |
422 |
242 |
|
|
|
ncbi_fcs_gx |
ncbi_fcs_gx |
FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). |
2023-09-21 |
https://github.com/ncbi/fcs-gx |
0.5.5 |
ncbi-fcs-gx |
0.5.5 |
Up-to-date |
Sequence Analysis |
Sequence assembly validation, Sequence trimming, Sequence contamination filtering |
Sequence assembly validation, Sequence trimming, Sequence contamination filtering |
Sequence analysis, Sequence assembly |
Sequence analysis, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx |
ncbi_fcs |
NCBI fcs |
The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
175 |
175 |
2259 |
2259 |
485 |
485 |
26859 |
26859 |
27 |
27 |
955 |
955 |
1 |
1 |
9 |
9 |
30082 |
30082 |
688 |
688 |
|
sequence-analysis/ncbi-fcs |
|
necat |
necat |
Error correction and de-novo assembly for ONT Nanopore reads |
2021-11-29 |
https://github.com/xiaochuanle/NECAT |
0.0.1_update20200803 |
necat |
0.0.1_update20200803 |
Up-to-date |
Assembly |
De-novo assembly |
De-novo assembly |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat |
necat |
NECAT |
NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
228 |
228 |
1106 |
1106 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1106 |
1106 |
228 |
228 |
|
|
|
newick_utils |
newick_display |
Perform operations on Newick trees |
2018-10-01 |
http://cegg.unige.ch/newick_utils |
1.6+galaxy1 |
newick_utils |
1.6 |
To update |
Visualization, Metagenomics |
Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction |
|
Phylogeny, Genomics, Computer science |
Phylogeny, Genomics, Computer science |
iuc |
https://github.com/tjunier/newick_utils |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils |
newick_utilities |
Newick Utilities |
The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1756 |
1893 |
51682 |
53373 |
2196 |
2332 |
18983 |
20195 |
1114 |
1145 |
9635 |
9912 |
48 |
49 |
310 |
312 |
83792 |
80610 |
5419 |
5114 |
https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.eu/published/workflow?id=c1e26abe61c69688, https://usegalaxy.eu/published/workflow?id=c67d2e75eeb4fd19, https://usegalaxy.eu/published/workflow?id=c8bc4af6dd3b5d02, https://usegalaxy.eu/published/workflow?id=dadca1020f586338, https://usegalaxy.eu/published/workflow?id=dc57118a95b10a80, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.eu/published/workflow?id=ec50dd6d56f50db1, https://usegalaxy.eu/published/workflow?id=f21d6a40a10a8ae8, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.org.au/published/workflow?id=2717e90438c7fb8c, https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0, https://usegalaxy.org.au/published/workflow?id=a01c3004bcef9dd3, https://usegalaxy.org.au/published/workflow?id=a52609119b30e64d, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=005924662f68a480, https://usegalaxy.org/published/workflow?id=0596162a499b4074, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=603e5c61c57bcf3f, https://usegalaxy.org/published/workflow?id=6a1eb7e7bececba1, https://usegalaxy.org/published/workflow?id=6f090b2c259847d2, https://usegalaxy.org/published/workflow?id=775335812a6b7a61, https://usegalaxy.org/published/workflow?id=9c4038fa15af6995, https://usegalaxy.org/published/workflow?id=bc01b8b203ecc754, https://usegalaxy.org/published/workflow?id=d653eaefcf6b4697, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1418?version=1, https://workflowhub.eu/workflows/1465?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/653?version=1 |
evolution/abc_intro_phylo, microbiome/mothur-miseq-sop, microbiome/mothur-miseq-sop-short, microbiome/pathogen-detection-from-nanopore-foodborne-data |
|
nextclade |
nextalign, nextclade |
Identify differences between your sequences and a reference sequence used by Nextstrain |
2021-03-29 |
https://github.com/nextstrain/nextclade |
2.7.0 |
nextalign |
2.14.0 |
To update |
Sequence Analysis |
Methylation analysis, Variant calling |
Methylation analysis, Variant calling |
Genomics, Sequence analysis, Cladistics |
Genomics, Cladistics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade |
nextclade |
Nextclade |
Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. |
|
0 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
373 |
373 |
4718 |
4718 |
309 |
309 |
11632 |
11632 |
258 |
258 |
2460 |
2460 |
11 |
11 |
723 |
723 |
19533 |
19533 |
951 |
951 |
https://usegalaxy.eu/published/workflow?id=0189bab68f828d86, https://usegalaxy.eu/published/workflow?id=1d1ebdeddf23bdb9, https://usegalaxy.eu/published/workflow?id=3f046b416b10b871, https://usegalaxy.eu/published/workflow?id=4c75ab0be3c56494, https://usegalaxy.eu/published/workflow?id=5c15f251642bfa1f, https://usegalaxy.eu/published/workflow?id=74f19aff1b9cdd6b, https://usegalaxy.eu/published/workflow?id=9feebfc6c34da287, https://usegalaxy.fr/published/workflow?id=2345fad7dac13daa, https://usegalaxy.fr/published/workflow?id=591c57173e259ca6, https://usegalaxy.fr/published/workflow?id=e4735d214a68b790, https://usegalaxy.fr/published/workflow?id=feb57548b3ce914d, https://usegalaxy.org.au/published/workflow?id=7563b3ef697a69fd, https://usegalaxy.org.au/published/workflow?id=af12a3ec85859563, https://usegalaxy.org/published/workflow?id=0fa2ce12c2874b1d, https://usegalaxy.org/published/workflow?id=426e3951dac0704e, https://usegalaxy.org/published/workflow?id=4b41a8247f52c463, https://usegalaxy.org/published/workflow?id=8b81b9a3b49bbf98, https://usegalaxy.org/published/workflow?id=d96bd5c9fb553f2c, https://workflowhub.eu/workflows/155?version=6, https://workflowhub.eu/workflows/520?version=1 |
variant-analysis/sars-cov-2-variant-discovery |
|
ngmlr |
ngmlr |
CoNvex Gap-cost alignMents for Long Reads |
2020-10-27 |
https://github.com/philres/ngmlr |
0.2.7 |
ngmlr |
0.2.7 |
Up-to-date |
Next Gen Mappers |
DNA mapping, Sequence alignment, Genetic variation analysis |
DNA mapping, Sequence alignment, Genetic variation analysis |
Sequencing, Mapping, DNA structural variation |
Sequencing, Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr |
ngmlr |
NGMLR |
An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
53 |
53 |
1408 |
1408 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1408 |
1408 |
53 |
53 |
https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5 |
|
|
ngsutils |
ngsutils_bam_filter |
NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. |
2015-11-10 |
https://github.com/ngsutils/ngsutils |
|
ngsutils |
0.5.9 |
To update |
SAM |
Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering |
Read pre-processing, Variant calling, Formatting, Sequence contamination filtering |
Genomics, Transcriptomics |
Transcriptomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils |
ngsutils |
NGSUtils |
NGSUtils is a suite of software tools for working with next-generation sequencing datasets |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
702 |
894 |
27862 |
37369 |
902 |
1390 |
17094 |
25161 |
128 |
176 |
10945 |
13368 |
21 |
21 |
148 |
148 |
76046 |
56049 |
2481 |
1753 |
https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=2a123e08436a89f1, https://usegalaxy.eu/published/workflow?id=45fc2dada84d251e, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://usegalaxy.eu/published/workflow?id=f33b5135ee99e0dc, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.org.au/published/workflow?id=a7726d18d2a5fcf2, https://usegalaxy.org/published/workflow?id=1f48b44fa22ac5fc, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=71f8a4090877f171, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/102?version=1, https://workflowhub.eu/workflows/1480?version=1, https://workflowhub.eu/workflows/1631?version=1 |
assembly/metagenomics-assembly, microbiome/metagenomics-assembly |
|
nonpareil |
nonpareil |
Estimate average coverage in metagenomic datasets |
2017-11-03 |
http://nonpareil.readthedocs.io |
3.5.5 |
nonpareil |
3.5.5 |
Up-to-date |
Metagenomics |
Operation |
Operation |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil |
nonpareil |
nonpareil |
Estimate metagenomic coverage and sequence diversity |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
16 |
19 |
105 |
195 |
23 |
26 |
122 |
168 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
363 |
227 |
45 |
39 |
|
|
|
novoplasty |
novoplasty |
NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. |
2020-05-18 |
https://github.com/ndierckx/NOVOPlasty |
4.3.1 |
novoplasty |
4.3.5 |
To update |
Assembly |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
502 |
502 |
11073 |
11073 |
1 |
1 |
1 |
1 |
137 |
137 |
3542 |
3542 |
11 |
11 |
37 |
37 |
14653 |
14653 |
651 |
651 |
https://usegalaxy.eu/published/workflow?id=5436eb1c430a38dd |
|
|
nugen_nudup |
nugen_nudup |
Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. |
2016-11-18 |
https://github.com/tecangenomics/nudup |
2.3.3 |
nudup |
2.3.3 |
Up-to-date |
SAM, Metagenomics, Sequence Analysis, Transcriptomics |
Duplication detection, Sequence analysis |
Duplication detection, Sequence analysis |
Sequencing, Genomics |
Sequencing, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup |
nudup |
NuDup |
Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
obitools |
obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq |
OBITools is a set of programs developed to simplify the manipulation of sequence files |
2017-03-22 |
http://metabarcoding.org/obitools |
1.2.13 |
obitools |
1.2.13 |
Up-to-date |
Sequence Analysis |
Sequence analysis, Sequence analysis |
Sequence analysis, Sequence analysis |
Sequence analysis, DNA, Sequencing |
Sequence analysis, DNA, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools |
obitools |
OBITools |
Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. |
|
0 |
10 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
483 |
493 |
45330 |
45705 |
0 |
0 |
0 |
0 |
107 |
107 |
5011 |
5011 |
25 |
25 |
1398 |
1398 |
52114 |
51739 |
625 |
615 |
https://usegalaxy.eu/published/workflow?id=513389e1a8c6bba9, https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d, https://usegalaxy.eu/published/workflow?id=edf7e2128f5aef8d, https://usegalaxy.org.au/published/workflow?id=470eb26144325590, https://workflowhub.eu/workflows/1702?version=1, https://workflowhub.eu/workflows/655?version=1 |
ecology/Obitools-metabarcoding |
|
ococo |
ococo |
Variant detection of SNVs |
2017-12-07 |
https://github.com/karel-brinda/ococo |
0.1.2.6 |
ococo |
0.1.2.7 |
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
71 |
101 |
1253 |
2070 |
186 |
208 |
1426 |
1552 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3622 |
2679 |
309 |
257 |
https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df |
|
|
odgi |
odgi_build, odgi_viz |
Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. |
2020-04-06 |
https://github.com/vgteam/odgi |
0.3 |
odgi |
0.9.3 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi |
|
|
|
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
3 |
4 |
7 |
29 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
29 |
7 |
4 |
3 |
|
|
|
omark |
omark |
Proteome quality assessment software |
2023-11-15 |
https://github.com/DessimozLab/OMArk |
0.3.1 |
|
|
To update |
Sequence Analysis |
Sequence assembly validation, Differential protein expression profiling |
Sequence assembly validation, Differential protein expression profiling |
Proteomics, Sequence analysis, Statistics and probability |
Proteomics, Sequence analysis, Statistics and probability |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark |
omark |
OMArk |
OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence of contamination from other species. OMArk relies on the OMA orthology database, from which it exploits orthology relationships, and on the OMAmer software for fast placement of all proteins into gene families. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
89 |
89 |
707 |
707 |
17 |
17 |
44 |
44 |
6 |
6 |
11 |
11 |
15 |
15 |
347 |
347 |
1109 |
1109 |
127 |
127 |
https://usegalaxy.eu/published/workflow?id=31bc2a44fb89aa89, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=6550f72070b24082, https://usegalaxy.eu/published/workflow?id=8976041ef89e4548, https://usegalaxy.org.au/published/workflow?id=dd9272826e6dd98d, https://usegalaxy.org.au/published/workflow?id=e263fcb6c98e231b, https://usegalaxy.org.au/published/workflow?id=ec7efff3d3249177, https://usegalaxy.org/published/workflow?id=4605309321799e9b, https://usegalaxy.org/published/workflow?id=80a7124c40438cc9, https://usegalaxy.org/published/workflow?id=f4111a169255535c, https://workflowhub.eu/workflows/1096?version=2, https://workflowhub.eu/workflows/1255?version=3, https://workflowhub.eu/workflows/1500?version=1, https://workflowhub.eu/workflows/1746?version=1 |
genome-annotation/braker3, genome-annotation/comparison-braker-helixer-annotation, genome-annotation/helixer |
|
ont_fast5_api |
ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 |
ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. |
2020-06-08 |
https://github.com/nanoporetech/ont_fast5_api/ |
3.1.3 |
ont-fast5-api |
4.1.3 |
To update |
Nanopore |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api |
|
|
|
|
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
4 |
49 |
51 |
2529 |
3106 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3106 |
2529 |
51 |
49 |
https://usegalaxy.eu/published/workflow?id=d5b1fab611ddfeb0, https://usegalaxy.eu/published/workflow?id=e271d95a671182ec |
|
|
onto_toolkit |
onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def |
ONTO-Toolkit is a collection of tools for managing ontologies. |
2017-11-04 |
http://search.cpan.org/~easr/ONTO-PERL-1.45/ |
1.45 |
perl-onto-perl |
1.45 |
Up-to-date |
Ontology Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit |
|
|
|
|
0 |
0 |
17 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
17 |
17 |
8 |
11 |
75 |
666 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
666 |
75 |
11 |
8 |
|
|
|
openalex_explorer |
openalex_explorer |
Fetch citing papers from OpenAlex using DOI, ID and title |
2025-05-29 |
https://openalex.org/ |
0.1.0+galaxy0 |
python |
|
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/openalex |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
3 |
3 |
|
|
|
optdoe |
optdoe |
Optimal Design Of Experiment |
2022-10-27 |
https://github.com/pablocarb/doebase |
v2.0.2 |
doebase |
|
To update |
Synthetic Biology |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
optitype |
optitype |
Precision HLA typing from NGS data |
2021-02-17 |
https://github.com/FRED-2/OptiType |
1.3.5 |
optitype |
1.3.5 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
62 |
62 |
585 |
585 |
18 |
18 |
99 |
99 |
6 |
6 |
97 |
97 |
0 |
0 |
0 |
0 |
781 |
781 |
86 |
86 |
https://usegalaxy.eu/published/workflow?id=db270d0eb035609e, https://usegalaxy.org.au/published/workflow?id=2249ab6710f5e84d, https://usegalaxy.org/published/workflow?id=1d925422fc6094a0, https://workflowhub.eu/workflows/1430?version=1, https://workflowhub.eu/workflows/1794?version=1 |
proteomics/neoantigen-predicting-hla-binding |
|
orfipy |
orfipy |
Galaxy wrapper for ORFIPY |
2022-04-07 |
https://github.com/urmi-21/orfipy |
0.0.4 |
orfipy |
0.0.4 |
Up-to-date |
Sequence Analysis |
Coding region prediction, Database search, Transcriptome assembly, De-novo assembly |
Coding region prediction, Database search, Transcriptome assembly, De-novo assembly |
Computer science, RNA-Seq, Transcriptomics, Small molecules |
Computer science, RNA-Seq, Transcriptomics, Small molecules |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy |
orfipy |
orfipy |
A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
172 |
172 |
1509 |
1509 |
343 |
343 |
2776 |
2776 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4285 |
4285 |
515 |
515 |
https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df |
genome-annotation/gene-centric |
|
orthofinder |
orthofinder_onlygroups |
Accurate inference of orthologous gene groups made easy |
2017-05-22 |
https://github.com/davidemms/OrthoFinder |
2.5.5 |
orthofinder |
3.1.0 |
To update |
Phylogenetics, Sequence Analysis |
Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment |
Genome comparison, Genome alignment |
Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis |
Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder |
OrthoFinder |
OrthoFinder |
OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
801 |
801 |
3870 |
3870 |
0 |
0 |
0 |
0 |
133 |
133 |
1450 |
1450 |
36 |
36 |
221 |
221 |
5541 |
5541 |
970 |
970 |
|
|
|
packaged_annotation_loader |
packaged_annotation_loader |
Tool to make cached genome annotation data available as a list of datasets collection |
2022-01-04 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader |
0.1 |
python |
|
To update |
Data Source |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
pacu |
pacu_map, pacu_snp |
PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. |
2024-08-13 |
https://github.com/BioinformaticsPlatformWIV-ISP/PACU |
0.0.5 |
pacu_snp |
0.0.7 |
To update |
Sequence Analysis, Phylogenetics |
Clustering |
Clustering |
Phylogenetics, Sequence analysis |
Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu |
pacu |
PACU |
PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads). |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
19 |
19 |
223 |
223 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
223 |
223 |
19 |
19 |
|
|
|
pairtools |
pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats |
Flexible tools for Hi-C data processing |
2024-03-26 |
https://pairtools.readthedocs.io |
1.1.3 |
pairtools |
1.1.3 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/open2c/pairtools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools |
|
|
|
|
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
25 |
25 |
742 |
742 |
8 |
8 |
415 |
415 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1157 |
1157 |
33 |
33 |
https://usegalaxy.org/published/workflow?id=c03ada2070e9ca8a, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1164?version=2, https://workflowhub.eu/workflows/625?version=26 |
|
|
panaroo |
panaroo |
A Bacterial Pangenome Analysis Pipeline |
2025-02-28 |
https://gthlab.au/panaroo/#/ |
1.5.2 |
panaroo |
1.5.2 |
Up-to-date |
Sequence Analysis |
De-novo assembly, Genome assembly, Clustering |
De-novo assembly, Genome assembly, Clustering |
Workflows, Sequence assembly, Gene and protein families, Plant biology, Sequencing |
Workflows, Sequence assembly, Gene and protein families, Plant biology, Sequencing |
galaxy-australia |
https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/panaroo |
panaroo |
Panaroo |
Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
67 |
67 |
297 |
297 |
0 |
0 |
0 |
0 |
39 |
39 |
312 |
312 |
0 |
0 |
0 |
0 |
609 |
609 |
106 |
106 |
|
|
|
pangolin |
pangolin |
Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. |
2021-03-06 |
https://github.com/cov-lineages/pangolin |
4.3 |
pangolin |
4.3.1 |
To update |
Sequence Analysis |
Tree-based sequence alignment, Variant classification |
Tree-based sequence alignment, Variant classification |
Virology |
Virology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin |
pangolin_cov-lineages |
pangolin |
Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
595 |
595 |
7737 |
7737 |
416 |
416 |
9068 |
9068 |
277 |
277 |
3099 |
3099 |
12 |
12 |
603 |
603 |
20507 |
20507 |
1300 |
1300 |
https://usegalaxy.eu/published/workflow?id=0189bab68f828d86, https://usegalaxy.eu/published/workflow?id=1d1ebdeddf23bdb9, https://usegalaxy.eu/published/workflow?id=3f046b416b10b871, https://usegalaxy.eu/published/workflow?id=4c75ab0be3c56494, https://usegalaxy.eu/published/workflow?id=5c15f251642bfa1f, https://usegalaxy.eu/published/workflow?id=74f19aff1b9cdd6b, https://usegalaxy.eu/published/workflow?id=9feebfc6c34da287, https://usegalaxy.fr/published/workflow?id=2345fad7dac13daa, https://usegalaxy.fr/published/workflow?id=591c57173e259ca6, https://usegalaxy.fr/published/workflow?id=e4735d214a68b790, https://usegalaxy.fr/published/workflow?id=feb57548b3ce914d, https://usegalaxy.org.au/published/workflow?id=7563b3ef697a69fd, https://usegalaxy.org.au/published/workflow?id=af12a3ec85859563, https://usegalaxy.org/published/workflow?id=0fa2ce12c2874b1d, https://usegalaxy.org/published/workflow?id=426e3951dac0704e, https://usegalaxy.org/published/workflow?id=4b41a8247f52c463, https://usegalaxy.org/published/workflow?id=8b81b9a3b49bbf98, https://usegalaxy.org/published/workflow?id=d96bd5c9fb553f2c, https://workflowhub.eu/workflows/1391?version=1, https://workflowhub.eu/workflows/155?version=6 |
galaxy-interface/workflow-automation, variant-analysis/sars-cov-2-variant-discovery |
|
panta |
panta |
Efficient inference of large prokaryotic pangenomes with PanTA. |
2025-09-15 |
https://github.com/amromics/panta |
1.0.1 |
panta |
1.0.1 |
Up-to-date |
Genome annotation, Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
parse_mito_blast |
parse_mito_blast |
Filtering blast out from querying assembly against mitochondrial database. |
2022-05-12 |
https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py |
1.0.2 |
parse_mito_blast |
1.0.2 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
136 |
136 |
1872 |
1872 |
95 |
95 |
1193 |
1193 |
33 |
33 |
178 |
178 |
0 |
0 |
0 |
0 |
3243 |
3243 |
264 |
264 |
https://usegalaxy.eu/published/workflow?id=012762cb4acb068b, https://usegalaxy.eu/published/workflow?id=0f044c9f62773a88, https://usegalaxy.eu/published/workflow?id=10150b1a188f6d07, https://usegalaxy.eu/published/workflow?id=12a018217ee146ca, https://usegalaxy.eu/published/workflow?id=2497292e98937a5f, https://usegalaxy.eu/published/workflow?id=2c2f0b4312bae4f4, https://usegalaxy.eu/published/workflow?id=33a052f9a3d5551d, https://usegalaxy.eu/published/workflow?id=3dec7c9b02c3d1ee, https://usegalaxy.eu/published/workflow?id=8a14cda6140acab7, https://usegalaxy.eu/published/workflow?id=8c7e972020799d57, https://usegalaxy.eu/published/workflow?id=8d64614d1971065a, https://usegalaxy.eu/published/workflow?id=9588311136ac8794, https://usegalaxy.eu/published/workflow?id=c4fc3adf8f7ff2bc, https://usegalaxy.eu/published/workflow?id=ec6b2c926fffab5f, https://usegalaxy.org.au/published/workflow?id=0edb9c8b767fa74b, https://usegalaxy.org.au/published/workflow?id=29ce205d98faf47e, https://usegalaxy.org.au/published/workflow?id=3d47e0de658b3304, https://usegalaxy.org.au/published/workflow?id=4047f9f242542716, https://usegalaxy.org.au/published/workflow?id=5fb44f257e445f56, https://usegalaxy.org.au/published/workflow?id=8034bd0690b4cbe8, https://usegalaxy.org.au/published/workflow?id=83441e3de699d157, https://usegalaxy.org.au/published/workflow?id=897a1255cef5c310, https://usegalaxy.org.au/published/workflow?id=97e55a900db3863b, https://usegalaxy.org.au/published/workflow?id=c92fead7c30c7497, https://usegalaxy.org.au/published/workflow?id=d2dcd3b54e5082a6, https://usegalaxy.org.au/published/workflow?id=d417e920ff97e4c1, https://usegalaxy.org.au/published/workflow?id=d720c98f7227b6d5, https://usegalaxy.org/published/workflow?id=1473cdcbd664d147, https://usegalaxy.org/published/workflow?id=1b80302437db5937, https://usegalaxy.org/published/workflow?id=5c259623a010fe77, https://usegalaxy.org/published/workflow?id=5e38c7b36e4918ad, https://usegalaxy.org/published/workflow?id=605160c81d098703, https://usegalaxy.org/published/workflow?id=7c9a55db0b0eb178, https://usegalaxy.org/published/workflow?id=b7fe3873ee5e3a02, https://usegalaxy.org/published/workflow?id=c8f9e048ddae7d03, https://usegalaxy.org/published/workflow?id=cace9f1359874352, https://usegalaxy.org/published/workflow?id=d2c408df40dc311b, https://usegalaxy.org/published/workflow?id=ddf7a594b9609d68, https://usegalaxy.org/published/workflow?id=e887adf3afc3253d, https://usegalaxy.org/published/workflow?id=ea206593698adbfd, https://usegalaxy.org/published/workflow?id=fc2b48600853f3ea, https://workflowhub.eu/workflows/1594?version=1, https://workflowhub.eu/workflows/645?version=13 |
assembly/assembly-decontamination |
|
pathview |
pathview |
Pathview is a tool set for pathway based data integration and visualization. |
2019-08-26 |
https://bioconductor.org/packages/release/bioc/html/pathview.html |
1.34.0 |
bioconductor-pathview |
1.46.0 |
To update |
Statistics, RNA, Micro-array Analysis |
Pathway or network analysis, Pathway or network visualisation |
Pathway or network analysis, Pathway or network visualisation |
Molecular interactions, pathways and networks, Systems biology, Data visualisation |
Molecular interactions, pathways and networks, Systems biology, Data visualisation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview |
pathview |
pathview |
Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1546 |
1688 |
8322 |
9128 |
1410 |
1484 |
7998 |
8673 |
244 |
244 |
1526 |
1526 |
21 |
22 |
258 |
275 |
19602 |
18104 |
3438 |
3221 |
https://usegalaxy.org.au/published/workflow?id=5490661d0153962b, https://workflowhub.eu/workflows/1713?version=1 |
transcriptomics/ref-based |
|
pbgcpp |
pbgcpp |
Compute genomic consensus and call variants using PacBio reads mapped to a reference |
2022-03-10 |
https://github.com/PacificBiosciences/gcpp |
2.0.2 |
pbgcpp |
2.0.2 |
Up-to-date |
Variant Analysis |
Variant calling |
Variant calling |
Mapping |
Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp |
genomicconsensus |
GenomicConsensus |
The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
pbmm2 |
pbmm2 |
A minimap2 SMRT wrapper for PacBio data. |
2022-03-10 |
https://github.com/PacificBiosciences/pbmm2 |
1.17.0 |
pbmm2 |
1.17.0 |
Up-to-date |
Next Gen Mappers |
Pairwise sequence alignment, Sorting |
Pairwise sequence alignment, Sorting |
Mapping |
Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 |
pbmm2 |
pbmm2 |
pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
41 |
41 |
229 |
229 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
229 |
229 |
41 |
41 |
|
|
|
pcdl |
pcdl_get_anndata, pcdl_get_cell_attribute, pcdl_get_cell_attribute_list, pcdl_get_cell_df, pcdl_get_celltype_list, pcdl_get_conc_attribute, pcdl_get_conc_df, pcdl_get_substrate_list, pcdl_get_unit_dict, pcdl_get_version, pcdl_make_cell_vtk, pcdl_make_conc_vtk, pcdl_make_gif, pcdl_make_graph_gml, pcdl_make_movie, pcdl_plot_contour, pcdl_plot_scatter, pcdl_plot_timeseries |
pcdl PhysiCell Data Loader. |
2025-06-06 |
https://github.com/elmbeech/physicelldataloader |
3.0.1+galaxy0 |
|
|
To update |
Systems Biology, Data Export, Graphics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl |
|
|
|
|
0 |
0 |
18 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
pdfimages |
pdfimages |
PDF image extractor. |
2025-07-31 |
https://gitlab.freedesktop.org/poppler/poppler/ |
25.07.0 |
poppler |
|
To update |
Imaging, Natural Language Processing |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pdfimages/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pdfimages |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
15 |
15 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
15 |
15 |
2 |
2 |
|
|
|
pe_histogram |
pe_histogram |
Contains a tool that produces an insert size histogram for a paired-end BAM file. |
2016-06-16 |
https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram |
1.0.2 |
openjdk |
|
To update |
Graphics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
709 |
709 |
8778 |
8778 |
1037 |
1176 |
10416 |
11753 |
168 |
168 |
1076 |
1076 |
72 |
72 |
195 |
195 |
21802 |
20465 |
2125 |
1986 |
https://usegalaxy.eu/published/workflow?id=1089e5c66dbcc1a3, https://usegalaxy.eu/published/workflow?id=111527fe542846af, https://usegalaxy.eu/published/workflow?id=1ee43d90b69829e9, https://usegalaxy.eu/published/workflow?id=25aa944237d7fb82, https://usegalaxy.eu/published/workflow?id=2f51a82838722bec, https://usegalaxy.eu/published/workflow?id=30e7dc81e323cbdb, https://usegalaxy.eu/published/workflow?id=3b8ef7905c902b27, https://usegalaxy.eu/published/workflow?id=45f63151bf4f1a49, https://usegalaxy.eu/published/workflow?id=48f63ef14a12f306, https://usegalaxy.eu/published/workflow?id=4daa0c33d6d50379, https://usegalaxy.eu/published/workflow?id=54b91dd86f463391, https://usegalaxy.eu/published/workflow?id=7e0ba4c14803448e, https://usegalaxy.eu/published/workflow?id=8132c3b710fd6d48, https://usegalaxy.eu/published/workflow?id=93a7047396080fda, https://usegalaxy.eu/published/workflow?id=94b9287365ea4d0d, https://usegalaxy.eu/published/workflow?id=ad4b347f9b68e127, 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epigenetics/atac-seq, epigenetics/cut_and_run |
|
peakzilla |
peakzilla |
Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. |
2024-02-25 |
https://github.com/steinmann/peakzilla |
1.0 |
python |
|
To update |
ChIP-seq |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
19 |
19 |
73 |
73 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
73 |
73 |
19 |
19 |
|
|
|
pear |
iuc_pear |
PEAR evaluates all possible paired-end read overlaps |
2015-02-11 |
https://cme.h-its.org/exelixis/web/software/pear/ |
0.9.6 |
pear |
0.9.6 |
Up-to-date |
Fastq Manipulation |
Sequence merging |
Sequence merging |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear |
pear |
PEAR |
Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
1 |
0 |
416 |
448 |
9796 |
10458 |
665 |
1869 |
8692 |
23290 |
202 |
335 |
4780 |
8865 |
0 |
0 |
0 |
0 |
42613 |
23268 |
2652 |
1283 |
https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org/published/workflow?id=9a1fb6ecff886358, https://workflowhub.eu/workflows/232?version=1 |
|
|
pgxrpi |
pgx_freqplot, pgx_loader |
pgxLoader and pgxFreqplot functions from pgxRpi |
2025-02-27 |
https://github.com/progenetix/pgxRpi |
1.2.0 |
bioconductor-pgxrpi |
1.2.0 |
Up-to-date |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pgxrpi |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pgxRpi |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
pharokka |
pharokka |
rapid standardised annotation tool for bacteriophage genomes and metagenomes |
2023-02-14 |
https://github.com/gbouras13/pharokka |
1.3.2 |
\n pharokka\n |
|
To update |
Genome annotation |
Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly |
Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly |
Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA |
Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka |
pharokka |
Pharokka |
Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
1 |
0 |
766 |
766 |
16933 |
16933 |
1 |
1 |
21 |
21 |
117 |
117 |
1202 |
1202 |
0 |
0 |
0 |
0 |
18156 |
18156 |
884 |
884 |
|
|
|
phyloseq |
phyloseq_add_rank_names, phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_bar, phyloseq_plot_ordination, phyloseq_plot_richness, phyloseq_tax_glom |
Handling and analysis of high-throughput microbiome census data |
2022-03-03 |
https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html |
1.50.0 |
bioconductor-phyloseq |
1.50.0 |
Up-to-date |
Metagenomics |
Deposition, Analysis, Visualisation |
Deposition, Analysis, Visualisation |
Microbiology, Sequence analysis, Metagenomics |
Microbiology, Sequence analysis, Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq |
phyloseq |
phyloseq |
Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. |
|
0 |
1 |
7 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
251 |
251 |
3161 |
3161 |
156 |
156 |
1022 |
1022 |
35 |
35 |
190 |
190 |
14 |
14 |
163 |
163 |
4536 |
4536 |
456 |
456 |
https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=e3918808605cf8cd, https://usegalaxy.org/published/workflow?id=4faff660f6defa10, https://workflowhub.eu/workflows/1395?version=2 |
microbiome/dada-16S |
|
phyml |
phyml |
PhyML is a phylogeny software based on the maximum-likelihood principle. |
2019-05-27 |
http://www.atgc-montpellier.fr/phyml/ |
3.3.20220408 |
phyml |
3.3.20220408 |
Up-to-date |
Phylogenetics |
Phylogenetic tree generation (maximum likelihood and Bayesian methods) |
|
Phylogenetics, Bioinformatics, Phylogenetics |
Phylogenetics, Bioinformatics, Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml |
phyml |
PhyML |
Phylogenetic estimation software using Maximum Likelihood |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
286 |
335 |
2452 |
2654 |
0 |
0 |
0 |
0 |
215 |
240 |
1475 |
1564 |
79 |
79 |
334 |
334 |
4552 |
4261 |
654 |
580 |
https://usegalaxy.fr/published/workflow?id=63b49f322ec366b5, https://usegalaxy.fr/published/workflow?id=894143d81af8dff0 |
|
|
picard |
picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile |
Picard SAM/BAM manipulation tools. |
2017-01-11 |
http://broadinstitute.github.io/picard/ |
3.1.1 |
picard |
3.4.0 |
To update |
SAM |
Formatting |
Formatting |
Sequencing |
Sequencing |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard |
picard_samtofastq |
picard_samtofastq |
Create a FASTQ file. |
|
0 |
31 |
31 |
31 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
31 |
4 |
31 |
0 |
0 |
0 |
0 |
0 |
31 |
0 |
0 |
0 |
0 |
0 |
0 |
31 |
31 |
31 |
5984 |
6700 |
343073 |
472216 |
11191 |
18752 |
341066 |
667776 |
1462 |
1651 |
57833 |
72802 |
1018 |
1021 |
41496 |
41992 |
1254786 |
783468 |
28124 |
19655 |
https://usegalaxy.eu/published/workflow?id=02655d0e4af0ee0d, https://usegalaxy.eu/published/workflow?id=03d1d2e0dc6e2024, https://usegalaxy.eu/published/workflow?id=0599f049e4697839, https://usegalaxy.eu/published/workflow?id=07b74e4cf53cb633, https://usegalaxy.eu/published/workflow?id=0a72d640d415e866, https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=0e5b701ed5ca69a7, https://usegalaxy.eu/published/workflow?id=1089e5c66dbcc1a3, https://usegalaxy.eu/published/workflow?id=111527fe542846af, https://usegalaxy.eu/published/workflow?id=112422839b68db02, https://usegalaxy.eu/published/workflow?id=146cef3acb2eba75, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=1761092d0e7deece, https://usegalaxy.eu/published/workflow?id=1b38e0d69e366be1, https://usegalaxy.eu/published/workflow?id=1c5588d6ac7f773f, https://usegalaxy.eu/published/workflow?id=1dba8278fb2786fb, 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https://workflowhub.eu/workflows/395?version=15, https://workflowhub.eu/workflows/399?version=19, https://workflowhub.eu/workflows/625?version=26 |
epigenetics/atac-seq, epigenetics/cut_and_run, genome-annotation/funannotate, introduction/galaxy-intro-ngs-data-managment, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts, variant-analysis/non-dip, variant-analysis/sars-cov-2 |
|
pick_value |
pick_value |
Compose a text parameter value using text, integer and float values |
2023-01-23 |
|
0.2.0 |
|
|
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
157 |
157 |
6779 |
6779 |
188 |
188 |
12737 |
12737 |
16 |
16 |
746 |
746 |
4 |
4 |
332 |
332 |
20594 |
20594 |
365 |
365 |
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https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1164?version=2, https://workflowhub.eu/workflows/1201?version=4, https://workflowhub.eu/workflows/1256?version=1, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/1327?version=6, https://workflowhub.eu/workflows/1352?version=3, https://workflowhub.eu/workflows/1873?version=1, https://workflowhub.eu/workflows/1876?version=1, https://workflowhub.eu/workflows/1882?version=2, https://workflowhub.eu/workflows/612?version=24, https://workflowhub.eu/workflows/625?version=26, https://workflowhub.eu/workflows/628?version=1, https://workflowhub.eu/workflows/631?version=6, https://workflowhub.eu/workflows/632?version=11, https://workflowhub.eu/workflows/642?version=24, https://workflowhub.eu/workflows/694?version=8 |
statistics/flexynesis_classification |
|
picrust |
picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes |
PICRUSt wrappers |
2016-11-08 |
https://picrust.github.io/picrust/ |
1.1.1 |
picrust |
1.1.4 |
To update |
Metagenomics |
Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding |
Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding |
Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing |
Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust |
picrust |
PICRUSt |
PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. |
|
0 |
6 |
5 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
44 |
63 |
562 |
1142 |
0 |
0 |
0 |
0 |
38 |
41 |
2348 |
2626 |
20 |
20 |
442 |
442 |
4210 |
3352 |
124 |
102 |
|
|
|
picrust2 |
picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions |
PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States |
2021-07-09 |
https://github.com/picrust/picrust2/wiki |
2.5.3 |
picrust2 |
2.6.2 |
To update |
Metagenomics |
Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis |
Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis |
Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing |
Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing |
iuc |
https://github.com/picrust/picrust2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 |
picrust2 |
PICRUSt2 |
PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. |
|
0 |
7 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
0 |
327 |
327 |
6432 |
6432 |
1 |
1 |
1 |
1 |
64 |
64 |
2888 |
2888 |
0 |
0 |
0 |
0 |
9321 |
9321 |
392 |
392 |
https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34 |
|
|
pilon |
pilon |
pilon is a tool for assembly improvement and variant analysis in bacteria |
2016-08-11 |
https://github.com/broadinstitute/pilon/wiki |
1.20.1 |
pilon |
1.24 |
To update |
Variant Analysis |
Sequence assembly, Analysis, Read alignment |
Sequence assembly, Analysis |
Assembly |
Assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon |
pilon |
pilon |
Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1417 |
1484 |
10881 |
12166 |
1340 |
1411 |
8461 |
9526 |
985 |
1018 |
5002 |
5466 |
25 |
25 |
126 |
126 |
27284 |
24470 |
3938 |
3767 |
https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=3588c40cab9b4e1d, https://usegalaxy.org.au/published/workflow?id=02c74095a7128c9d, https://usegalaxy.org.au/published/workflow?id=22bd45f60c60a338, https://usegalaxy.org.au/published/workflow?id=2cb16d321a804b1a, https://usegalaxy.org.au/published/workflow?id=7c343e5b55474d19, https://usegalaxy.org.au/published/workflow?id=8a40059343cf4b87, https://usegalaxy.org.au/published/workflow?id=b5403e4fff2961f9, https://usegalaxy.org/published/workflow?id=bff206b4625375bc, https://workflowhub.eu/workflows/1617?version=1 |
assembly/chloroplast-assembly |
|
pimento |
pimento_are_there_primers, pimento_auto, pimento_choose_primer_cutoff, pimento_find_cutoffs, pimento_gen_bcv, pimento_std |
A PrIMEr infereNce TOolkit to facilitate large-scale calling of metabarcoding amplicon sequence variants. |
2025-08-04 |
https://github.com/EBI-Metagenomics/PIMENTO |
1.0.2 |
mi-pimento |
1.0.2 |
Up-to-date |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento |
|
|
|
|
0 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
1 |
1 |
|
|
|
pipelign |
pipelign |
Multipe sequence alignment |
2019-08-20 |
https://github.com/asmmhossain/pipelign/ |
0.2 |
pipelign |
0.2 |
Up-to-date |
Next Gen Mappers |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
313 |
329 |
1909 |
1972 |
715 |
796 |
9356 |
9994 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11966 |
11265 |
1125 |
1028 |
|
|
|
pizzly |
pizzly |
Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. |
2017-09-03 |
https://github.com/pmelsted/pizzly/ |
0.37.3.1 |
pizzly |
0.37.3 |
To update |
Transcriptomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
25 |
30 |
2337 |
2381 |
71 |
89 |
2125 |
2362 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4743 |
4462 |
119 |
96 |
|
|
|
plasclass |
plasclass |
PlasClass is a tool to classify sequences of plasmid or chromosomal origin |
2025-07-31 |
https://github.com/Shamir-Lab/PlasClass |
0.1.1 |
plasclass |
0.1.1 |
Up-to-date |
Sequence Analysis |
Sequence classification, Sequence assembly, k-mer counting |
Sequence classification, Sequence assembly, k-mer counting |
Metagenomics, Sequence assembly, DNA, Metagenomic sequencing |
Metagenomics, Sequence assembly, DNA, Metagenomic sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass |
PlasClass |
PlasClass |
PlasClass is a tool for easy classification of sequences as either plasmid or chromosomal. For example, it can be used to classify the contigs in a (metagenomic) assembly. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
plasflow |
PlasFlow |
PlasFlow - Prediction of plasmid sequences in metagenomic contigs. |
2018-09-05 |
https://github.com/smaegol/PlasFlow |
1.1.0 |
plasflow |
1.1.0 |
Up-to-date |
Sequence Analysis |
Sequence analysis |
Sequence analysis |
Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning |
Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow |
plasflow |
PlasFlow |
PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
876 |
1004 |
55069 |
56639 |
757 |
797 |
7929 |
8195 |
87 |
87 |
3496 |
3496 |
0 |
0 |
0 |
0 |
68330 |
66494 |
1888 |
1720 |
https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=32d2f5340098bcbd, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=b4de76c0a4d0e23a, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/406?version=1 |
microbiome/plasmid-metagenomics-nanopore |
|
plasmidfinder |
plasmidfinder |
"PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage" |
2022-09-19 |
https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ |
2.1.6 |
plasmidfinder |
2.1.6 |
Up-to-date |
Sequence Analysis |
Genome assembly, Scaffolding, Multilocus sequence typing |
Genome assembly, Scaffolding, Multilocus sequence typing |
Whole genome sequencing, Sequence assembly, Mapping, Probes and primers |
Whole genome sequencing, Sequence assembly, Mapping, Probes and primers |
iuc |
https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder |
PlasmidFinder |
PlasmidFinder |
PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1015 |
1015 |
35994 |
35994 |
623 |
623 |
11939 |
11939 |
211 |
211 |
3278 |
3278 |
48 |
48 |
10730 |
10730 |
61941 |
61941 |
1897 |
1897 |
https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3f5fe28793ed0c6c, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, https://usegalaxy.eu/published/workflow?id=61948fcaefa1418a, https://usegalaxy.eu/published/workflow?id=6b69ab27c565257b, https://usegalaxy.eu/published/workflow?id=8792eaecb69fbc26, https://usegalaxy.eu/published/workflow?id=a18aed4b03ffd27e, https://usegalaxy.eu/published/workflow?id=b1afc8d1e81fc904, https://usegalaxy.eu/published/workflow?id=bcd50e655809cfcb, https://usegalaxy.eu/published/workflow?id=d8db0b2e30370b84, https://usegalaxy.eu/published/workflow?id=dfb8e0f3c534000e, https://usegalaxy.eu/published/workflow?id=fd63b9884fda75b6, https://usegalaxy.fr/published/workflow?id=7964ddc68853458f, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org/published/workflow?id=04c5ea133de3204c, https://usegalaxy.org/published/workflow?id=3940186d02245b1d, https://usegalaxy.org/published/workflow?id=49da012e2839c046, https://usegalaxy.org/published/workflow?id=4f8bdd61c524b901, https://usegalaxy.org/published/workflow?id=649cdc14757e5755, https://usegalaxy.org/published/workflow?id=8cb8a588a0495cfa, https://usegalaxy.org/published/workflow?id=993534c11310a207, https://usegalaxy.org/published/workflow?id=d2a5f6a5181aada5, https://workflowhub.eu/workflows/1050?version=12, https://workflowhub.eu/workflows/1513?version=1 |
genome-annotation/bacterial-genome-annotation |
|
plink |
plink |
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. |
2020-09-14 |
https://www.cog-genomics.org/plink |
1.90b6.21 |
plink |
1.90b6.21 |
Up-to-date |
Genome-Wide Association Study |
Genetic variation analysis |
Genetic variation analysis |
GWAS study |
GWAS study |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink |
plink |
PLINK |
Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
191 |
191 |
1210 |
1210 |
105 |
105 |
1251 |
1251 |
0 |
0 |
0 |
0 |
7 |
7 |
67 |
67 |
2528 |
2528 |
303 |
303 |
|
|
|
polypolish |
polypolish |
"Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix." |
2022-09-22 |
https://github.com/rrwick/Polypolish |
0.6.1 |
polypolish |
0.6.1 |
Up-to-date |
Sequence Analysis |
Genome assembly, Read mapping, Mapping assembly, Sequencing error detection |
Genome assembly, Read mapping, Mapping assembly, Sequencing error detection |
Sequence assembly, Sequence composition, complexity and repeats, Mapping |
Sequence assembly, Sequence composition, complexity and repeats, Mapping |
iuc |
https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish |
Polypolish |
Polypolish |
Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
147 |
147 |
1066 |
1066 |
0 |
0 |
0 |
0 |
26 |
26 |
615 |
615 |
10 |
10 |
79 |
79 |
1760 |
1760 |
183 |
183 |
https://workflowhub.eu/workflows/1613?version=1 |
assembly/mrsa-nanopore |
|
porechop |
porechop |
Porechop - Finding and removing adapters from Oxford Nanopore reads |
2018-09-13 |
https://github.com/rrwick/Porechop |
|
porechop |
0.2.4 |
To update |
Fasta Manipulation, Fastq Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3888 |
4063 |
445549 |
452222 |
3090 |
3144 |
150171 |
150874 |
1362 |
1432 |
46371 |
65797 |
9 |
9 |
10935 |
10935 |
679828 |
653026 |
8648 |
8349 |
https://usegalaxy.eu/published/workflow?id=0590554db9794d13, https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c, https://usegalaxy.eu/published/workflow?id=181e751be8dd9abc, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=30dc526dcfa500df, https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302, https://usegalaxy.eu/published/workflow?id=346b46e6316c6950, https://usegalaxy.eu/published/workflow?id=4a39d38fde81e35d, https://usegalaxy.eu/published/workflow?id=57d3109f32defa3b, https://usegalaxy.eu/published/workflow?id=70d3ebf31940bfb3, https://usegalaxy.eu/published/workflow?id=86cf02cc0868d238, https://usegalaxy.eu/published/workflow?id=889f2782ad82bd69, https://usegalaxy.eu/published/workflow?id=8b2f53745e720d0f, https://usegalaxy.eu/published/workflow?id=a705370bc2c13d5c, https://usegalaxy.eu/published/workflow?id=ab646c6ab6de7061, https://usegalaxy.eu/published/workflow?id=bf48b0eb15e8ff75, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=fc0b9efa7d2e61e6, https://usegalaxy.org.au/published/workflow?id=25d52afddaa3451b, https://usegalaxy.org.au/published/workflow?id=479c6b0a96ea1610, https://usegalaxy.org.au/published/workflow?id=4c7e0703aace6aa3, https://usegalaxy.org.au/published/workflow?id=59618ed15510f531, https://usegalaxy.org.au/published/workflow?id=69d91340fc7effa2, https://usegalaxy.org.au/published/workflow?id=803ef29108e36e58, https://usegalaxy.org.au/published/workflow?id=c4d23297f6fbf5f3, https://usegalaxy.org.au/published/workflow?id=c997a34b55425155, https://usegalaxy.org/published/workflow?id=00596e862edb23f2, https://usegalaxy.org/published/workflow?id=21161075002d6778, https://usegalaxy.org/published/workflow?id=2ded909e7e3a9962, https://usegalaxy.org/published/workflow?id=48dafc35989f13b1, https://usegalaxy.org/published/workflow?id=5626a440a5798458, https://usegalaxy.org/published/workflow?id=562bcaa9b4d2e8a4, https://usegalaxy.org/published/workflow?id=574e42683dc3961b, https://usegalaxy.org/published/workflow?id=60f0d0d5d6e93941, https://usegalaxy.org/published/workflow?id=69d8863d40524120, https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1, https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8, https://usegalaxy.org/published/workflow?id=a8b9252fad5fe06a, https://usegalaxy.org/published/workflow?id=b7817a12dbee583c, https://usegalaxy.org/published/workflow?id=badd4b56dbdeaba7, https://usegalaxy.org/published/workflow?id=cfa9e6e722b086c8, https://usegalaxy.org/published/workflow?id=d5436cee11a34de9, https://workflowhub.eu/workflows/1061?version=1, https://workflowhub.eu/workflows/1114?version=1, https://workflowhub.eu/workflows/1439?version=1, https://workflowhub.eu/workflows/1473?version=1, https://workflowhub.eu/workflows/1492?version=2 |
assembly/mrsa-nanopore, microbiome/beer-data-analysis, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data |
|
poretools |
poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot |
A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. |
2017-12-17 |
https://poretools.readthedocs.io/en/latest/ |
0.6.1a1 |
poretools |
0.6.1a1 |
Up-to-date |
Fasta Manipulation, Fastq Manipulation |
Nucleic acid sequence analysis |
Nucleic acid sequence analysis |
DNA, Sequencing |
DNA, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools |
poretools |
Poretools |
Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. |
|
0 |
13 |
13 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
13 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
13 |
13 |
172 |
274 |
15702 |
21152 |
392 |
508 |
31358 |
42781 |
125 |
130 |
9684 |
11349 |
0 |
0 |
0 |
0 |
75282 |
56744 |
912 |
689 |
|
|
|
ppanggolin |
ppanggolin_all, ppanggolin_msa, ppanggolin_projection, ppanggolin_rarefaction |
Microbial Partitioned PanGenome |
2025-01-22 |
https://github.com/labgem/PPanGGOLiN |
2.2.5 |
ppanggolin |
2.2.5 |
Up-to-date |
Genome annotation |
Rarefaction, Essential dynamics, Sequence assembly, Genome annotation |
Rarefaction, Essential dynamics, Sequence assembly, Genome annotation |
Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping |
Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin |
ppanggolin |
PPanGGOLiN |
PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species |
|
0 |
0 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
55 |
55 |
249 |
249 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
16 |
67 |
67 |
316 |
316 |
71 |
71 |
|
genome-annotation/bacterial-pangenomics |
|
presto |
presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 |
pRESTO toolkit for immune repertoire analysis. |
2017-08-30 |
https://presto.readthedocs.io/ |
0.6.2 |
presto |
0.7.6 |
To update |
Sequence Analysis |
Nucleic acid sequence analysis |
Nucleic acid sequence analysis |
Sequencing, DNA, Immunology |
Sequencing, DNA, Immunology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto |
presto |
pRESTO |
Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
331 |
401 |
75739 |
81623 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
81623 |
75739 |
401 |
331 |
https://usegalaxy.org/published/workflow?id=34f3aac3aed0f97a, https://usegalaxy.org/published/workflow?id=51f936d1a4e849fa |
|
|
prinseq |
prinseq |
PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets |
2016-05-30 |
http://prinseq.sourceforge.net/manual.html |
@TOOL_VERSION+galaxy2 |
prinseq |
0.20.4 |
To update |
Fastq Manipulation, Metagenomics |
Read pre-processing, Sequence trimming, Sequence contamination filtering |
Read pre-processing, Sequence trimming, Sequence contamination filtering |
Transcriptomics, Metagenomics, Genomics |
Transcriptomics, Metagenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq |
prinseq |
PRINSEQ |
PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
345 |
412 |
15643 |
16651 |
1317 |
1501 |
10523 |
12474 |
0 |
0 |
0 |
0 |
11 |
11 |
17 |
17 |
29142 |
26183 |
1924 |
1673 |
https://usegalaxy.eu/published/workflow?id=0609a4b1941d1a68, https://usegalaxy.eu/published/workflow?id=76e9cd837ea5e7da, https://usegalaxy.eu/published/workflow?id=8f415b0c409f56f7, https://usegalaxy.eu/published/workflow?id=9fddc44294236e8f, https://usegalaxy.eu/published/workflow?id=d6ff6be33b8bfe85, https://usegalaxy.eu/published/workflow?id=da19c0eaa757fa39, https://usegalaxy.org/published/workflow?id=20b7ae4b517a80fd, https://usegalaxy.org/published/workflow?id=46f184a0e95f3c1c, https://usegalaxy.org/published/workflow?id=5f878c4cc3bff68c, https://usegalaxy.org/published/workflow?id=a71fcbc60caae8b6, https://usegalaxy.org/published/workflow?id=afb67b4b9952f57d, https://workflowhub.eu/workflows/1271?version=3, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1850?version=1, https://workflowhub.eu/workflows/1854?version=1 |
microbiome/mgnify-amplicon |
|
prodigal |
prodigal |
A protein-coding gene prediction software tool for bacterial and archaeal genomes |
2024-03-14 |
https://github.com/hyattpd/Prodigal |
2.6.3 |
prodigal |
2.6.3 |
Up-to-date |
Genome annotation |
Genome annotation |
Genome annotation |
Genomics, Sequence analysis |
Genomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal |
prodigal |
Prodigal |
Fast, reliable protein-coding gene prediction for prokaryotic genomes. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
611 |
611 |
6456 |
6456 |
0 |
0 |
0 |
0 |
70 |
70 |
1515 |
1515 |
19 |
19 |
1487 |
1487 |
9458 |
9458 |
700 |
700 |
https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b, https://workflowhub.eu/workflows/1663?version=1 |
ecology/marine_omics_bgc |
|
progressivemauve |
progressivemauve, xmfa2gff3 |
Mauve/ProgressiveMauve Multiple Sequence Aligner |
2015-05-15 |
http://darlinglab.org/mauve/user-guide/progressivemauve.html |
|
progressivemauve |
snapshot_2015_02_13 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
788 |
861 |
2637 |
3053 |
1096 |
1189 |
3329 |
3750 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
6804 |
5967 |
2051 |
1885 |
|
|
|
prokka |
prokka |
Rapid annotation of prokaryotic genomes |
2016-10-07 |
http://github.com/tseemann/prokka |
1.14.6 |
prokka |
1.14.6 |
Up-to-date |
Sequence Analysis |
Gene prediction, Coding region prediction, Genome annotation |
Coding region prediction, Genome annotation |
Genomics, Model organisms, Virology |
Genomics, Model organisms, Virology |
crs4 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka |
prokka |
Prokka |
Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
1 |
1 |
10459 |
11098 |
819587 |
847581 |
14547 |
16587 |
462648 |
506432 |
5094 |
6142 |
199279 |
229418 |
422 |
424 |
7463 |
7481 |
1590912 |
1488977 |
34251 |
30522 |
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assembly/chloroplast-assembly, assembly/unicycler-assembly, genome-annotation/annotation-with-prokka |
|
prot_scriber |
prot_scriber |
Protein annotation of short human readable descriptions |
2022-05-10 |
https://github.com/usadellab/prot-scriber |
0.1.6 |
prot-scriber |
0.1.6 |
Up-to-date |
Proteomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
9 |
9 |
13 |
13 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
13 |
13 |
9 |
9 |
|
|
|
proteinortho |
proteinortho, proteinortho_clustering, proteinortho_grab_proteins, proteinortho_summary |
Proteinortho is a tool to detect orthologous proteins/genes within different species. |
2020-02-05 |
https://gitlab.com/paulklemm_PHD/proteinortho |
6.3.6 |
proteinortho |
6.3.6 |
Up-to-date |
Proteomics |
Sequence clustering, Sequence analysis |
Sequence clustering, Sequence analysis |
Comparative genomics |
Comparative genomics |
iuc |
https://gitlab.com/paulklemm_PHD/proteinortho |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho |
proteinortho |
Proteinortho |
Proteinortho is a tool to detect orthologous genes within different species |
|
0 |
0 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
432 |
463 |
5028 |
5485 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
23 |
23 |
5508 |
5051 |
467 |
436 |
https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1 |
ecology/phylogeny-data-prep |
|
psiclass |
psiclass |
PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. |
2023-09-06 |
https://github.com/splicebox/PsiCLASS |
1.0.3 |
psiclass |
1.0.3 |
Up-to-date |
Transcriptomics |
Transcriptome assembly |
Transcriptome assembly |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass |
psiclass |
PsiCLASS |
Reference-based transcriptome assembler for single or multiple RNA-seq samples |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
11 |
11 |
46 |
46 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
46 |
46 |
11 |
11 |
|
|
|
pureclip |
pureclip |
PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data |
2018-04-26 |
https://github.com/skrakau/PureCLIP |
1.0.4 |
pureclip |
1.3.1 |
To update |
Sequence Analysis, RNA, CLIP-seq |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
84 |
105 |
1337 |
1705 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1705 |
1337 |
105 |
84 |
https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=8fb156020285e049 |
|
|
purge_dups |
purge_dups |
Purge haplotigs and overlaps in an assembly based on read depth |
2021-02-03 |
https://github.com/dfguan/purge_dups |
1.2.6 |
purge_dups |
1.2.6 |
Up-to-date |
Assembly |
Genome assembly, Read binning, Scaffolding |
Genome assembly, Read binning, Scaffolding |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups |
purge_dups |
purge_dups |
Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
365 |
365 |
19303 |
19303 |
97 |
97 |
1776 |
1776 |
80 |
80 |
3001 |
3001 |
0 |
0 |
0 |
0 |
24080 |
24080 |
542 |
542 |
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https://workflowhub.eu/workflows/701?version=1, https://workflowhub.eu/workflows/751?version=17 |
assembly/vgp_genome_assembly |
|
pycoqc |
pycoqc |
QC metrics for ONT Basecalling |
2021-03-02 |
https://github.com/tleonardi/pycoQC |
2.5.2 |
pycoqc |
2.5.2 |
Up-to-date |
Nanopore |
Sequencing quality control, Statistical calculation |
Sequencing quality control, Statistical calculation |
Sequence analysis, Data quality management, Sequencing |
Sequence analysis, Data quality management, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc |
pycoqc |
pycoQC |
PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
832 |
832 |
23549 |
23549 |
1182 |
1182 |
4440 |
4440 |
606 |
606 |
1143 |
1143 |
158 |
158 |
322 |
322 |
29454 |
29454 |
2778 |
2778 |
https://usegalaxy.org.au/published/workflow?id=01393562b82f1884, https://usegalaxy.org.au/published/workflow?id=0d1d4392c3042fbd, https://usegalaxy.org.au/published/workflow?id=31dbe7344d72b903, https://usegalaxy.org.au/published/workflow?id=364025bd13970867, https://usegalaxy.org.au/published/workflow?id=419e09e4a2fa6d38, https://usegalaxy.org.au/published/workflow?id=5f4e164c18810cca, https://usegalaxy.org.au/published/workflow?id=866b69c5ee6601fe, https://usegalaxy.org.au/published/workflow?id=8fe84de499e96485, https://usegalaxy.org.au/published/workflow?id=98f285d6f0253b81, https://usegalaxy.org.au/published/workflow?id=c87b645aedfb857d, https://usegalaxy.org.au/published/workflow?id=da3d4b39b0d655e7, https://usegalaxy.org.au/published/workflow?id=ed43af416c6a7d3b, https://usegalaxy.org.au/published/workflow?id=fdf32312e8567093 |
sequence-analysis/quality-control |
|
pygenometracks |
pygenomeTracks |
pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. |
2018-06-08 |
https://github.com/deeptools/pyGenomeTracks |
3.8 |
pygenometracks |
3.9 |
To update |
Visualization |
Visualisation, Formatting |
Visualisation, Formatting |
Model organisms, Imaging, Workflows |
Model organisms, Imaging, Workflows |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks |
pygenometracks |
pyGenomeTracks |
reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1301 |
1446 |
13377 |
16146 |
1427 |
1472 |
11997 |
12438 |
210 |
210 |
5014 |
5054 |
44 |
44 |
81 |
81 |
33719 |
30469 |
3172 |
2982 |
https://usegalaxy.eu/published/workflow?id=02655d0e4af0ee0d, https://usegalaxy.eu/published/workflow?id=2a9c812f59b7b36c, https://usegalaxy.eu/published/workflow?id=4464d3b0fc782a1a, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=506a451679fe25b4, https://usegalaxy.eu/published/workflow?id=72201ffaf488f278, https://usegalaxy.eu/published/workflow?id=9843ae66c3b367b7, https://usegalaxy.eu/published/workflow?id=985044b4b2c51425, https://usegalaxy.eu/published/workflow?id=9f8a93cfffb31cd6, https://usegalaxy.eu/published/workflow?id=9fc8b89954c04ee1, https://usegalaxy.eu/published/workflow?id=a28c207730e7e13d, https://usegalaxy.eu/published/workflow?id=f394d1b12779ba41, https://usegalaxy.org.au/published/workflow?id=13ce18408ee7acc9, https://usegalaxy.org.au/published/workflow?id=99821674db7682bb, https://usegalaxy.org/published/workflow?id=06eaa5b141fe7a08, https://usegalaxy.org/published/workflow?id=0bc1b8888d8b20c4, https://usegalaxy.org/published/workflow?id=1dc312e3fba9f810, https://usegalaxy.org/published/workflow?id=4998f171ec922c7d, https://usegalaxy.org/published/workflow?id=582f3de3971fc38c, https://usegalaxy.org/published/workflow?id=7353afb9301780e5, https://usegalaxy.org/published/workflow?id=b31ab9e76409a9b7, https://usegalaxy.org/published/workflow?id=e33f6a058c5f57e5, https://usegalaxy.org/published/workflow?id=f13432eef7ac28e9, https://usegalaxy.org/published/workflow?id=f80b80aa7fb196ba, https://usegalaxy.org/published/workflow?id=fb789920b057fe8d, https://workflowhub.eu/workflows/1568?version=1, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/1715?version=1, https://workflowhub.eu/workflows/1847?version=1, https://workflowhub.eu/workflows/420?version=3 |
epigenetics/atac-seq, epigenetics/hicexplorer, transcriptomics/differential-isoform-expression, transcriptomics/ref-based |
|
pysradb_search |
pysradb_search |
pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. |
2022-11-10 |
https://github.com/saketkc/pysradb |
1.4.2 |
pysradb |
2.3.0 |
To update |
Sequence Analysis |
Deposition, Data retrieval |
Deposition, Data retrieval |
Sequencing, Gene transcripts, Bioinformatics |
Sequencing, Gene transcripts, Bioinformatics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb |
pysradb |
pysradb |
Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
44 |
44 |
178 |
178 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
178 |
178 |
44 |
44 |
|
|
|
qfilt |
qfilt |
Filter sequencing data |
2018-06-06 |
https://github.com/veg/qfilt |
1.0.0+galaxy1 |
qfilt |
0.0.1 |
To update |
Fastq Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
qiime |
qiime_collapse_samples, qiime_make_otu_table |
QIIME to perform microbial community analysis |
2017-01-16 |
http://www.qiime.org |
|
qiime |
1.9.1 |
To update |
Metagenomics |
Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control |
Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control |
Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics |
Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on |
qiime_add_on |
qiime_add_on |
QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. |
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
183 |
242 |
2193 |
2749 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
9 |
9 |
18 |
18 |
2769 |
2213 |
252 |
193 |
https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4 |
|
|
qiime |
qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file |
QIIME to perform microbial community analysis |
2017-01-16 |
http://www.qiime.org |
|
qiime |
1.9.1 |
To update |
Metagenomics |
Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control |
Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control |
Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics |
Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core |
qiime_core |
qiime_core |
QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. |
|
0 |
0 |
32 |
32 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
32 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
31 |
31 |
418 |
483 |
34279 |
42817 |
1 |
1 |
1617 |
1617 |
1 |
1 |
2 |
16 |
17 |
17 |
4517 |
4550 |
49000 |
40415 |
502 |
437 |
https://usegalaxy.eu/published/workflow?id=3acfb87be6db2303, https://usegalaxy.eu/published/workflow?id=58955868b504c60d, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1 |
sequence-analysis/Manage_AB1_Sanger |
|
qiime_extract_viz |
qiime_extract_viz |
Extract vizualization from QIIME artifacts |
2022-10-06 |
http://www.qiime.org |
0.1.0 |
unzip |
|
To update |
Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
31 |
31 |
277 |
277 |
0 |
0 |
0 |
0 |
9 |
9 |
186 |
186 |
0 |
0 |
0 |
0 |
463 |
463 |
40 |
40 |
https://usegalaxy.eu/published/workflow?id=be9ff4159593cc34 |
|
|
qq_tools |
qq_manhattan |
|
2020-10-07 |
https://CRAN.R-project.org/package=qqman |
0.1.0 |
r-qqman |
0.1.4 |
To update |
Visualization, Variant Analysis |
|
|
|
|
iuc |
|
https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
35 |
35 |
35 |
35 |
1 |
1 |
https://usegalaxy.fr/published/workflow?id=4ec0bc782472fa10 |
|
|
qualimap |
qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq |
Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. |
2019-10-10 |
http://qualimap.bioinfo.cipf.es/ |
2.3 |
qualimap |
2.3 |
Up-to-date |
Sequence Analysis, Transcriptomics, SAM |
Sequencing quality control |
Sequencing quality control |
Data quality management |
Data quality management |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap |
qualimap |
QualiMap |
Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. |
|
0 |
4 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
4 |
2949 |
3172 |
735774 |
740034 |
3586 |
3810 |
117198 |
120922 |
847 |
882 |
36259 |
41650 |
70 |
70 |
6924 |
6924 |
909530 |
896155 |
7934 |
7452 |
https://usegalaxy.eu/published/workflow?id=0189bab68f828d86, https://usegalaxy.eu/published/workflow?id=0be293debca8fb9b, https://usegalaxy.eu/published/workflow?id=0f6a7bd5362e4a2b, https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=2573209308aaad23, https://usegalaxy.eu/published/workflow?id=2c3d05023c02113e, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=2d9d4445a1871230, https://usegalaxy.eu/published/workflow?id=3f046b416b10b871, https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a, https://usegalaxy.eu/published/workflow?id=40d2c7ac42bd5302, https://usegalaxy.eu/published/workflow?id=429ae28a178cd07c, https://usegalaxy.eu/published/workflow?id=45fc2dada84d251e, https://usegalaxy.eu/published/workflow?id=476db04368d5e90c, https://usegalaxy.eu/published/workflow?id=4b4bfc79205d83f1, https://usegalaxy.eu/published/workflow?id=4c75ab0be3c56494, 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https://usegalaxy.org/published/workflow?id=953d9cbe05e632a8, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://usegalaxy.org/published/workflow?id=98b2ac8fc75781f8, https://usegalaxy.org/published/workflow?id=9adf8691809326e5, https://usegalaxy.org/published/workflow?id=9fc9f1db50019929, https://usegalaxy.org/published/workflow?id=b1b75a9323d25085, https://usegalaxy.org/published/workflow?id=b34ba9b2e4d8f050, https://usegalaxy.org/published/workflow?id=bd355e8ce58a139e, https://usegalaxy.org/published/workflow?id=bf3ccae8d5b6ef58, https://usegalaxy.org/published/workflow?id=c12e6b7896f8e114, https://usegalaxy.org/published/workflow?id=c7b2d2ccc4b0dec5, https://usegalaxy.org/published/workflow?id=cdf5dffbed938d49, https://usegalaxy.org/published/workflow?id=d3428dd172a78102, https://usegalaxy.org/published/workflow?id=d4ea6cdd40522eb1, https://usegalaxy.org/published/workflow?id=d96bd5c9fb553f2c, https://usegalaxy.org/published/workflow?id=e282f505ba9f729f, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://usegalaxy.org/published/workflow?id=eb4f7dbca0114270, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/110?version=11, https://workflowhub.eu/workflows/111?version=5, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/155?version=6, https://workflowhub.eu/workflows/1647?version=1, https://workflowhub.eu/workflows/1876?version=1, https://workflowhub.eu/workflows/439?version=3, https://workflowhub.eu/workflows/519?version=1, https://workflowhub.eu/workflows/628?version=1 |
variant-analysis/aiv-analysis, variant-analysis/pox-tiled-amplicon, variant-analysis/tb-variant-analysis |
|
quast |
quast |
Quast (Quality ASsessment Tool) evaluates genome assemblies. |
2016-09-07 |
http://quast.bioinf.spbau.ru/ |
5.3.0 |
quast |
5.3.0 |
Up-to-date |
Assembly |
Visualisation, Sequence assembly validation |
Visualisation, Sequence assembly validation |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast |
quast |
QUAST |
QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
11028 |
11672 |
120605 |
126603 |
13078 |
14773 |
78457 |
86986 |
4849 |
5353 |
46644 |
50987 |
613 |
619 |
14902 |
14963 |
279539 |
260608 |
32417 |
29568 |
https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=01dc0619e050dc91, https://usegalaxy.eu/published/workflow?id=0404013d5c27210d, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=0ebfab0e957b7267, https://usegalaxy.eu/published/workflow?id=1524b189069b42a5, https://usegalaxy.eu/published/workflow?id=165089132248a0b0, https://usegalaxy.eu/published/workflow?id=1860e02bcb894a64, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=30b514cfb9cce524, https://usegalaxy.eu/published/workflow?id=3303a04887a47675, https://usegalaxy.eu/published/workflow?id=34a07bf6407510ef, https://usegalaxy.eu/published/workflow?id=374797e58377c40f, https://usegalaxy.eu/published/workflow?id=37da7b42cb063a3a, 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https://usegalaxy.org/published/workflow?id=cdcf91a8ddb5dcd1, https://usegalaxy.org/published/workflow?id=db08887d7d6dc147, https://usegalaxy.org/published/workflow?id=e745c45651d829b8, https://usegalaxy.org/published/workflow?id=f4d623a19b32370e, https://usegalaxy.org/published/workflow?id=f926e70bee242785, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be, https://workflowhub.eu/workflows/1043?version=11, https://workflowhub.eu/workflows/1352?version=3, https://workflowhub.eu/workflows/1390?version=2, https://workflowhub.eu/workflows/1580?version=1, https://workflowhub.eu/workflows/1595?version=1, https://workflowhub.eu/workflows/1598?version=1, https://workflowhub.eu/workflows/1602?version=1, https://workflowhub.eu/workflows/1607?version=1, https://workflowhub.eu/workflows/1613?version=1, https://workflowhub.eu/workflows/1621?version=1, https://workflowhub.eu/workflows/1622?version=1, https://workflowhub.eu/workflows/1634?version=1, https://workflowhub.eu/workflows/1646?version=1, https://workflowhub.eu/workflows/1882?version=2, https://workflowhub.eu/workflows/225?version=1, https://workflowhub.eu/workflows/229?version=1, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/750?version=3, https://workflowhub.eu/workflows/794?version=2 |
assembly/assembly-quality-control, assembly/general-introduction, assembly/hifi-assembly, assembly/largegenome, assembly/metagenomics-assembly, assembly/mrsa-illumina, assembly/mrsa-nanopore, assembly/unicycler-assembly, assembly/vgp_genome_assembly, assembly/vgp_workflow_training, microbiome/metagenomics-assembly |
|
query_impc |
query_impc |
Contains a tool to query the IMPC database. |
2023-10-11 |
https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc |
0.9.0 |
requests |
|
To update |
Convert Formats, Web Services |
|
|
|
|
iuc |
https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
2 |
2 |
|
|
|
query_tabular |
filter_tabular, query_tabular, sqlite_to_tabular |
Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output |
2017-07-14 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular |
3.3.1 |
python |
|
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular |
|
|
|
|
0 |
3 |
3 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
2 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
869 |
887 |
150015 |
159379 |
898 |
898 |
14092 |
14092 |
149 |
149 |
7881 |
7895 |
5 |
6 |
96 |
98 |
181464 |
172084 |
1940 |
1921 |
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assembly/metagenomics-assembly, digital-humanities/open-refine-tutorial, ecology/Ecoregionalization_tutorial, galaxy-interface/ncbi-sarf, microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-3-verification, microbiome/metagenomics-assembly, microbiome/mgnify-amplicon, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-3-verification, proteomics/metaproteomics, proteomics/metaquantome-data-creation, proteomics/neoantigen-fragpipe-discovery, proteomics/neoantigen-fusion-database-generation, proteomics/neoantigen-hla-binding-novel-peptides, proteomics/neoantigen-non-reference-database-generation, proteomics/neoantigen-peptide-verification, proteomics/neoantigen-predicting-hla-binding, proteomics/neoantigen-variant-annotation, proteomics/proteogenomics-dbcreation, proteomics/proteogenomics-dbsearch, proteomics/proteogenomics-novel-peptide-analysis, transcriptomics/rna-interactome |
|
quickmerge |
quickmerge |
Merge long-read and hybrid assemblies to increase contiguity |
2022-07-08 |
https://github.com/mahulchak/quickmerge |
0.3 |
quickmerge |
0.3 |
Up-to-date |
Assembly |
Genome assembly, Scaffolding, De-novo assembly, Genotyping |
Genome assembly, Scaffolding, De-novo assembly, Genotyping |
Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype |
Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge |
quickmerge |
quickmerge |
Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
quicktree |
quicktree |
neighbour-joining phylogenetic inference |
2024-11-21 |
https://github.com/khowe/quicktree |
2.5 |
quicktree |
2.5 |
Up-to-date |
Phylogenetics |
Phylogenetic inference (from molecular sequences) |
Phylogenetic inference (from molecular sequences) |
Phylogenetics |
Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/quicktree |
quicktree |
QuickTree |
QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
69 |
69 |
466 |
466 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
466 |
466 |
69 |
69 |
https://workflowhub.eu/workflows/1650?version=1 |
sequence-analysis/tapscan-streptophyte-algae |
|
raceid |
raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory |
RaceID3, StemID2, FateID - scRNA analysis |
2018-03-03 |
https://github.com/dgrun/RaceID3_StemID2_package/ |
0.2.3 |
r-raceid |
0.1.3 |
To update |
Single Cell, Transcriptomics |
Expression profile clustering, Expression analysis, Molecular dynamics |
Expression profile clustering, Expression analysis, Molecular dynamics |
Cell biology, Molecular interactions, pathways and networks, RNA-Seq, Gene expression |
Cell biology, Molecular interactions, pathways and networks, RNA-Seq, Gene expression |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid |
RaceID |
RaceID |
Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data |
|
0 |
5 |
5 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
5 |
85 |
164 |
973 |
4613 |
433 |
438 |
3133 |
3209 |
4 |
5 |
2567 |
2969 |
1 |
1 |
1 |
1 |
10792 |
6674 |
608 |
523 |
https://usegalaxy.eu/published/workflow?id=2f8d9fb85242eca7, https://usegalaxy.org.au/published/workflow?id=9dfa217eae285c30, https://workflowhub.eu/workflows/1547?version=1 |
single-cell/scrna-raceid |
|
ragtag |
ragtag |
Reference-guided scaffolding of draft genomes tool. |
2021-11-10 |
https://github.com/malonge/RagTag |
2.1.0 |
ragtag |
2.1.0 |
Up-to-date |
Assembly |
Genome assembly |
Genome assembly |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag |
ragtag |
ragtag |
RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
774 |
774 |
8106 |
8106 |
6 |
6 |
59 |
59 |
108 |
108 |
2145 |
2145 |
32 |
32 |
416 |
416 |
10726 |
10726 |
920 |
920 |
https://usegalaxy.org.au/published/workflow?id=7f37c5366bce5489 |
|
|
rapidnj |
rapidnj |
Galaxy wrapper for the RapidNJ tool |
2020-05-11 |
https://birc.au.dk/software/rapidnj/ |
2.3.2 |
rapidnj |
2.3.2 |
Up-to-date |
Phylogenetics |
Phylogenetic tree generation |
|
Phylogeny |
Phylogeny |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj |
rapidnj |
RapidNJ |
A tool for fast canonical neighbor-joining tree construction. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
57 |
57 |
3022 |
3022 |
285 |
303 |
1941 |
2185 |
31 |
31 |
291 |
291 |
13 |
13 |
44 |
44 |
5542 |
5298 |
404 |
386 |
https://usegalaxy.eu/published/workflow?id=86900be4282d4b1d, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://usegalaxy.org/published/workflow?id=005924662f68a480, https://usegalaxy.org/published/workflow?id=0596162a499b4074, https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=b0f85c802c1ea7f8, https://workflowhub.eu/workflows/1518?version=1 |
genome-annotation/gene-centric |
|
rasusa |
rasusa |
Randomly subsample sequencing reads to a specified coverage |
2024-02-16 |
https://github.com/mbhall88/rasusa |
2.0.0 |
rasusa |
2.2.2 |
To update |
Sequence Analysis |
Sequence assembly validation, Sequencing quality control |
Sequence assembly validation |
Genomics, Sequence analysis, Sequence assembly, Sequencing, RNA-Seq |
Genomics, Sequence analysis, Sequence assembly, RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa |
rasusa |
rasusa |
Rasusa: Randomly subsample sequencing reads to aspecified coverageProduces an unbiased subsample of your reads |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
24 |
24 |
104 |
104 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
104 |
104 |
24 |
24 |
|
|
|
raven |
raven |
Raven is a de novo genome assembler for long uncorrected reads. |
2020-11-04 |
https://github.com/lbcb-sci/raven |
1.8.3 |
raven-assembler |
1.8.3 |
Up-to-date |
Assembly |
De-novo assembly, Genome assembly, Read pre-processing |
De-novo assembly, Genome assembly, Read pre-processing |
Sequence assembly, Whole genome sequencing, Genomics |
Sequence assembly, Whole genome sequencing, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven |
raven |
Raven |
a de novo genome assembler for long reads.Raven is a de novo genome assembler for long uncorrected reads. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
610 |
610 |
15837 |
15837 |
0 |
0 |
0 |
0 |
276 |
276 |
13041 |
13041 |
24 |
24 |
217 |
217 |
29095 |
29095 |
910 |
910 |
|
|
|
raxml |
raxml |
RAxML - A Maximum Likelihood based phylogenetic inference |
2015-11-05 |
http://www.exelixis-lab.org/web/software/raxml/ |
8.2.12 |
raxml |
8.2.13 |
To update |
Phylogenetics |
Sequence analysis, Phylogenetic tree analysis |
Sequence analysis |
Phylogenetics, Sequence analysis |
Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml |
raxml |
RAxML |
A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1422 |
1464 |
15492 |
16986 |
1144 |
1144 |
19599 |
19633 |
731 |
1034 |
5870 |
7945 |
21 |
21 |
305 |
305 |
44869 |
41266 |
3663 |
3318 |
https://usegalaxy.eu/published/workflow?id=470656ef317c9dd5, https://usegalaxy.eu/published/workflow?id=875b3ca170ac12a1, https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://workflowhub.eu/workflows/1577?version=1 |
evolution/mtb_phylogeny |
|
rcorrector |
rcorrector |
Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. |
2018-05-02 |
https://github.com/mourisl/Rcorrector |
1.0.3+galaxy1 |
rcorrector |
1.0.7 |
To update |
Fastq Manipulation |
Sequencing error detection |
Sequencing error detection |
RNA, RNA-Seq, Sequencing |
RNA, RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector |
rcorrector |
Rcorrector |
This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
78 |
78 |
803 |
803 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
803 |
803 |
78 |
78 |
|
|
|
read_it_and_keep |
read_it_and_keep |
Rapid decontamination of SARS-CoV-2 sequencing reads |
2022-01-28 |
https://github.com/GenomePathogenAnalysisService/read-it-and-keep |
0.2.2 |
read-it-and-keep |
0.3.0 |
To update |
Sequence Analysis |
Filtering, Genome alignment |
Filtering, Genome alignment |
Pathology, Genomics |
Pathology, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep |
read_it_and_keep |
read_it_and_keep |
Read-it-and-keep is a bioinformatics tool designed to filter and extract sequencing reads according to user-defined criteria, such as the presence of specific motifs or coverage of regions of interest. This type of filtering can be particularly useful for targeted analyses, where only relevant sequences are retained for further study, optimising computing and storage resources. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
81 |
81 |
3781 |
3781 |
8 |
8 |
9 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3790 |
3790 |
89 |
89 |
https://usegalaxy.eu/published/workflow?id=3fb550d7c2bc390a, https://usegalaxy.eu/published/workflow?id=4a764275d4bf9f31, https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539, https://usegalaxy.eu/published/workflow?id=d88145e7475e0b7b, https://workflowhub.eu/workflows/519?version=1, https://workflowhub.eu/workflows/521?version=1 |
|
|
recentrifuge |
recentrifuge |
"With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics." |
2022-05-04 |
https://github.com/khyox/recentrifuge |
1.16.1 |
recentrifuge |
1.16.1 |
Up-to-date |
Metagenomics |
Taxonomic classification, Expression analysis, Cross-assembly |
Taxonomic classification, Expression analysis, Cross-assembly |
Metagenomics, Microbial ecology, Metagenomic sequencing |
Metagenomics, Microbial ecology, Metagenomic sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge |
Recentrifuge |
Recentrifuge |
Robust comparative analysis and contamination removal for metagenomics. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
306 |
306 |
2546 |
2546 |
160 |
160 |
593 |
593 |
37 |
37 |
105 |
105 |
27 |
27 |
2397 |
2397 |
5641 |
5641 |
530 |
530 |
https://usegalaxy.eu/published/workflow?id=0a82eb8b44d9d502, https://usegalaxy.eu/published/workflow?id=0abd32dbc5207b88, https://usegalaxy.eu/published/workflow?id=0c47571d20535426, https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=47e14222073e7192, https://usegalaxy.eu/published/workflow?id=884a4415b669690c, https://usegalaxy.eu/published/workflow?id=aafcfcb585c5ca75, https://usegalaxy.eu/published/workflow?id=bb63b5bb983fd49c, https://usegalaxy.eu/published/workflow?id=bdc7cfaac0db2eab, https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264, https://usegalaxy.eu/published/workflow?id=c14d2e8b3c191bc4, https://usegalaxy.eu/published/workflow?id=c930a54a30dcc7e3, https://usegalaxy.eu/published/workflow?id=e69b555faa6bb962, https://usegalaxy.eu/published/workflow?id=ebb131f2a6172081, https://usegalaxy.fr/published/workflow?id=3d3b40398d1cd1ae, https://usegalaxy.org/published/workflow?id=1be5c982c2d36a6c, https://usegalaxy.org/published/workflow?id=2a782ad24271f570, https://usegalaxy.org/published/workflow?id=323c651ca583c9e5, https://usegalaxy.org/published/workflow?id=4f698eaeef30e364, https://usegalaxy.org/published/workflow?id=623fc80c7f91a33a, https://usegalaxy.org/published/workflow?id=9f68718f025bed30, https://usegalaxy.org/published/workflow?id=b6a795834009ce06, https://usegalaxy.org/published/workflow?id=de9bf4c1024f8d53, https://usegalaxy.org/published/workflow?id=dfd73857c0eb2a21, https://usegalaxy.org/published/workflow?id=f378960ee55f567e, https://workflowhub.eu/workflows/1052?version=11, https://workflowhub.eu/workflows/1644?version=1, https://workflowhub.eu/workflows/1674?version=1, https://workflowhub.eu/workflows/1881?version=1, https://workflowhub.eu/workflows/1882?version=2 |
ecology/bacterial-isolate-species-contamination-checking, sequence-analysis/quality-contamination-control |
|
red |
red |
Red (REpeat Detector) |
2022-09-14 |
https://github.com/BioinformaticsToolsmith/Red |
2018.09.10 |
red |
2018.09.10 |
Up-to-date |
Sequence Analysis |
RNA-Seq analysis, Editing |
RNA-Seq analysis, Editing |
RNA, Sequencing, Data visualisation |
RNA, Sequencing, Data visualisation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/red |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/red |
red |
RED |
This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
362 |
362 |
1237 |
1237 |
277 |
277 |
556 |
556 |
86 |
86 |
369 |
369 |
60 |
60 |
177 |
177 |
2339 |
2339 |
785 |
785 |
https://usegalaxy.eu/published/workflow?id=3d604dad4f1f5b3d, https://usegalaxy.eu/published/workflow?id=4a71a1e08a4a8e61, https://usegalaxy.eu/published/workflow?id=f9279495683a8ac3, https://workflowhub.eu/workflows/1538?version=2, https://workflowhub.eu/workflows/753?version=1 |
genome-annotation/repeatmasker |
|
repeat_masker |
repeatmasker_wrapper |
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. |
2018-04-21 |
http://www.repeatmasker.org/ |
4.1.5 |
repeatmasker |
4.2.1 |
To update |
Sequence Analysis |
Genome annotation |
Genome annotation |
Sequence analysis, Sequence composition, complexity and repeats |
Sequence composition, complexity and repeats |
bgruening |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker |
repeatmasker |
RepeatMasker |
A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1428 |
1448 |
10157 |
10293 |
1181 |
1219 |
9955 |
10202 |
413 |
413 |
4594 |
4594 |
91 |
91 |
610 |
610 |
25699 |
25316 |
3171 |
3113 |
https://usegalaxy.eu/published/workflow?id=09c534f738426a6d, https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=4a71a1e08a4a8e61, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.eu/published/workflow?id=f9279495683a8ac3, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=a71349ba0bff403a, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org.au/published/workflow?id=ffb1117077f68a9f, https://usegalaxy.org/published/workflow?id=effc17e170263ae6, https://usegalaxy.org/published/workflow?id=f2f633d2b02b6050, https://usegalaxy.org/published/workflow?id=fb8b997f516288e1, https://workflowhub.eu/workflows/1538?version=2, https://workflowhub.eu/workflows/1656?version=1, https://workflowhub.eu/workflows/358?version=1, https://workflowhub.eu/workflows/575?version=1, https://workflowhub.eu/workflows/753?version=1, https://workflowhub.eu/workflows/875?version=3 |
ecology/phylogeny-data-prep, genome-annotation/repeatmasker |
|
repeatmodeler |
repeatmodeler |
RepeatModeler - Model repetitive DNA |
2021-08-26 |
https://www.repeatmasker.org/RepeatModeler/ |
2.0.5 |
|
|
To update |
Genome annotation |
Repeat sequence detection |
Repeat sequence detection |
Sequence composition, complexity and repeats, Sequence composition, complexity and repeats |
Sequence composition, complexity and repeats, Sequence composition, complexity and repeats |
csbl |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler |
repeatmodeler |
RepeatModeler |
De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
725 |
725 |
9423 |
9423 |
424 |
424 |
2473 |
2473 |
240 |
240 |
8995 |
8995 |
30 |
30 |
270 |
270 |
21161 |
21161 |
1419 |
1419 |
https://usegalaxy.eu/published/workflow?id=09c534f738426a6d, https://usegalaxy.eu/published/workflow?id=327beb1edda305ff, https://usegalaxy.eu/published/workflow?id=4077e77b6af919c4, https://usegalaxy.eu/published/workflow?id=f9279495683a8ac3, https://usegalaxy.fr/published/workflow?id=ae05ff8487f58fd6, https://usegalaxy.org.au/published/workflow?id=a71349ba0bff403a, https://usegalaxy.org.au/published/workflow?id=a9068ea858222e2b, https://usegalaxy.org.au/published/workflow?id=ffb1117077f68a9f, https://usegalaxy.org/published/workflow?id=effc17e170263ae6, https://workflowhub.eu/workflows/575?version=1, https://workflowhub.eu/workflows/875?version=3 |
genome-annotation/repeatmasker |
|
repmatch_gff3 |
repmatch_gff3 |
Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. |
2015-12-18 |
|
|
matplotlib |
|
To update |
ChIP-seq |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3 |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
96 |
224 |
254 |
727 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
727 |
254 |
224 |
96 |
|
|
|
reshape2 |
cast, melt |
Flexibly restructure and aggregate data using just the two functions melt and dcast |
2017-05-26 |
https://cran.r-project.org/web/packages/reshape2/index.html |
1.4.2 |
r-reshape2 |
|
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 |
|
|
|
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
112 |
123 |
3506 |
3687 |
100 |
131 |
421 |
585 |
0 |
0 |
0 |
0 |
3 |
3 |
6 |
6 |
4278 |
3933 |
257 |
215 |
https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.org/published/workflow?id=173ecc0c88090d0e, https://usegalaxy.org/published/workflow?id=734e08331f8f34b7, https://usegalaxy.org/published/workflow?id=b094b6e1e7d48416, https://usegalaxy.org/published/workflow?id=ddb737f2ad0589e8, https://workflowhub.eu/workflows/1189?version=2 |
|
|
resize_coordinate_window |
resize_coordinate_window |
Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. |
2016-01-13 |
|
1.0.2 |
python |
|
To update |
Genomic Interval Operations |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
6 |
9 |
13 |
86 |
22 |
60 |
36 |
221 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
307 |
49 |
69 |
28 |
https://usegalaxy.eu/published/workflow?id=6bce1d419a179c50, https://usegalaxy.org/published/workflow?id=7643e66a9b4e9c11 |
|
|
revoluzer |
revoluzer_crex, revoluzer_distmat |
revoluzer wrappers |
2024-03-19 |
https://gitlab.com/Bernt/revoluzer/ |
0.1.8 |
revoluzer |
0.1.8 |
Up-to-date |
Phylogenetics |
Structural variation detection |
Structural variation detection |
Molecular evolution, Phylogeny |
Molecular evolution, Phylogeny |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer |
revoluzer |
revoluzer |
Various tools for genome rearrangement analysis. CREx, TreeREx, etc |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
68 |
68 |
3932 |
3932 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3932 |
3932 |
68 |
68 |
|
|
|
rgcca |
rgcca |
multi-block analysis |
2020-09-02 |
https://github.com/rgcca-factory/RGCCA |
3.0.2 |
rgccacmd |
3.0.3 |
To update |
Statistics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
7 |
7 |
46 |
46 |
40 |
40 |
94 |
94 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
140 |
140 |
47 |
47 |
|
|
|
rgrnastar |
rna_star, rna_starsolo |
RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper |
2015-05-18 |
https://github.com/alexdobin/STAR |
2.7.11b |
star |
2.7.11b |
Up-to-date |
Next Gen Mappers, Transcriptomics, Single Cell |
Sequence alignment |
Sequence alignment |
RNA-Seq, Transcriptomics |
RNA-Seq, Transcriptomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar |
star |
STAR |
Ultrafast universal RNA-seq data aligner |
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11597 |
13300 |
454740 |
555235 |
17153 |
22174 |
406678 |
513360 |
1461 |
1710 |
55618 |
62678 |
1016 |
1019 |
12202 |
12241 |
1143514 |
929238 |
38203 |
31227 |
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genome-annotation/braker3, genome-annotation/comparison-braker-helixer-annotation, genome-annotation/funannotate, proteomics/neoantigen-fusion-database-generation, single-cell/scrna-preprocessing, single-cell/scrna-preprocessing-tenx, transcriptomics/clipseq, transcriptomics/differential-isoform-expression, transcriptomics/ref-based |
|
ribowaltz |
ribowaltz_process, ribowaltz_plot |
Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data |
2022-09-22 |
https://github.com/LabTranslationalArchitectomics/riboWaltz |
1.2.0 |
ribowaltz |
2.0 |
To update |
Transcriptomics, RNA |
|
|
Computational biology |
Computational biology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz |
riboWaltz |
riboWaltz |
riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
21 |
21 |
204 |
204 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
204 |
204 |
21 |
21 |
|
|
|
rnaquast |
rna_quast |
rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. |
2020-10-05 |
https://github.com/ablab/rnaquast |
2.3.0 |
rnaquast |
2.3.0 |
Up-to-date |
Assembly, RNA |
De-novo assembly, Transcriptome assembly, Sequence assembly validation |
De-novo assembly, Transcriptome assembly, Sequence assembly validation |
Sequence assembly, Transcriptomics, RNA-Seq |
Sequence assembly, Transcriptomics, RNA-Seq |
iuc |
https://git.ufz.de/lehmanju/rnaquast |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast |
rnaQUAST |
rnaQUAST |
Quality assessment tool for de novo transcriptome assemblies. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
375 |
375 |
1887 |
1887 |
196 |
196 |
767 |
767 |
31 |
31 |
326 |
326 |
11 |
11 |
103 |
103 |
3083 |
3083 |
613 |
613 |
https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://workflowhub.eu/workflows/1688?version=1 |
transcriptomics/differential-isoform-expression |
|
roary |
roary |
Roary the pangenome pipeline |
2017-06-21 |
https://sanger-pathogens.github.io/Roary/ |
3.13.0 |
roary |
3.13.0 |
Up-to-date |
Sequence Analysis |
Genome assembly |
Genome assembly |
DNA, Genomics, Mapping |
DNA, Genomics, Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary |
roary |
Roary |
A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2251 |
2377 |
21218 |
23887 |
2319 |
2454 |
17744 |
18851 |
653 |
749 |
5251 |
7169 |
47 |
47 |
187 |
187 |
50094 |
44400 |
5627 |
5270 |
https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=e16e524c557d7928, https://usegalaxy.org.au/published/workflow?id=05f3abecd4ddd4a1, https://usegalaxy.org.au/published/workflow?id=3fd2195b6928d5e0, https://usegalaxy.org/published/workflow?id=78d8b738f5715a8a |
|
|
rp2biosensor |
rp2biosensor |
Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output |
2023-01-05 |
https://github.com/brsynth/rp2biosensor |
3.2.1 |
rp2biosensor |
|
To update |
Synthetic Biology |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
rp2paths |
rp2paths |
Enumerate and seperate the different pathways generated by RetroPath2.0 |
2022-10-17 |
https://github.com/brsynth/rp2paths |
1.5.1 |
rp2paths |
|
To update |
Synthetic Biology |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
https://workflowhub.eu/workflows/1581?version=1 |
synthetic-biology/retrosynthesis_analysis |
|
rpbasicdesign |
rpbasicdesign |
Extracting enzyme IDs from rpSBML files |
2022-03-30 |
https://github.com/brsynth/rpbasicdesign |
1.2.2 |
rpbasicdesign |
|
To update |
Synthetic Biology |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign |
|
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
https://workflowhub.eu/workflows/1576?version=1 |
synthetic-biology/basic_assembly_analysis |
|
rpfba |
rpfba |
Perform FBA for the RetroPath2.0 heterologous pathways |
2022-01-17 |
https://github.com/brsynth/rptools/releases |
5.12.3 |
rptools |
|
To update |
Synthetic Biology |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba |
|
|
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|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
https://workflowhub.eu/workflows/1572?version=1 |
synthetic-biology/pathway_analysis |
|
rptools |
rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz |
Suite of tools that work on rpSBML format |
2022-11-16 |
https://github.com/brsynth/rptools |
5.13.1 |
rptools |
|
To update |
Synthetic Biology |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
rrmscorer |
rrmscorer |
Predicts RNA Recognition Motif (RRM) scores for protein sequences. |
2025-09-17 |
https://bio2byte.be/rrmscorer/ |
1.0.11 |
rrmscorer |
1.0.11 |
Up-to-date |
Sequence Analysis |
Multiple sequence alignment, Calculation, Visualisation |
Multiple sequence alignment, Calculation, Visualisation |
Computational biology |
Computational biology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer |
RRMScorer |
RRMScorer |
RRMScorer provides quick predictions for any RNA recognition motif (RRM) and any RNA target purely based on their sequences. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
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0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
rrparser |
rrparser |
Reaction Rules Parser |
2022-06-27 |
https://github.com/brsynth/RRParser |
2.7.0 |
rrparser |
|
To update |
Synthetic Biology |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
https://workflowhub.eu/workflows/1581?version=1 |
synthetic-biology/retrosynthesis_analysis |
|
rseqc |
rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin |
an RNA-seq quality control package |
2017-02-27 |
https://code.google.com/p/rseqc/ |
5.0.3 |
rseqc |
5.0.4 |
To update |
Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization |
Data handling |
Data handling |
Sequencing |
Sequencing |
nilesh |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc |
rseqc |
RSeQC |
Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. |
|
0 |
22 |
22 |
22 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
22 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
22 |
0 |
0 |
0 |
0 |
0 |
0 |
22 |
22 |
22 |
4113 |
5223 |
155237 |
181534 |
4079 |
5016 |
146353 |
197501 |
629 |
697 |
28108 |
32069 |
809 |
810 |
78294 |
78366 |
489470 |
407992 |
11746 |
9630 |
https://usegalaxy.eu/published/workflow?id=1ee43d90b69829e9, https://usegalaxy.eu/published/workflow?id=1f9a9a7998ef5ab3, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=47a0407867a90f95, https://usegalaxy.eu/published/workflow?id=5e4135eeb4972709, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=985044b4b2c51425, https://usegalaxy.eu/published/workflow?id=9b025479fade745d, https://usegalaxy.eu/published/workflow?id=9c7a218993788493, https://usegalaxy.eu/published/workflow?id=a28c207730e7e13d, https://usegalaxy.eu/published/workflow?id=a52c5dd688def9ba, https://usegalaxy.eu/published/workflow?id=b7a3cbcd32734e8b, https://usegalaxy.eu/published/workflow?id=cc37667c2d1f9056, https://usegalaxy.eu/published/workflow?id=ccef778cfd9024d1, https://usegalaxy.eu/published/workflow?id=f33b5135ee99e0dc, https://usegalaxy.fr/published/workflow?id=334189184455d9a2, https://usegalaxy.fr/published/workflow?id=5d83e0886f2a7465, https://usegalaxy.fr/published/workflow?id=74b4d11c07f7f0a4, https://usegalaxy.fr/published/workflow?id=826cffb2458e4067, https://usegalaxy.org.au/published/workflow?id=6e1e24f9e0326930, https://usegalaxy.org.au/published/workflow?id=75113a1b41904d2a, https://usegalaxy.org.au/published/workflow?id=85aede91db0122e4, https://usegalaxy.org.au/published/workflow?id=a763e53653b10ce0, https://usegalaxy.org.au/published/workflow?id=af7b95f46485308c, https://usegalaxy.org.au/published/workflow?id=b08342866a118a5e, https://usegalaxy.org.au/published/workflow?id=bb0feff5d764df60, https://usegalaxy.org.au/published/workflow?id=ce7f6a1c824920e2, https://usegalaxy.org.au/published/workflow?id=e1fd89e7248b6661, https://usegalaxy.org/published/workflow?id=044c5ce43f2e1829, https://usegalaxy.org/published/workflow?id=582f3de3971fc38c, https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6, https://usegalaxy.org/published/workflow?id=682b1c7e2ad9d443, https://usegalaxy.org/published/workflow?id=7022c4d9af725e5c, https://usegalaxy.org/published/workflow?id=73f5b1a6fd3c703f, https://usegalaxy.org/published/workflow?id=76b8ed1c68678b62, https://usegalaxy.org/published/workflow?id=7e9269e78e989480, https://usegalaxy.org/published/workflow?id=a743746151101352, https://usegalaxy.org/published/workflow?id=b11796364c22235e, https://usegalaxy.org/published/workflow?id=b1a98a2d5ebda1c5, https://usegalaxy.org/published/workflow?id=e035be74e3c85bf5, https://usegalaxy.org/published/workflow?id=e33f6a058c5f57e5, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a, https://usegalaxy.org/published/workflow?id=fb789920b057fe8d, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1675?version=1, https://workflowhub.eu/workflows/1688?version=1, https://workflowhub.eu/workflows/1692?version=1, https://workflowhub.eu/workflows/1695?version=1, https://workflowhub.eu/workflows/1715?version=1, https://workflowhub.eu/workflows/688?version=1 |
transcriptomics/differential-isoform-expression, transcriptomics/minerva-pathways, transcriptomics/ref-based, transcriptomics/rna-seq-reads-to-counts |
|
ruvseq |
ruvseq |
Remove Unwanted Variation from RNA-Seq Data |
2018-08-30 |
https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html |
1.26.0 |
bioconductor-ruvseq |
1.40.0 |
To update |
Transcriptomics, RNA, Statistics |
Differential gene expression analysis |
Differential gene expression analysis |
Gene expression, RNA-seq |
Gene expression |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq |
ruvseq |
RUVSeq |
This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
155 |
200 |
1182 |
1507 |
272 |
319 |
2100 |
2428 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3935 |
3282 |
519 |
427 |
|
|
|
salsa |
salsa |
A tool to scaffold long read assemblies with Hi-C |
2021-01-14 |
https://github.com/marbl/SALSA |
2.3 |
salsa2 |
2.3 |
Up-to-date |
Assembly |
Genome assembly, De-novo assembly, Scaffolding |
Genome assembly, De-novo assembly, Scaffolding |
Sequence assembly, DNA binding sites, Mapping |
Sequence assembly, DNA binding sites, Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 |
SALSA |
SALSA |
> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
130 |
130 |
495 |
495 |
103 |
103 |
1074 |
1074 |
24 |
24 |
410 |
410 |
0 |
0 |
0 |
0 |
1979 |
1979 |
257 |
257 |
https://usegalaxy.org.au/published/workflow?id=434127690544d0e9, https://usegalaxy.org.au/published/workflow?id=e07866576cc2f467, https://workflowhub.eu/workflows/1607?version=1 |
assembly/vgp_genome_assembly |
|
samblaster |
samblaster |
samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files |
2016-12-18 |
https://github.com/GregoryFaust/samblaster |
0.1.26 |
samblaster |
0.1.26 |
Up-to-date |
SAM, Fastq Manipulation, Variant Analysis |
Split read mapping |
Split read mapping |
DNA, Sequencing, Mapping |
DNA, Sequencing, Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster |
samblaster |
SAMBLASTER |
A tool to mark duplicates and extract discordant and split reads from SAM files. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
samtools |
|
|
2017-01-24 |
https://github.com/samtools/samtools |
1.22 |
samtools |
1.22.1 |
To update |
SAM |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
sansa |
sansa_annotate |
Sansa is a tool for structural variant annotation. |
2020-12-05 |
https://github.com/dellytools/sansa |
0.2.2 |
sansa |
0.2.3 |
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
43 |
43 |
157 |
157 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
157 |
157 |
43 |
43 |
|
|
|
sarscov2formatter |
sarscov2formatter |
sarscov2formatter custom script |
2020-05-01 |
https://github.com/nickeener/sarscov2formatter |
1.0 |
sarscov2formatter |
1.0 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
14 |
16 |
40 |
174 |
26 |
30 |
48 |
402 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
576 |
88 |
46 |
40 |
https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e |
|
|
sarscov2summary |
sarscov2summary |
sarscov2summary custom script |
2020-05-01 |
https://github.com/nickeener/sarscov2summary |
0.1 |
sarscov2summary |
0.5 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3 |
5 |
3 |
140 |
3 |
6 |
4 |
253 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
393 |
7 |
11 |
6 |
https://usegalaxy.org/published/workflow?id=a46ad0b9240d1a13, https://usegalaxy.org/published/workflow?id=e1cc0886cd27b92e |
|
|
sbml2sbol |
sbml2sbol |
Convert SBML to SBOL format |
2022-10-15 |
https://github.com/neilswainston/SbmlToSbol |
0.1.13 |
sbml2sbol |
|
To update |
Synthetic Biology |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
scanpy |
scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders |
Scanpy – Single-Cell Analysis in Python |
2019-03-04 |
https://scanpy.readthedocs.io |
1.10.2 |
scanpy |
1.7.2 |
To update |
Single Cell, Spatial Omics, Transcriptomics |
Differential gene expression analysis, Principal component visualisation, Expression profile clustering |
Differential gene expression analysis, Principal component visualisation, Expression profile clustering |
Gene expression, Cell biology, Genetics, Single-cell sequencing |
Gene expression, Cell biology, Genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy |
scanpy |
SCANPY |
Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. |
|
0 |
6 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
6 |
771 |
868 |
70187 |
77433 |
456 |
465 |
42066 |
42163 |
120 |
121 |
22195 |
23258 |
2 |
2 |
114 |
114 |
142968 |
134562 |
1456 |
1349 |
https://usegalaxy.eu/published/workflow?id=0d7c643d7720ee31, https://usegalaxy.eu/published/workflow?id=171d6fca2c3339e2, https://usegalaxy.eu/published/workflow?id=21315ffd2df2f159, https://usegalaxy.eu/published/workflow?id=37e51e215684bdcc, https://usegalaxy.eu/published/workflow?id=4756053b2596b6cf, https://usegalaxy.eu/published/workflow?id=715ca378c1d68de3, https://usegalaxy.eu/published/workflow?id=77e85bde57477194, https://usegalaxy.eu/published/workflow?id=78dc6fca5b58ec05, https://usegalaxy.eu/published/workflow?id=921cab3e6faf30be, https://usegalaxy.eu/published/workflow?id=9adf0402b641042c, https://usegalaxy.eu/published/workflow?id=9d15b328d8408715, https://usegalaxy.eu/published/workflow?id=ae79275d3568ad31, https://usegalaxy.eu/published/workflow?id=b3cf397fd4d1bea8, https://usegalaxy.eu/published/workflow?id=b5627201bb4f6943, https://usegalaxy.eu/published/workflow?id=d70dc4cfeedb690b, https://usegalaxy.eu/published/workflow?id=d7c0c972c471d514, https://usegalaxy.eu/published/workflow?id=ddced7b107e4707a, https://usegalaxy.eu/published/workflow?id=e2391c40d24d403f, https://usegalaxy.eu/published/workflow?id=e472096116cbe392, https://usegalaxy.eu/published/workflow?id=e4e969e9943cdaa5, https://usegalaxy.eu/published/workflow?id=f05754467a439134, https://usegalaxy.org.au/published/workflow?id=102eb726f63f3190, https://usegalaxy.org.au/published/workflow?id=106080375ad4eaaa, https://usegalaxy.org.au/published/workflow?id=218ffb4438833bdd, https://usegalaxy.org.au/published/workflow?id=57321b64220d5835, https://usegalaxy.org.au/published/workflow?id=8055596d732590d6, https://usegalaxy.org.au/published/workflow?id=8bc01c1fdd62ad12, https://usegalaxy.org/published/workflow?id=dd43ae9a5b303086, https://usegalaxy.org/published/workflow?id=ea3257e0ef9f505a, https://usegalaxy.org/published/workflow?id=f35ccb693cd874c1, https://workflowhub.eu/workflows/1077?version=1, https://workflowhub.eu/workflows/1256?version=1, https://workflowhub.eu/workflows/1356?version=1, https://workflowhub.eu/workflows/1362?version=1, https://workflowhub.eu/workflows/1485?version=1, https://workflowhub.eu/workflows/1490?version=1, https://workflowhub.eu/workflows/1496?version=1, https://workflowhub.eu/workflows/1501?version=1, https://workflowhub.eu/workflows/1502?version=1, https://workflowhub.eu/workflows/1519?version=1, https://workflowhub.eu/workflows/1550?version=1, https://workflowhub.eu/workflows/1551?version=1, https://workflowhub.eu/workflows/1556?version=1, https://workflowhub.eu/workflows/1574?version=1, https://workflowhub.eu/workflows/467?version=4, https://workflowhub.eu/workflows/468?version=3 |
single-cell/pseudobulk-analysis, single-cell/scatac-preprocessing-tenx, single-cell/scatac-standard-processing-snapatac2, single-cell/scrna-case_basic-pipeline, single-cell/scrna-case_cell-cycle, single-cell/scrna-plant, single-cell/scrna-scanpy-pbmc3k |
|
scater |
scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne |
Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. |
2019-07-18 |
http://bioconductor.org/packages/scater/ |
1.22.0 |
bioconductor-scater |
1.34.1 |
To update |
Single Cell, Transcriptomics, Visualization |
Read pre-processing, Sequencing quality control, Sequence visualisation |
Read pre-processing, Sequence visualisation |
RNA-Seq, Quality affairs, Molecular genetics |
RNA-Seq, Quality affairs, Molecular genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater |
scater |
scater |
Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. |
|
0 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
5 |
77 |
94 |
1007 |
1409 |
0 |
0 |
0 |
0 |
7 |
8 |
1094 |
1215 |
0 |
0 |
0 |
0 |
2624 |
2101 |
102 |
84 |
https://usegalaxy.eu/published/workflow?id=f055b8fa294d4be8, https://usegalaxy.org.au/published/workflow?id=3c9140288202aa76, https://workflowhub.eu/workflows/1511?version=1 |
single-cell/scrna-scater-qc |
|
sceasy_convert |
sceasy_convert |
Converter between difference single-cell formats |
2023-11-10 |
https://github.com/cellgeni/sceasy/ |
0.0.7 |
r-sceasy |
0.0.7 |
Up-to-date |
Single Cell, Spatial Omics, Convert Formats |
Data handling |
Data handling |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy |
sceasy |
sceasy |
sceasy is a package that helps easy conversion of different single-cell data formats to each other. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
301 |
310 |
1543 |
1615 |
103 |
104 |
521 |
522 |
5 |
5 |
349 |
349 |
1 |
1 |
2 |
2 |
2488 |
2415 |
420 |
410 |
https://usegalaxy.eu/published/workflow?id=0e6e181234b48121, https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=9a9bbd8046da7b19, https://usegalaxy.eu/published/workflow?id=a0f1959a9f4533f7, https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d, https://workflowhub.eu/workflows/1533?version=1, https://workflowhub.eu/workflows/1537?version=1 |
single-cell/EBI-retrieval, single-cell/scrna-case_alevin, single-cell/scrna-data-ingest |
|
schicexplorer |
schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol |
scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. |
2019-12-16 |
https://github.com/joachimwolff/schicexplorer |
4 |
schicexplorer |
7 |
To update |
Sequence Analysis, Transcriptomics, Visualization, Single Cell |
Validation, Visualisation, Standardisation and normalisation |
Validation, Visualisation, Standardisation and normalisation |
Workflows, DNA, Chromosome conformation capture, ChIP-seq, Epigenetics |
Workflows, DNA, Chromosome conformation capture, ChIP-seq, Epigenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer |
hicexplorer |
HiCExplorer |
A web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization.HiCExplorer — HiCExplorer 3.6 documentation.scHiCExplorer — scHiCExplorer 7 documentation.Free document hosting provided by Read the Docs. |
|
0 |
16 |
16 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
16 |
16 |
8 |
11 |
99 |
821 |
12 |
12 |
32 |
32 |
2 |
2 |
1351 |
1351 |
0 |
0 |
0 |
0 |
2204 |
1482 |
25 |
22 |
|
|
|
scikit_bio |
scikit_bio_diversity_beta_diversity |
scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics |
2016-05-31 |
http://scikit-bio.org/ |
0.4.2 |
scikit-bio |
0.4.2 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
303 |
445 |
1472 |
2106 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2107 |
1473 |
446 |
304 |
https://usegalaxy.org/published/workflow?id=7251c6e0dad8f927 |
|
|
scoary |
scoary |
Scoary calculates the assocations between all genes in the accessory genome and the traits. |
2021-03-18 |
https://github.com/AdmiralenOla/Scoary |
1.6.16 |
scoary |
1.6.16 |
Up-to-date |
Metagenomics |
Analysis |
Analysis |
Genotype and phenotype, Model organisms, GWAS study, Functional genomics |
Genotype and phenotype, Model organisms, GWAS study, Functional genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary |
scoary |
Scoary |
Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
113 |
113 |
1366 |
1366 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1366 |
1366 |
113 |
113 |
|
|
|
scpipe |
scpipe |
A flexible preprocessing pipeline for single-cell RNA-sequencing data |
2018-08-12 |
http://bioconductor.org/packages/release/bioc/html/scPipe.html |
1.0.0+galaxy2 |
bioconductor-scpipe |
2.6.0 |
To update |
Transcriptomics, Single Cell |
Genome annotation, Validation, Alignment, Visualisation |
Genome annotation, Validation, Alignment, Visualisation |
Gene expression, RNA-Seq, Sequencing |
Gene expression, RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe |
scpipe |
scPipe |
A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
25 |
40 |
149 |
643 |
50 |
63 |
656 |
799 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
1443 |
806 |
104 |
76 |
https://usegalaxy.eu/published/workflow?id=0a692a2e643b9e1a |
|
|
seaborn |
seaborn, seaborn_pairgrid |
Seaborn is a Python data visualization library based on Matplotlib. |
2025-05-13 |
https://seaborn.pydata.org/ |
0.13.2 |
seaborn |
|
To update |
Visualization |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seaborn |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seaborn |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
seacr |
seacr |
SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. |
2020-02-05 |
https://github.com/FredHutch/SEACR |
1.3 |
seacr |
1.3 |
Up-to-date |
Epigenetics, ChIP-seq |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
150 |
155 |
6871 |
7014 |
289 |
289 |
8117 |
8117 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
15131 |
14988 |
444 |
439 |
https://usegalaxy.eu/published/workflow?id=719314fa5263b501 |
|
|
selenzy_wrapper |
selenzy_wrapper |
Performs enzyme selection from a reaction query. |
2022-06-29 |
https://github.com/brsynth/selenzy-wrapper |
0.3.0 |
selenzy_wrapper |
0.3.0 |
Up-to-date |
Synthetic Biology |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
semibin |
semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train |
SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks |
2022-10-14 |
https://semibin.readthedocs.io/en/latest/ |
2.1.0 |
semibin |
2.2.0 |
To update |
Metagenomics |
Sequence assembly, Read binning |
Sequence assembly, Read binning |
Metagenomics, Machine learning, Microbial ecology, Sequence assembly |
Metagenomics, Machine learning, Microbial ecology, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin |
semibin |
SemiBin |
Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. |
|
0 |
0 |
6 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
0 |
53 |
53 |
2779 |
2779 |
9 |
9 |
18 |
18 |
0 |
0 |
0 |
0 |
2 |
2 |
75 |
75 |
2872 |
2872 |
64 |
64 |
https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=0563f58718be932d, https://usegalaxy.eu/published/workflow?id=1e5f1d9a51032e44, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=7ecd92cb382d8168, https://usegalaxy.eu/published/workflow?id=97312d273b6e8bd9, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://workflowhub.eu/workflows/1352?version=3 |
|
|
seq2hla |
seq2hla |
Precision HLA typing and expression from RNAseq data |
2020-02-20 |
https://github.com/TRON-Bioinformatics/seq2HLA |
2.3 |
seq2hla |
2.3 |
Up-to-date |
Sequence Analysis |
Read mapping, Genetic variation analysis |
Read mapping, Genetic variation analysis |
Transcriptomics, Mapping |
Transcriptomics, Mapping |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla |
seq2hla |
Seq2HLA |
seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
62 |
65 |
432 |
482 |
11 |
11 |
49 |
49 |
6 |
6 |
102 |
102 |
0 |
0 |
0 |
0 |
633 |
583 |
82 |
79 |
https://usegalaxy.eu/published/workflow?id=c3f2350f0be2d9c9, https://usegalaxy.eu/published/workflow?id=db270d0eb035609e, https://usegalaxy.org.au/published/workflow?id=2249ab6710f5e84d, https://usegalaxy.org/published/workflow?id=1d925422fc6094a0, https://workflowhub.eu/workflows/1430?version=1, https://workflowhub.eu/workflows/1794?version=1 |
proteomics/neoantigen-predicting-hla-binding |
|
seqcomplexity |
seqcomplexity |
Sequence complexity for raw reads |
2022-06-07 |
https://github.com/stevenweaver/seqcomplexity |
0.1.2 |
seqcomplexity |
0.1.2 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
25 |
25 |
84 |
84 |
55 |
55 |
133 |
133 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
217 |
217 |
80 |
80 |
|
|
|
seqkit |
seqkit_fx2tab, seqkit_grep, seqkit_head, seqkit_locate, seqkit_sort, seqkit_split2, seqkit_stats, seqkit_translate |
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation |
2022-06-01 |
https://bioinf.shenwei.me/seqkit/ |
2.10.1 |
seqkit |
2.10.1 |
Up-to-date |
Sequence Analysis |
DNA transcription, Sequence trimming, DNA translation, Sequence conversion |
DNA transcription, Sequence trimming, DNA translation |
Database management, Sequence analysis |
Database management, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit |
seqkit |
seqkit |
FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. |
|
0 |
6 |
6 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
396 |
396 |
13926 |
13926 |
0 |
0 |
0 |
0 |
120 |
120 |
2190 |
2190 |
69 |
69 |
648 |
648 |
16764 |
16764 |
585 |
585 |
https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://usegalaxy.org.au/published/workflow?id=ed3e48a73b5aaa56, https://workflowhub.eu/workflows/601?version=2, https://workflowhub.eu/workflows/602?version=2, https://workflowhub.eu/workflows/697?version=1 |
|
|
seqprep |
seqprep |
Tool for merging paired-end Illumina reads and trimming adapters. |
2024-01-15 |
https://github.com/jstjohn/SeqPrep |
1.3.2 |
seqprep |
1.3.2 |
Up-to-date |
Fastq Manipulation, Sequence Analysis |
Nucleic acid design |
Nucleic acid design |
Genomics, Sequence assembly, Sequencing, Probes and primers |
Genomics, Sequence assembly, Sequencing, Probes and primers |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep |
seqprep |
SeqPrep |
Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
227 |
227 |
3602 |
3602 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3602 |
3602 |
227 |
227 |
|
microbiome/mgnify-amplicon |
|
seqsero2 |
seqsero2 |
Salmonella serotype prediction from genome sequencing data |
2023-11-07 |
https://github.com/denglab/SeqSero2 |
1.3.1 |
seqsero2 |
1.3.1 |
Up-to-date |
Sequence Analysis |
Genome indexing, Antimicrobial resistance prediction, Genome alignment |
Genome indexing, Antimicrobial resistance prediction, Genome alignment |
Whole genome sequencing, Sequence assembly, Genomics |
Whole genome sequencing, Sequence assembly, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 |
seqsero2 |
SeqSero2 |
rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode) |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
116 |
116 |
14011 |
14011 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
2 |
14013 |
14013 |
118 |
118 |
https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://workflowhub.eu/workflows/407?version=1 |
|
|
seqtk |
seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq |
Toolkit for processing sequences in FASTA/Q formats |
2015-01-13 |
https://github.com/lh3/seqtk |
1.5 |
seqtk |
1.5 |
Up-to-date |
Sequence Analysis |
Data handling, Sequence file editing |
Data handling, Sequence file editing |
Data management |
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk |
seqtk |
seqtk |
A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. |
|
0 |
15 |
15 |
15 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
15 |
0 |
14 |
0 |
0 |
0 |
0 |
0 |
15 |
0 |
0 |
0 |
0 |
0 |
0 |
15 |
15 |
14 |
804 |
862 |
270417 |
273634 |
956 |
1098 |
107899 |
122221 |
260 |
262 |
158312 |
159084 |
55 |
55 |
18691 |
18691 |
573630 |
555319 |
2277 |
2075 |
https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=52cb9bacc26b013e, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=69be516a48761365, https://usegalaxy.eu/published/workflow?id=83a1b8949d87e3da, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.eu/published/workflow?id=ce5c16ac23c4fbb1, https://usegalaxy.eu/published/workflow?id=d2f75f70c33394ee, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4, https://usegalaxy.eu/published/workflow?id=efb58bba65393347, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=324c683a8e2fa5b0, https://usegalaxy.org.au/published/workflow?id=462beb964c99619d, https://usegalaxy.org.au/published/workflow?id=5cfea39918e8632d, https://usegalaxy.org.au/published/workflow?id=79ca45e45d76871f, https://usegalaxy.org.au/published/workflow?id=9c60b83feaa22415, https://usegalaxy.org.au/published/workflow?id=b59fada651043735, https://usegalaxy.org.au/published/workflow?id=fc3c83b11f527977, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=1ba0239e55ac0d07, https://usegalaxy.org/published/workflow?id=1ddabc7d272dc702, https://usegalaxy.org/published/workflow?id=33d90e718ce500ef, https://usegalaxy.org/published/workflow?id=34f3aac3aed0f97a, https://usegalaxy.org/published/workflow?id=35c2626849348f2c, https://usegalaxy.org/published/workflow?id=51f936d1a4e849fa, https://usegalaxy.org/published/workflow?id=69514a75e4c9af08, https://usegalaxy.org/published/workflow?id=7610b7797d71993a, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://usegalaxy.org/published/workflow?id=cdea4f88ccbd155f, https://usegalaxy.org/published/workflow?id=eb4f7dbca0114270, https://workflowhub.eu/workflows/1260?version=2, https://workflowhub.eu/workflows/1327?version=6, https://workflowhub.eu/workflows/1480?version=1, https://workflowhub.eu/workflows/1612?version=1, https://workflowhub.eu/workflows/1616?version=1, https://workflowhub.eu/workflows/1629?version=1, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1631?version=1, https://workflowhub.eu/workflows/1635?version=1, https://workflowhub.eu/workflows/1653?version=1, https://workflowhub.eu/workflows/517?version=1, https://workflowhub.eu/workflows/518?version=1, https://workflowhub.eu/workflows/880?version=1 |
assembly/assembly-with-preprocessing, assembly/metagenomics-assembly, contributing/create-new-tutorial, microbiome/metagenomics-assembly, sequence-analysis/Manage_AB1_Sanger, sequence-analysis/human-reads-removal, variant-analysis/aiv-analysis |
|
sequali |
sequali |
Fast sequencing data quality metrics for short and long reads |
2025-03-19 |
https://sequali.readthedocs.io/ |
1.0.2 |
sequali |
1.0.2 |
Up-to-date |
Fastq Manipulation |
Sequencing quality control, Statistical calculation |
Sequencing quality control, Statistical calculation |
Data quality management, Sequence analysis |
Data quality management, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sequali |
sequali |
Sequali |
Fast sequencing data quality metrics |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
9 |
16 |
16 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
16 |
9 |
9 |
|
|
|
seqwish |
seqwish |
Alignment to variation graph inducer |
2020-04-06 |
https://github.com/ekg/seqwish |
0.7.5 |
seqwish |
0.7.11 |
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
2 |
0 |
271 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
271 |
0 |
2 |
0 |
https://usegalaxy.eu/published/workflow?id=9ba580ba8b01db40 |
|
|
seurat |
seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension |
Seurat - R toolkit for single cell genomics |
2018-08-20 |
https://satijalab.org/seurat/ |
5.0 |
r-seurat |
3.0.2 |
To update |
Single Cell, Transcriptomics, Sequence Analysis |
|
|
RNA-Seq, Transcriptomics |
RNA-Seq, Transcriptomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat |
seurat |
Seurat |
Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. |
|
0 |
7 |
7 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
120 |
120 |
6468 |
6468 |
109 |
109 |
2871 |
2871 |
9 |
9 |
1332 |
1332 |
4 |
4 |
105 |
105 |
10776 |
10776 |
242 |
242 |
https://usegalaxy.eu/published/workflow?id=10c5d0560b977a6f, https://usegalaxy.eu/published/workflow?id=26deb6f2521742ea, https://usegalaxy.eu/published/workflow?id=290373b2f5fb8c6c, https://usegalaxy.eu/published/workflow?id=c52e8b5ab3e8e958, https://usegalaxy.eu/published/workflow?id=d773cbc76253afbf, https://usegalaxy.org/published/workflow?id=59554bfcad77e307, https://workflowhub.eu/workflows/1555?version=1, https://workflowhub.eu/workflows/1560?version=1, https://workflowhub.eu/workflows/1570?version=1 |
single-cell/scrna-case_FilterPlotandExplore_SeuratTools, single-cell/scrna-seurat-pbmc3k |
|
sfold |
sfold |
Predict the probable RNA secondary structures through structure ensemble sampling |
2024-10-09 |
https://github.com/Ding-RNA-Lab/Sfold |
2.2.0 |
|
|
To update |
RNA |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sfold |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
2 |
|
|
|
shasta |
shasta |
Fast de novo assembly of long read sequencing data |
2020-11-11 |
https://github.com/chanzuckerberg/shasta |
0.6.0 |
shasta |
0.14.0 |
To update |
Assembly, Nanopore |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
399 |
399 |
1291 |
1291 |
0 |
0 |
0 |
0 |
98 |
98 |
791 |
791 |
0 |
0 |
0 |
0 |
2082 |
2082 |
497 |
497 |
|
|
|
shorah_amplicon |
shorah_amplicon |
Reconstruct haplotypes using ShoRAH in amplicon mode |
2018-11-27 |
https://github.com/cbg-ethz/shorah/blob/master/README.md |
1.1.3 |
shorah |
1.99.2 |
To update |
Sequence Analysis |
Haplotype mapping, Variant calling |
Haplotype mapping, Variant calling |
Metagenomics, Sequencing, Genetics |
Metagenomics, Sequencing, Genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah |
shorah |
ShoRAH |
Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
shovill |
shovill |
Faster de novo assembly pipeline based around Spades |
2017-10-24 |
https://github.com/tseemann/shovill |
1.1.0 |
shovill |
1.1.0 |
Up-to-date |
Assembly |
Genome assembly |
Genome assembly |
Genomics, Microbiology, Sequence assembly |
Genomics, Microbiology, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill |
shovill |
shovill |
Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3269 |
3491 |
70801 |
76107 |
4933 |
5212 |
51724 |
55190 |
1425 |
1669 |
30312 |
35794 |
83 |
83 |
9136 |
9136 |
176227 |
161973 |
10455 |
9710 |
https://usegalaxy.eu/published/workflow?id=0404013d5c27210d, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=3303a04887a47675, https://usegalaxy.eu/published/workflow?id=3d937648809ca4e7, https://usegalaxy.eu/published/workflow?id=4216424f032c055f, https://usegalaxy.eu/published/workflow?id=42c0da2e86318b37, https://usegalaxy.eu/published/workflow?id=4f245ac304ab76d9, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=723e718f37e9ab91, https://usegalaxy.eu/published/workflow?id=7aa32aba3fde0708, https://usegalaxy.eu/published/workflow?id=7e48134082dab0a3, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=a727e22dc0431614, https://usegalaxy.eu/published/workflow?id=b5ffba506152b1a1, https://usegalaxy.eu/published/workflow?id=b90585626a793502, https://usegalaxy.eu/published/workflow?id=b93333efdab316d8, https://usegalaxy.eu/published/workflow?id=ba1fda2318046543, https://usegalaxy.eu/published/workflow?id=cbe3769f1abb9fa5, https://usegalaxy.eu/published/workflow?id=e532d98f4b368666, https://usegalaxy.eu/published/workflow?id=fca458178b3c794a, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=52065a4100b11184, https://usegalaxy.org.au/published/workflow?id=7a0c4804e4d4c905, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org.au/published/workflow?id=d78f885b4b86635f, https://usegalaxy.org.au/published/workflow?id=f2541030f6d70b59, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://usegalaxy.org/published/workflow?id=0e30324072570abb, https://usegalaxy.org/published/workflow?id=4161cfd67ed94b5d, https://usegalaxy.org/published/workflow?id=4d1279007d0137fa, https://usegalaxy.org/published/workflow?id=524602abe59b18f7, https://usegalaxy.org/published/workflow?id=5cd56232e873beab, https://usegalaxy.org/published/workflow?id=8ebc2b1ae24ed884, https://usegalaxy.org/published/workflow?id=9ac1e4efe310b3b3, https://usegalaxy.org/published/workflow?id=9e5c5ddb60a24889, https://usegalaxy.org/published/workflow?id=b76a9ce44ea019f1, https://usegalaxy.org/published/workflow?id=c454c930ccfb0d3f, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=db08887d7d6dc147, https://usegalaxy.org/published/workflow?id=e75bd7d392e65209, https://usegalaxy.org/published/workflow?id=f4d623a19b32370e, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/102?version=1, https://workflowhub.eu/workflows/103?version=1, https://workflowhub.eu/workflows/1043?version=11, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1602?version=1, https://workflowhub.eu/workflows/1767?version=1, https://workflowhub.eu/workflows/407?version=1, https://workflowhub.eu/workflows/470?version=1 |
assembly/mrsa-illumina |
|
sickle |
sickle |
A windowed adaptive trimming tool for FASTQ files using quality |
2015-11-03 |
https://github.com/najoshi/sickle |
1.33.3 |
sickle-trim |
1.33 |
To update |
Fastq Manipulation, Sequence Analysis |
Sequence trimming |
Sequence trimming |
Data quality management |
Data quality management |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle |
sickle |
sickle |
A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
627 |
731 |
20571 |
21706 |
1315 |
1394 |
11397 |
12999 |
0 |
0 |
0 |
0 |
147 |
149 |
1215 |
1324 |
36029 |
33183 |
2274 |
2089 |
https://usegalaxy.eu/published/workflow?id=b6eb5fe7e37f680a, https://usegalaxy.fr/published/workflow?id=334189184455d9a2, https://usegalaxy.fr/published/workflow?id=74b4d11c07f7f0a4, https://usegalaxy.org/published/workflow?id=fca70e1bf761c6a2 |
|
|
simpleweather |
simple_weather |
provides simple weather in text format |
2016-07-19 |
http://wttr.in/ |
0.1.2 |
curl |
|
To update |
Visualization, Web Services |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
simtext |
abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix |
A text mining framework for interactive analysis and visualization of similarities among biomedical entities. |
2021-02-28 |
https://github.com/dlal-group/simtext |
0.0.2 |
r-argparse |
1.0.1 |
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tools/simtext |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext |
|
|
|
|
0 |
2 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
32 |
32 |
234 |
234 |
0 |
0 |
0 |
0 |
5 |
5 |
608 |
608 |
0 |
0 |
0 |
0 |
842 |
842 |
37 |
37 |
https://workflowhub.eu/workflows/1603?version=1 |
statistics/text-mining_simtext |
|
sina |
sina |
SINA reference based multiple sequence alignment |
2019-10-11 |
https://sina.readthedocs.io/en/latest/ |
1.7.2 |
sina |
1.7.2 |
Up-to-date |
Sequence Analysis |
Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment |
Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment |
Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy |
Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina |
sina |
SINA |
Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
123 |
143 |
1180 |
1492 |
377 |
460 |
2041 |
2558 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4050 |
3221 |
603 |
500 |
|
|
|
sinto |
sinto_barcode, sinto_fragments |
Sinto single-cell analysis tools |
2023-04-12 |
https://github.com/timoast/sinto |
0.10.1 |
sinto |
0.10.1 |
Up-to-date |
Single Cell, Epigenetics |
|
|
Bioinformatics, Cell biology |
Bioinformatics, Cell biology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto |
sinto |
sinto |
Sinto is a toolkit for processing aligned single-cell data. |
|
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
48 |
48 |
350 |
350 |
28 |
28 |
221 |
221 |
1 |
1 |
190 |
190 |
0 |
0 |
0 |
0 |
761 |
761 |
77 |
77 |
https://workflowhub.eu/workflows/1506?version=1 |
single-cell/scatac-preprocessing-tenx |
|
slamdunk |
alleyoop, slamdunk |
Slamdunk maps and quantifies SLAMseq reads |
2018-10-05 |
http://t-neumann.github.io/slamdunk |
0.4.3 |
slamdunk |
0.4.3 |
Up-to-date |
RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
10 |
13 |
159 |
402 |
55 |
57 |
1312 |
1380 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1782 |
1471 |
70 |
65 |
|
|
|
sleuth |
sleuth |
Sleuth is a program for differential analysis of RNA-Seq data. |
2023-05-30 |
https://github.com/pachterlab/sleuth |
0.30.2 |
r-sleuth |
0.30.2 |
Up-to-date |
Transcriptomics, RNA, Statistics |
Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation |
Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation |
RNA-Seq, Gene expression, Statistics and probability |
RNA-Seq, Gene expression, Statistics and probability |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth |
sleuth |
sleuth |
A statistical model and software application for RNA-seq differential expression analysis. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
42 |
42 |
204 |
204 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
204 |
204 |
42 |
42 |
|
|
|
smallgenomeutilities |
smgu_frameshift_deletions_checks |
Set of utilities for manipulating small viral genome data. |
2023-05-30 |
https://github.com/cbg-ethz/smallgenomeutilities |
0.5.2 |
smallgenomeutilities |
0.5.2 |
Up-to-date |
Sequence Analysis |
Read pre-processing, Sequence alignment, Genetic variation analysis |
Read pre-processing, Sequence alignment, Genetic variation analysis |
Genomics, Population genetics, Workflows, Virology, Sequencing |
Genomics, Population genetics, Workflows, Virology, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities |
v-pipe |
V-pipe |
Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
15 |
15 |
168 |
168 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
168 |
168 |
15 |
15 |
|
|
|
smudgeplot |
smudgeplot |
Inference of ploidy and heterozygosity structure using whole genome sequencing |
2022-06-30 |
https://github.com/KamilSJaron/smudgeplot |
0.2.5 |
smudgeplot |
0.4.0 |
To update |
Assembly |
Sequence trimming, Genotyping, k-mer counting |
Sequence trimming, Genotyping, k-mer counting |
Sequence assembly, Genetic variation, Mathematics |
Sequence assembly, Genetic variation, Mathematics |
galaxy-australia |
https://github.com/galaxyproject/tools-iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot |
smudgeplots |
Smudgeplots |
Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
146 |
146 |
805 |
805 |
90 |
90 |
242 |
242 |
78 |
78 |
1315 |
1315 |
0 |
0 |
0 |
0 |
2362 |
2362 |
314 |
314 |
https://usegalaxy.eu/published/workflow?id=bc32937d505135ab, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/1641?version=1, https://workflowhub.eu/workflows/603?version=2, https://workflowhub.eu/workflows/698?version=1 |
assembly/ERGA-post-assembly-QC |
|
snap |
snap, snap_training |
SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. |
2017-10-12 |
https://github.com/KorfLab/SNAP |
2013_11_29 |
snap |
2013_11_29 |
Up-to-date |
Sequence Analysis |
Gene prediction |
Gene prediction |
DNA, DNA polymorphism, Genetics |
DNA polymorphism, Genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap |
snap |
SNAP |
The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
348 |
410 |
1443 |
1821 |
258 |
292 |
813 |
939 |
100 |
101 |
578 |
594 |
0 |
0 |
0 |
0 |
3354 |
2834 |
803 |
706 |
https://usegalaxy.eu/published/workflow?id=26ad77bc07a7e512, https://usegalaxy.eu/published/workflow?id=6ca20e710f4f3ffb, https://usegalaxy.org.au/published/workflow?id=7e40485d1ed45b7c, https://workflowhub.eu/workflows/1504?version=1 |
genome-annotation/annotation-with-maker |
|
snapatac2 |
snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing |
SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis |
2024-05-16 |
https://kzhang.org/SnapATAC2/ |
2.6.4 |
|
|
To update |
Single Cell, Epigenetics |
Essential dynamics, Dimensionality reduction, Gene expression profiling |
Essential dynamics, Dimensionality reduction, Gene expression profiling |
Epigenomics, Cell biology, Chromosome conformation capture, Mapping, Sequencing |
Epigenomics, Cell biology, Chromosome conformation capture, Mapping, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 |
snapatac |
SnapATAC |
SnapATAC (Single Nucleus Analysis Pipeline for ATAC-seq) is a fast, accurate and comprehensive method for analyzing single cell ATAC-seq datasets. |
|
0 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
14 |
14 |
2521 |
2521 |
14 |
14 |
65 |
65 |
1 |
1 |
1633 |
1633 |
0 |
0 |
0 |
0 |
4219 |
4219 |
29 |
29 |
https://usegalaxy.eu/published/workflow?id=15cb6b690d23e6ef, https://usegalaxy.eu/published/workflow?id=d20fbb95f15386f5, https://usegalaxy.eu/published/workflow?id=e4e969e9943cdaa5, https://workflowhub.eu/workflows/1077?version=1, https://workflowhub.eu/workflows/1078?version=1, https://workflowhub.eu/workflows/1089?version=1, https://workflowhub.eu/workflows/1551?version=1, https://workflowhub.eu/workflows/1561?version=1 |
single-cell/scatac-batch-correction-snapatac2, single-cell/scatac-standard-processing-snapatac2 |
|
sniffles |
sniffles |
Galaxy wrapper for sniffles |
2020-08-29 |
https://github.com/fritzsedlazeck/Sniffles |
2.5.2 |
sniffles |
2.6.3 |
To update |
Sequence Analysis |
Sequence analysis, Structural variation detection |
Sequence analysis, Structural variation detection |
DNA structural variation, Sequencing |
Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles |
sniffles |
Sniffles |
An algorithm for structural variation detection from third generation sequencing alignment. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
205 |
205 |
1813 |
1813 |
246 |
246 |
1546 |
1546 |
98 |
98 |
2716 |
2716 |
4 |
4 |
11 |
11 |
6086 |
6086 |
553 |
553 |
https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=35a9136ddf37d589, https://usegalaxy.eu/published/workflow?id=cb54883452a73019, https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7, https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org.au/published/workflow?id=d69a765cfc82a399 |
|
|
snipit |
snipit |
Summarise snps relative to a reference sequence |
2022-07-17 |
https://github.com/aineniamh/snipit |
1.6 |
snipit |
1.6 |
Up-to-date |
Variant Analysis, Sequence Analysis |
Base position variability plotting |
Base position variability plotting |
Virology |
Virology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit |
snipit |
snipit |
Summarise snps relative to a reference sequence |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
88 |
88 |
1354 |
1354 |
16 |
16 |
84 |
84 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1438 |
1438 |
104 |
104 |
https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://workflowhub.eu/workflows/1260?version=2 |
|
|
snippy |
snippy_core, snippy, snippy_clean_full_aln |
Contains the snippy tool for characterising microbial snps |
2017-07-13 |
https://github.com/tseemann/snippy |
|
snippy |
4.6.0 |
To update |
Sequence Analysis |
Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling |
Phylogenetic tree visualisation, Variant calling |
Genomics, Model organisms, DNA polymorphism, Phylogenetics |
Genomics, Model organisms, DNA polymorphism, Phylogenetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy |
snippy |
snippy |
Rapid haploid variant calling and core SNP phylogeny generation. |
|
0 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
3483 |
3838 |
188403 |
199916 |
4057 |
4306 |
138187 |
142349 |
2223 |
2852 |
67168 |
78979 |
60 |
60 |
8769 |
8769 |
430013 |
402527 |
11056 |
9823 |
https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383, https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=464b642261ed7452, https://usegalaxy.eu/published/workflow?id=4f9f7065975b3f97, https://usegalaxy.eu/published/workflow?id=515ef1601bc24a6c, https://usegalaxy.eu/published/workflow?id=628062a8cf93261f, https://usegalaxy.eu/published/workflow?id=65249196143d7930, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=920aab45ff028ed4, https://usegalaxy.eu/published/workflow?id=94c3d329c31c712f, https://usegalaxy.eu/published/workflow?id=968f0ac2617aa524, https://usegalaxy.eu/published/workflow?id=a183da6b56cd1d60, https://usegalaxy.eu/published/workflow?id=b556b0a67ad979da, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.eu/published/workflow?id=fde21b5f5c169114, https://usegalaxy.org.au/published/workflow?id=1719e0eb54b41f68, https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2, https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://usegalaxy.org/published/workflow?id=00596e862edb23f2, https://usegalaxy.org/published/workflow?id=562bcaa9b4d2e8a4, https://usegalaxy.org/published/workflow?id=5674956f5c18b85b, https://usegalaxy.org/published/workflow?id=69d8863d40524120, https://usegalaxy.org/published/workflow?id=7dd6e4150bb81ad1, https://usegalaxy.org/published/workflow?id=80ac6adead9f97d8, https://usegalaxy.org/published/workflow?id=d4f0a7ccb09f1e55, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://usegalaxy.org/published/workflow?id=ee4679b3e9e830b7, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1573?version=1, https://workflowhub.eu/workflows/1639?version=1, https://workflowhub.eu/workflows/1647?version=1 |
evolution/mtb_transmission, variant-analysis/microbial-variants, variant-analysis/tb-variant-analysis |
|
snp_dists |
snp_dists |
Compute pairwise SNP distance matrix from a FASTA sequence alignment |
2019-10-18 |
https://github.com/tseemann/snp-dists |
0.8.2 |
snp-dists |
0.8.2 |
Up-to-date |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists |
|
|
|
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0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1166 |
1178 |
9794 |
10000 |
353 |
353 |
8021 |
8021 |
282 |
282 |
2937 |
2937 |
0 |
0 |
0 |
0 |
20958 |
20752 |
1813 |
1801 |
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evolution/mtb_transmission |
|
snp_sites |
snp_sites |
Finds SNP sites from a multi-FASTA alignment file |
2017-06-28 |
https://github.com/sanger-pathogens/snp-sites |
2.5.1 |
snp-sites |
2.5.1 |
Up-to-date |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites |
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10330 |
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3008 |
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16080 |
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evolution/mtb_transmission |
|
snpeff |
snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names |
SnpEff is a genetic variant annotation and effect prediction toolbox |
2014-11-11 |
http://snpeff.sourceforge.net/ |
5.2 |
biopython |
1.70 |
To update |
Genome-Wide Association Study, Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff |
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100316 |
146690 |
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16720 |
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introduction/galaxy-intro-ngs-data-managment, variant-analysis/dip, variant-analysis/exome-seq, variant-analysis/mapping-by-sequencing, variant-analysis/somatic-variants, variant-analysis/trio-analysis |
|
snpeff_sars_cov_2 |
snpeff_sars_cov_2 |
SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox |
2020-06-17 |
http://snpeff.sourceforge.net/ |
|
|
|
To update |
Genome-Wide Association Study, Variant Analysis |
SNP detection |
SNP detection |
DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs |
DNA polymorphism, Nucleic acid sites, features and motifs |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 |
snpeff |
snpEff |
Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1580 |
1592 |
704888 |
766978 |
1876 |
1910 |
84580 |
99497 |
607 |
607 |
30784 |
32363 |
29 |
29 |
3465 |
3465 |
902303 |
823717 |
4138 |
4092 |
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galaxy-interface/ncbi-sarf, introduction/galaxy-intro-ngs-data-managment, variant-analysis/sars-cov-2 |
|
snpfreqplot |
snpfreqplot |
A plotting app to visualise the SNPs across a region |
2020-12-02 |
https://github.com/BrownfieldPlantLab/SNPFreqPlot |
1.0 |
r-base |
|
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
399 |
399 |
3862 |
3862 |
525 |
525 |
1655 |
1655 |
103 |
103 |
1386 |
1386 |
9 |
9 |
347 |
347 |
7250 |
7250 |
1036 |
1036 |
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|
|
snpsift |
snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck |
snpEff SnpSift tools from Pablo Cingolani |
2014-11-11 |
http://snpeff.sourceforge.net/SnpSift.html |
|
snpsift |
5.3.0a |
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift |
|
|
|
|
0 |
8 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
0 |
0 |
0 |
0 |
0 |
8 |
0 |
0 |
0 |
0 |
0 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
8 |
2060 |
2117 |
5092180 |
5175645 |
3160 |
4102 |
368540 |
447226 |
502 |
515 |
105403 |
108005 |
39 |
40 |
11506 |
11523 |
5742399 |
5577629 |
6774 |
5761 |
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https://usegalaxy.org/published/workflow?id=fae519dcba6bfc72, https://usegalaxy.org/published/workflow?id=ff3ade25b35f4893, https://usegalaxy.org/published/workflow?id=ffae9c47980a5170, https://workflowhub.eu/workflows/1063?version=5, https://workflowhub.eu/workflows/109?version=9, https://workflowhub.eu/workflows/110?version=11, https://workflowhub.eu/workflows/1190?version=1, https://workflowhub.eu/workflows/138?version=9, https://workflowhub.eu/workflows/1391?version=1, https://workflowhub.eu/workflows/1479?version=1, https://workflowhub.eu/workflows/1540?version=1, https://workflowhub.eu/workflows/1642?version=1, https://workflowhub.eu/workflows/1876?version=1, https://workflowhub.eu/workflows/354?version=1, https://workflowhub.eu/workflows/356?version=1, https://workflowhub.eu/workflows/35?version=1, https://workflowhub.eu/workflows/36?version=1, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1 |
galaxy-interface/collections, galaxy-interface/workflow-automation, introduction/galaxy-intro-ngs-data-managment, microbiome/pathogen-detection-from-nanopore-foodborne-data, variant-analysis/sars-cov-2 |
|
snpsift_dbnsfp |
snpSift_dbnsfp |
snpEff SnpSift dbnsfp tool from Pablo Cingolani |
2014-11-11 |
http://snpeff.sourceforge.net/SnpSift.html#dbNSFP |
|
snpsift |
5.3.0a |
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
21 |
25 |
70 |
82 |
62 |
77 |
297 |
425 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
507 |
367 |
102 |
83 |
https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4 |
|
|
snpsift_genesets |
snpSift_geneSets |
Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome |
2014-11-11 |
http://snpeff.sourceforge.net/SnpSift.html#geneSets |
|
snpsift |
5.3.0a |
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
105 |
149 |
570 |
644 |
179 |
218 |
437 |
534 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1178 |
1007 |
367 |
284 |
|
|
|
socru |
socru |
Order and orientation of complete bacterial genomes |
2019-09-03 |
https://github.com/quadram-institute-bioscience/socru |
2.1.7 |
socru |
2.2.5 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
41 |
52 |
571 |
679 |
90 |
107 |
278 |
320 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
999 |
849 |
159 |
131 |
|
|
|
sonneityping |
sonneityping |
Scripts for parsing Mykrobe predict results for Shigella sonnei. |
2021-09-16 |
https://github.com/katholt/sonneityping |
20210201 |
sonneityping |
20210201 |
Up-to-date |
Sequence Analysis |
Antimicrobial resistance prediction, Variant calling, Genotyping |
Antimicrobial resistance prediction, Variant calling, Genotyping |
Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics |
Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics |
iuc |
https://github.com/katholt/sonneityping |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping |
sonneityping |
sonneityping |
Scripts for parsing Mykrobe predict results for Shigella sonnei. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
2 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
2 |
|
|
|
spacexr |
spacexr_cside, spacexr_rctd |
Cell type identification and cell type-specific differential expression in spatial transcriptomics |
2024-08-02 |
https://github.com/dmcable/spacexr/tree/master |
2.2.1 |
r-spacexr |
2.2.1 |
Up-to-date |
Spatial Omics, Single Cell |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/spacexr |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/spacexr |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
7 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
2 |
2 |
|
|
|
spades |
spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades |
SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. |
2016-12-21 |
https://github.com/ablab/spades |
4.2.0 |
spades |
4.2.0 |
Up-to-date |
Assembly, RNA, Metagenomics |
Genome assembly |
Genome assembly |
Sequence assembly |
Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades |
spades |
SPAdes |
St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. |
|
0 |
9 |
9 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
3 |
8 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
9 |
3 |
8250 |
8882 |
104429 |
116176 |
14023 |
14731 |
147425 |
154112 |
5211 |
6722 |
62902 |
76811 |
373 |
380 |
2677 |
2762 |
349861 |
317433 |
30715 |
27857 |
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assembly/debruijn-graph-assembly, assembly/metagenomics-assembly, microbiome/metagenomics-assembly |
|
spaln |
list_spaln_tables, spaln |
Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. |
2019-01-11 |
http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ |
2.4.9 |
python |
|
To update |
Sequence Analysis, Genome annotation |
|
|
|
|
iuc |
https://github.com/ogotoh/spaln |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln |
|
|
|
|
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
110 |
132 |
399 |
612 |
267 |
318 |
4249 |
4506 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5118 |
4648 |
450 |
377 |
|
|
|
spapros |
spapros_evaluation, spapros_selection |
Select and evaluate probe sets for targeted spatial transcriptomics. |
2024-08-25 |
https://github.com/theislab/spapros |
0.1.5 |
spapros |
0.1.5 |
Up-to-date |
Single Cell, Transcriptomics, Sequence Analysis |
Primer and probe design, Visualisation |
Primer and probe design, Visualisation |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros |
spapros |
spapros |
Spapros is a python package that provides a pipeline for probe set selection and evaluation for targeted spatial transcriptomics data. |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
1 |
1 |
https://usegalaxy.eu/published/workflow?id=9adf0402b641042c |
|
|
spotyping |
spotyping |
SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads |
2018-05-07 |
https://github.com/xiaeryu/SpoTyping-v2.0 |
2.1 |
spotyping |
2.1 |
Up-to-date |
Sequence Analysis |
Variant pattern analysis |
Variant pattern analysis |
Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation |
Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation |
iuc |
https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping |
spotyping |
SpoTyping |
Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
34 |
34 |
2042 |
2042 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2042 |
2042 |
34 |
34 |
|
|
|
spyboat |
spyboat |
Wavelet analysis for 3d-image stacks |
2020-11-28 |
http://github.com/tensionhead/spyboat |
0.1.2 |
spyboat |
|
To update |
Imaging, Graphics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
6 |
6 |
174 |
174 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
174 |
174 |
6 |
6 |
|
|
|
squirrel |
squirrel_phylo, squirrel_qc |
QC and Phylogenetic analysis of MPXV |
2025-01-16 |
https://github.com/aineniamh/squirrel |
1.0.13 |
squirrel |
1.2.2 |
To update |
Phylogenetics |
Phylogenetic analysis, Sequencing quality control |
Phylogenetic analysis, Sequencing quality control |
Virology |
Virology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel |
squirrel |
squirrel |
Some QUIck Reconstruction to Resolve Evolutionary LinksSquirrel provides a rapid way of producing reliable alignments for MPXV and also enable maximum-likelihood phylogenetics pipeline tree estimation. |
|
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
7 |
7 |
0 |
0 |
0 |
0 |
41 |
41 |
193 |
193 |
0 |
0 |
0 |
0 |
200 |
200 |
43 |
43 |
https://usegalaxy.org.au/published/workflow?id=b9fd488b0938d323 |
|
|
sra_tools |
fasterq_dump, fastq_dump, sam_dump |
NCBI Sequence Read Archive toolkit utilities |
2015-11-16 |
https://github.com/ncbi/sra-tools |
3.1.1 |
sra-tools |
3.2.1 |
To update |
Data Source, Fastq Manipulation |
Data handling |
Data handling |
DNA, Genomics, Sequencing |
DNA, Genomics, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools |
sra-tools |
SRA Software Toolkit |
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. |
|
0 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
12471 |
13217 |
237033 |
441031 |
27873 |
35613 |
529630 |
790405 |
3415 |
3922 |
56240 |
63877 |
411 |
416 |
6530 |
6602 |
1301915 |
829433 |
53168 |
44170 |
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assembly/assembly-with-preprocessing, galaxy-interface/ncbi-sarf, introduction/galaxy-intro-ngs-data-managment, transcriptomics/minerva-pathways, variant-analysis/baculovirus-isolate-variation, variant-analysis/sars-cov-2 |
|
srst2 |
srst2 |
SRST2 Short Read Sequence Typing for Bacterial Pathogens |
2022-08-22 |
http://katholt.github.io/srst2/ |
0.2.0 |
samtools |
1.22.1 |
To update |
Metagenomics |
Multilocus sequence typing |
Multilocus sequence typing |
Whole genome sequencing, Public health and epidemiology, Comparative genomics |
Whole genome sequencing, Public health and epidemiology, Comparative genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 |
srst2 |
srst2 |
Short Read Sequence Typing for Bacterial Pathogens |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
68 |
68 |
407 |
407 |
1 |
1 |
71 |
71 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
478 |
478 |
69 |
69 |
https://workflowhub.eu/workflows/407?version=1 |
|
|
stacks |
stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks |
Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq |
2016-03-07 |
http://catchenlab.life.illinois.edu/stacks/ |
|
stacks |
2.68 |
To update |
Sequence Analysis |
Data handling |
Data handling |
Mapping, Population genetics |
Mapping, Population genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks |
stacks |
Stacks |
Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. |
|
0 |
13 |
13 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
13 |
13 |
132 |
199 |
6924 |
14189 |
0 |
0 |
0 |
0 |
40 |
40 |
6127 |
6127 |
2 |
2 |
8 |
8 |
20324 |
13059 |
241 |
174 |
https://workflowhub.eu/workflows/1662?version=1, https://workflowhub.eu/workflows/1665?version=1, https://workflowhub.eu/workflows/1666?version=1, https://workflowhub.eu/workflows/1683?version=1 |
ecology/de-novo-rad-seq, ecology/genetic-map-rad-seq, ecology/ref-based-rad-seq |
|
stacks2 |
stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks |
Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq |
2018-12-01 |
http://catchenlab.life.illinois.edu/stacks/ |
2.55 |
stacks |
2.68 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 |
|
|
|
|
0 |
12 |
12 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
118 |
145 |
8146 |
11221 |
0 |
0 |
0 |
0 |
54 |
54 |
22200 |
22427 |
8 |
9 |
650 |
651 |
34299 |
30996 |
208 |
180 |
https://usegalaxy.eu/published/workflow?id=510bcef37f385495, https://usegalaxy.eu/published/workflow?id=f5d387583670f694, https://usegalaxy.org.au/published/workflow?id=1e71b5232b9b4d2a, https://usegalaxy.org.au/published/workflow?id=9b3f3d331d0b2892, https://usegalaxy.org.au/published/workflow?id=a401ad5349b44dfb, https://usegalaxy.org.au/published/workflow?id=ca45322bff44e73a, https://usegalaxy.org.au/published/workflow?id=f7adc76331620f34, https://workflowhub.eu/workflows/347?version=1, https://workflowhub.eu/workflows/348?version=1, https://workflowhub.eu/workflows/349?version=1, https://workflowhub.eu/workflows/350?version=1, https://workflowhub.eu/workflows/352?version=1 |
|
|
star_fusion |
star_fusion |
STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR |
2015-10-15 |
https://github.com/STAR-Fusion/STAR-Fusion |
0.5.4-3+galaxy1 |
star-fusion |
1.15.1 |
To update |
Sequence Analysis, Transcriptomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
84 |
108 |
1268 |
1483 |
204 |
337 |
1678 |
3284 |
4 |
4 |
300 |
300 |
0 |
0 |
0 |
0 |
5067 |
3246 |
449 |
292 |
|
|
|
staramr |
staramr_search |
Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. |
2024-09-19 |
https://github.com/phac-nml/staramr |
0.11.0 |
staramr |
0.11.0 |
Up-to-date |
Sequence Analysis |
Antimicrobial resistance prediction |
Antimicrobial resistance prediction |
Microbiology, Public health and epidemiology, Infectious disease |
Microbiology, Public health and epidemiology, Infectious disease |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/staramr |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr |
staramr |
staramr |
staramr (*AMR) scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes. The star|* in staramr indicates that it can handle all of the ResFinder, PointFinder, and PlasmidFinder databases. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2921 |
3072 |
31443 |
33124 |
2130 |
2130 |
14763 |
14763 |
1173 |
1182 |
8989 |
9237 |
97 |
97 |
9838 |
9838 |
66962 |
65033 |
6481 |
6321 |
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genome-annotation/amr-gene-detection, microbiome/plasmid-metagenomics-nanopore |
|
straindesign |
straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion |
Toolbox to optimize biological model |
2022-10-02 |
https://github.com/brsynth/straindesign |
3.2.2 |
straindesign |
3.2.3 |
To update |
Systems Biology, Synthetic Biology |
|
|
|
|
iuc |
https://github.com/brsynth/straindesign |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign |
|
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strelka |
strelka_germline, strelka_somatic |
Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision. |
2021-01-27 |
https://github.com/Illumina/strelka/ |
2.9.10 |
strelka |
2.9.10 |
Up-to-date |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka |
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88 |
88 |
992 |
992 |
342 |
342 |
1990 |
1990 |
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0 |
0 |
2982 |
2982 |
430 |
430 |
https://usegalaxy.eu/published/workflow?id=ddd604341afd9cf7 |
|
|
stringtie |
stringtie, stringtie_merge |
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. |
2014-09-13 |
http://ccb.jhu.edu/software/stringtie/ |
2.2.3 |
stringtie |
3.0.1 |
To update |
Transcriptomics |
Transcriptome assembly, RNA-Seq analysis |
Transcriptome assembly, RNA-Seq analysis |
Transcriptomics, RNA-Seq |
Transcriptomics, RNA-Seq |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie |
stringtie |
StringTie |
Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. |
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2 |
2 |
2 |
2 |
3884 |
4419 |
194508 |
217287 |
6876 |
11163 |
316022 |
446115 |
673 |
865 |
27958 |
33201 |
302 |
303 |
3783 |
3787 |
700390 |
542271 |
16750 |
11735 |
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genome-annotation/lncrna, proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation, transcriptomics/de-novo, transcriptomics/differential-isoform-expression |
|
structure |
structure |
for using multi-locus genotype data to investigate population structure. |
2017-09-22 |
https://web.stanford.edu/group/pritchardlab/structure.html |
2.3.4 |
structure |
2.3.4 |
Up-to-date |
Phylogenetics, Variant Analysis |
Genetic variation analysis |
Genetic variation analysis |
Population genetics |
Population genetics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure |
structure |
Structure |
The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. |
|
0 |
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1 |
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1 |
1 |
1 |
138 |
155 |
3903 |
4354 |
0 |
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0 |
0 |
0 |
0 |
0 |
3 |
3 |
330 |
330 |
4684 |
4233 |
158 |
141 |
|
|
|
structureharvester |
structureharvester |
for parsing STRUCTURE outputs and for performing the Evanno method |
2017-12-06 |
http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/ |
0.6.94 |
structureharvester |
0.6.94 |
Up-to-date |
Phylogenetics, Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester |
|
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suite_pretext |
pretext_graph, pretext_map, pretext_snapshot |
Process genome contacts maps processing images. |
2021-04-05 |
https://github.com/wtsi-hpag/PretextSnapshot |
0.0.7 |
pretextgraph |
0.0.9 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext |
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397 |
397 |
5173 |
5173 |
241 |
241 |
6703 |
6703 |
53 |
53 |
1729 |
1729 |
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13605 |
13605 |
691 |
691 |
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assembly/ERGA-post-assembly-QC, assembly/vgp_genome_assembly |
|
swiftlink |
swiftlink |
Parallel MCMC Linkage Analysis |
2017-11-21 |
https://github.com/ajm/swiftlink |
1.0 |
swiftlink |
1.0 |
Up-to-date |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
syndiva |
syndiva |
SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. |
2022-06-23 |
|
1.0 |
clustalo |
1.2.4 |
To update |
Proteomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
2 |
2 |
30 |
30 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
30 |
30 |
2 |
2 |
|
|
|
syri |
syri |
Synteny and Rearrangement Identifier |
2025-04-16 |
https://github.com/schneebergerlab/syri |
1.7.1 |
syri |
1.7.1 |
Up-to-date |
Sequence Analysis |
Haplotype mapping, Variant calling, Genotyping, Sequence assembly, Read mapping |
Haplotype mapping, Variant calling, Genotyping, Sequence assembly, Read mapping |
DNA polymorphism, Sequence assembly, DNA structural variation, Mapping, Sequencing |
DNA polymorphism, Sequence assembly, Mapping, Sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri |
SyRI |
SyRI |
SyRI is tool for finding genomic rearrangements and local sequence differences from whole-genome assemblies.Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
22 |
22 |
84 |
84 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
76 |
76 |
160 |
160 |
27 |
27 |
https://usegalaxy.fr/published/workflow?id=356dced9687596b7, https://usegalaxy.fr/published/workflow?id=ce4acd38084ee9ef |
|
|
table_compute |
table_compute |
Perform general-purpose table operations |
2019-06-05 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute |
1.2.4 |
pandas |
|
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1946 |
2210 |
235082 |
237980 |
1655 |
1819 |
12248 |
14832 |
262 |
285 |
17101 |
18230 |
99 |
100 |
892 |
926 |
271968 |
265323 |
4414 |
3962 |
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https://workflowhub.eu/workflows/1550?version=1, https://workflowhub.eu/workflows/1567?version=1, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1713?version=1, https://workflowhub.eu/workflows/1789?version=1, https://workflowhub.eu/workflows/1849?version=1, https://workflowhub.eu/workflows/561?version=11, https://workflowhub.eu/workflows/659?version=1 |
microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/neoantigen-hla-binding-novel-peptides, single-cell/bulk-deconvolution-evaluate, single-cell/bulk-music-2-preparescref, single-cell/bulk-music-3-preparebulk, single-cell/scrna-case_cell-cycle, statistics/flexynesis_cbio_import, statistics/flexynesis_classification, transcriptomics/ref-based, transcriptomics/rna-seq-analysis-clustering-viz |
|
tabular_to_fastq |
tabular_to_fastq |
Tabular to FASTQ converter |
2019-06-21 |
https://github.com/galaxyproject/sequence_utils |
1.1.5 |
galaxy_sequence_utils |
1.2.0 |
To update |
Fastq Manipulation |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
507 |
586 |
9277 |
11798 |
740 |
2407 |
7442 |
32030 |
92 |
124 |
892 |
1250 |
11 |
12 |
20 |
22 |
45100 |
17631 |
3129 |
1350 |
https://usegalaxy.eu/published/workflow?id=5e1b048040ea7535, https://usegalaxy.eu/published/workflow?id=8c7958cb05fba814, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=acb9131e84de1ae0, https://usegalaxy.org.au/published/workflow?id=533dbb3242ee4255, https://usegalaxy.org/published/workflow?id=14f62361a15f8a24, https://usegalaxy.org/published/workflow?id=1e1a299825f27f11, https://usegalaxy.org/published/workflow?id=1efb485f123233eb, https://usegalaxy.org/published/workflow?id=41b181f1d763e419, https://usegalaxy.org/published/workflow?id=4266aa248d5b1ea4, https://usegalaxy.org/published/workflow?id=5004f1087f5e87db, https://usegalaxy.org/published/workflow?id=5de035c08af915ea, https://usegalaxy.org/published/workflow?id=9304cc9410a96323, https://usegalaxy.org/published/workflow?id=bb9ee8e05f7042a9 |
single-cell/scrna-data-ingest |
|
tag_pileup_frequency |
tag_pileup_frequency |
Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. |
2016-05-05 |
https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup |
1.0.2 |
openjdk |
|
To update |
Statistics, SAM, Genomic Interval Operations |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
11 |
17 |
35 |
184 |
34 |
77 |
661 |
875 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1059 |
696 |
94 |
45 |
|
|
|
tasmanian_mismatch |
tasmanian_mismatch |
Analysis of positional mismatches |
2020-04-19 |
https://github.com/nebiolabs/tasmanian-mismatch |
1.0.9 |
tasmanian-mismatch |
1.0.9 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
11 |
23 |
23 |
32 |
32 |
292 |
292 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
315 |
315 |
43 |
43 |
https://usegalaxy.org/published/workflow?id=1ddabc7d272dc702, https://usegalaxy.org/published/workflow?id=cdea4f88ccbd155f |
|
|
taxonkit |
name2taxid, profile2cami |
TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit |
2024-07-26 |
https://bioinf.shenwei.me/taxonkit/ |
0.20.0 |
taxonkit |
0.20.0 |
Up-to-date |
Metagenomics |
Formatting, Data retrieval |
Formatting, Data retrieval |
Taxonomy, Biotechnology, Ecology |
Taxonomy, Biotechnology, Ecology |
iuc |
https://github.com/shenwei356/taxonkit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit |
taxonkit |
TaxonKit |
TaxonKit is a practical and efficient NCBI taxonomy toolkit. |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
1094 |
1094 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1094 |
1094 |
12 |
12 |
https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1 |
|
|
taxonomy_filter_refseq |
taxonomy_filter_refseq |
Filter RefSeq by taxonomy |
2019-01-13 |
https://github.com/pvanheus/ncbitaxonomy |
0.3.0 |
rust-ncbitaxonomy |
1.0.7 |
To update |
Sequence Analysis, Genome annotation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
taxonomy_krona_chart |
taxonomy_krona_chart |
Krona pie chart from taxonomic profile |
2015-08-06 |
http://sourceforge.net/projects/krona/ |
2.7.1+galaxy0 |
krona |
2.8.1 |
To update |
Assembly |
Visualisation |
Visualisation |
Metagenomics |
Metagenomics |
crs4 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart |
krona |
Krona |
Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
1 |
1 |
7406 |
7874 |
48617 |
51653 |
6438 |
7659 |
33268 |
41191 |
2005 |
2042 |
11003 |
11192 |
162 |
163 |
565 |
586 |
104622 |
93453 |
17738 |
16011 |
https://usegalaxy.eu/published/workflow?id=007ce6405d196df3, https://usegalaxy.eu/published/workflow?id=0590554db9794d13, https://usegalaxy.eu/published/workflow?id=05f5f040337786bf, https://usegalaxy.eu/published/workflow?id=08e25b733cd796e6, https://usegalaxy.eu/published/workflow?id=08eb5e55109c4d9c, https://usegalaxy.eu/published/workflow?id=096b75501c8e0888, https://usegalaxy.eu/published/workflow?id=0bafeb17c21ebc9c, https://usegalaxy.eu/published/workflow?id=10101558b211a782, https://usegalaxy.eu/published/workflow?id=14714876dda7186d, https://usegalaxy.eu/published/workflow?id=181e751be8dd9abc, https://usegalaxy.eu/published/workflow?id=19de5cbae7f48103, https://usegalaxy.eu/published/workflow?id=2cf09adb1ed6c3ec, https://usegalaxy.eu/published/workflow?id=309fc4fc2e0da89c, https://usegalaxy.eu/published/workflow?id=39d36a7ce0ef268d, https://usegalaxy.eu/published/workflow?id=437704898229dfb6, https://usegalaxy.eu/published/workflow?id=44e16f0782f54111, 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https://usegalaxy.org/published/workflow?id=e12324f5e3b930fd, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/101?version=1, https://workflowhub.eu/workflows/1059?version=1, https://workflowhub.eu/workflows/1199?version=2, https://workflowhub.eu/workflows/124?version=1, https://workflowhub.eu/workflows/1270?version=2, https://workflowhub.eu/workflows/1273?version=2, https://workflowhub.eu/workflows/1439?version=1, https://workflowhub.eu/workflows/1451?version=2, https://workflowhub.eu/workflows/1465?version=1, https://workflowhub.eu/workflows/1466?version=2, https://workflowhub.eu/workflows/1470?version=1, https://workflowhub.eu/workflows/1472?version=1, https://workflowhub.eu/workflows/1473?version=1, https://workflowhub.eu/workflows/1483?version=1, https://workflowhub.eu/workflows/1842?version=1, https://workflowhub.eu/workflows/1856?version=1, https://workflowhub.eu/workflows/53?version=1, https://workflowhub.eu/workflows/624?version=1 |
microbiome/beer-data-analysis, microbiome/general-tutorial, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/mgnify-amplicon, microbiome/mothur-miseq-sop, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/taxonomic-profiling |
|
taxpasta |
taxpasta |
standardise taxonomic profiles |
2023-08-30 |
https://taxpasta.readthedocs.io/en/latest/ |
0.7.0 |
taxpasta |
0.7.0 |
Up-to-date |
Sequence Analysis |
Standardisation and normalisation, Aggregation, Formatting, Conversion |
Standardisation and normalisation, Aggregation, Formatting, Conversion |
Taxonomy, Metagenomics |
Taxonomy, Metagenomics |
iuc |
https://github.com/taxprofiler/taxpasta |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta |
taxpasta |
taxpasta |
TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
51 |
51 |
323 |
323 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
18 |
18 |
341 |
341 |
52 |
52 |
https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=cb2df493f5e334f7 |
|
|
tb-profiler |
tb_profiler_collate, tb_profiler_profile |
Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. |
2019-04-02 |
https://github.com/jodyphelan/TBProfiler |
6.6.5 |
tb-profiler |
6.6.5 |
Up-to-date |
Sequence Analysis |
Antimicrobial resistance prediction |
Antimicrobial resistance prediction |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler |
tb-profiler |
tb-profiler |
A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). |
|
0 |
2 |
2 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
491 |
535 |
15947 |
16201 |
490 |
506 |
11483 |
11641 |
199 |
201 |
10939 |
10981 |
0 |
0 |
0 |
0 |
38823 |
38369 |
1242 |
1180 |
https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=89ed570bc0703472, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6, https://usegalaxy.eu/published/workflow?id=d0d6dae0d1eecc21, https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2, https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1564?version=1, https://workflowhub.eu/workflows/1647?version=1 |
evolution/mtb_transmission, variant-analysis/tb-variant-analysis |
|
tb_variant_filter |
tb_variant_filter |
M. tuberculosis H37Rv VCF filter |
2019-10-03 |
https://github.com/COMBAT-TB/tb_variant_filter |
0.4.0 |
tb_variant_filter |
0.4.0 |
Up-to-date |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/COMBAT-TB/tb_variant_filter |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
618 |
655 |
43892 |
44301 |
356 |
364 |
23229 |
23483 |
103 |
103 |
10184 |
10203 |
1 |
1 |
3000 |
3000 |
80987 |
80305 |
1123 |
1078 |
https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=2ebf65efe8ca4a7f, https://usegalaxy.eu/published/workflow?id=3a8fde248a4d0383, https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=65249196143d7930, https://usegalaxy.eu/published/workflow?id=6d333ed886aab471, https://usegalaxy.eu/published/workflow?id=8a248dda0131e8ad, https://usegalaxy.eu/published/workflow?id=a183da6b56cd1d60, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6, https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2, https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1569?version=1, https://workflowhub.eu/workflows/1573?version=1, https://workflowhub.eu/workflows/1647?version=1 |
evolution/mtb_transmission, variant-analysis/tb-variant-analysis |
|
tbl2gff3 |
tbl2gff3 |
Table to GFF3 |
2020-07-07 |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 |
1.2 |
bcbiogff |
0.6.6 |
To update |
Convert Formats, Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
661 |
661 |
2492 |
2492 |
255 |
255 |
604 |
604 |
148 |
148 |
649 |
649 |
17 |
17 |
53 |
53 |
3798 |
3798 |
1081 |
1081 |
https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=4ddbffe4b3fef275, https://usegalaxy.org.au/published/workflow?id=2e29b21cdec7d0cc, https://usegalaxy.org/published/workflow?id=547f86db467bf620, https://workflowhub.eu/workflows/1488?version=1, https://workflowhub.eu/workflows/1513?version=1 |
genome-annotation/amr-gene-detection, genome-annotation/bacterial-genome-annotation |
|
tbvcfreport |
tbvcfreport |
Generate HTML report from SnpEff M.tuberculosis VCF(s) |
2019-08-29 |
https://github.com/COMBAT-TB/tbvcfreport |
1.0.1 |
tbvcfreport |
1.0.1 |
Up-to-date |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
378 |
411 |
9773 |
9913 |
418 |
441 |
7332 |
7415 |
96 |
97 |
3675 |
3682 |
1 |
1 |
1 |
1 |
21011 |
20781 |
950 |
893 |
https://usegalaxy.eu/published/workflow?id=2b25eaebd3987612, https://usegalaxy.eu/published/workflow?id=2c79eee5ca5a3b09, https://usegalaxy.eu/published/workflow?id=3ff4dbcc7a602e6b, https://usegalaxy.eu/published/workflow?id=461d71caea871db8, https://usegalaxy.eu/published/workflow?id=c38e3ac59d8b86d6, https://usegalaxy.org.au/published/workflow?id=5693811cd933d2a2, https://usegalaxy.org.au/published/workflow?id=a61d4bda54de7cd1, https://usegalaxy.org/published/workflow?id=e7ce46762faccaac, https://workflowhub.eu/workflows/1035?version=1, https://workflowhub.eu/workflows/1647?version=1 |
variant-analysis/tb-variant-analysis |
|
te_finder |
te_finder |
Transposable element insertions finder |
2022-08-08 |
https://github.com/VistaSohrab/TEfinder |
1.0.1 |
samtools |
1.22.1 |
To update |
Sequence Analysis |
Genome indexing, Variant calling, PCR primer design |
Genome indexing, Variant calling, PCR primer design |
Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation |
Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder |
tefinder |
TEfinder |
A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
28 |
28 |
219 |
219 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
219 |
219 |
28 |
28 |
|
|
|
telescope_assign |
telescope_assign |
Single locus resolution of Transposable ELEment expression. |
2019-09-03 |
https://github.com/mlbendall/telescope/ |
1.0.3 |
telescope |
1.0.3 |
Up-to-date |
Genome annotation |
Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping |
Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping |
RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly |
RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope |
Telescope-expression |
Telescope |
Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
tesseract |
tesseract |
Tesseract is an OCR engine with support for unicode and the ability to recognize more than 100 languages out of the box. |
2025-06-18 |
https://github.com/tesseract-ocr/tesseract |
5.5.1 |
tesseract |
3.04.01 |
To update |
Natural Language Processing |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tesseract/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tesseract |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
83 |
83 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
83 |
83 |
10 |
10 |
|
|
|
tetoolkit |
tetoolkit_tetranscripts |
The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. |
2020-04-10 |
http://hammelllab.labsites.cshl.edu/software/ |
2.2.3 |
tetranscripts |
2.2.3 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/mhammell-laboratory/TEtranscripts |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
89 |
93 |
1167 |
1200 |
0 |
0 |
0 |
0 |
5 |
5 |
206 |
206 |
0 |
0 |
0 |
0 |
1406 |
1373 |
98 |
94 |
|
|
|
tetyper |
tetyper |
Type a specific transposable element (TE) of interest from paired-end sequencing data. |
2019-11-23 |
https://github.com/aesheppard/TETyper |
1.1 |
tetyper |
1.1 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
23 |
25 |
146 |
178 |
50 |
57 |
142 |
200 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
378 |
288 |
82 |
73 |
|
|
|
tn93 |
tn93_readreduce, tn93, tn93_cluster, tn93_filter |
Compute distances between sequences |
2018-06-06 |
https://github.com/veg/tn93/ |
1.0.15 |
tn93 |
1.0.15 |
Up-to-date |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 |
|
|
|
|
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
31 |
31 |
1952 |
1952 |
86 |
102 |
2566 |
2831 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4783 |
4518 |
133 |
117 |
|
|
|
tooldistillator |
tooldistillator, tooldistillator_summarize |
ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files |
2024-04-30 |
https://gitlab.com/ifb-elixirfr/abromics/tooldistillator |
1.0.0 |
tooldistillator |
1.0.0 |
Up-to-date |
Sequence Analysis |
Data parsing |
|
Microbiology, Bioinformatics, Sequence analysis |
Microbiology, Bioinformatics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator |
tooldistillator |
ToolDistillator |
ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. |
|
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
121 |
121 |
5042 |
5042 |
162 |
162 |
1550 |
1550 |
0 |
0 |
0 |
0 |
9 |
9 |
19253 |
19253 |
25845 |
25845 |
292 |
292 |
https://usegalaxy.eu/published/workflow?id=0404013d5c27210d, https://usegalaxy.eu/published/workflow?id=0a82eb8b44d9d502, https://usegalaxy.eu/published/workflow?id=0abd32dbc5207b88, https://usegalaxy.eu/published/workflow?id=0c47571d20535426, https://usegalaxy.eu/published/workflow?id=1ce523ef51f47134, https://usegalaxy.eu/published/workflow?id=2c1a6da84d891cf2, https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=32de10b9de8a999a, https://usegalaxy.eu/published/workflow?id=3303a04887a47675, https://usegalaxy.eu/published/workflow?id=34df701aa23a9fb3, https://usegalaxy.eu/published/workflow?id=36ea584e0f60893e, https://usegalaxy.eu/published/workflow?id=3d937648809ca4e7, https://usegalaxy.eu/published/workflow?id=41d207d06a32ba05, https://usegalaxy.eu/published/workflow?id=4216424f032c055f, https://usegalaxy.eu/published/workflow?id=47e14222073e7192, https://usegalaxy.eu/published/workflow?id=4a218fb93d78ba67, 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|
|
tracegroomer |
tracegroomer |
TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. |
2024-03-28 |
https://github.com/cbib/TraceGroomer |
0.1.4 |
tracegroomer |
0.1.4 |
Up-to-date |
Metabolomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
16 |
16 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
42 |
42 |
58 |
58 |
6 |
6 |
https://usegalaxy.fr/published/workflow?id=879408d684923861 |
|
|
tracy |
tracy_align, tracy_assemble, tracy_basecall, tracy_decompose |
A suite tools for basecalling, alignment, assembly and deconvolution of Sanger chromatograms using tracy. |
2021-10-12 |
https://github.com/gear-genomics/tracy/ |
0.7.8 |
tracy |
0.8.1 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy |
|
|
|
|
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
55 |
55 |
4837 |
4837 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4837 |
4837 |
55 |
55 |
|
|
|
transdecoder |
transdecoder |
TransDecoder finds coding regions within transcripts |
2015-11-09 |
https://transdecoder.github.io/ |
5.5.0 |
transdecoder |
5.7.1 |
To update |
Transcriptomics, RNA |
Coding region prediction, de Novo sequencing, De-novo assembly |
Coding region prediction, de Novo sequencing, De-novo assembly |
Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing |
Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder |
TransDecoder |
TransDecoder |
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1215 |
1323 |
7178 |
8593 |
1267 |
1357 |
6450 |
7010 |
372 |
432 |
3197 |
3705 |
37 |
38 |
495 |
505 |
19813 |
17320 |
3150 |
2891 |
https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.org.au/published/workflow?id=c04a62f528a69e79, https://workflowhub.eu/workflows/1716?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1, https://workflowhub.eu/workflows/879?version=1 |
transcriptomics/full-de-novo |
|
transit |
gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps |
TRANSIT |
2019-03-01 |
https://github.com/mad-lab/transit/ |
3.2.3 |
transit |
3.3.19 |
To update |
Genome annotation |
Transposon prediction |
Transposon prediction |
DNA, Sequencing, Mobile genetic elements |
DNA, Sequencing, Mobile genetic elements |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit |
transit |
TRANSIT |
A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. |
|
0 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
5 |
5 |
97 |
104 |
1908 |
2076 |
210 |
244 |
2813 |
4134 |
42 |
42 |
640 |
640 |
0 |
0 |
0 |
0 |
6850 |
5361 |
390 |
349 |
https://usegalaxy.eu/published/workflow?id=2a123e08436a89f1, https://workflowhub.eu/workflows/1530?version=1 |
genome-annotation/tnseq |
|
transtermhp |
transtermhp |
Finds rho-independent transcription terminators in bacterial genomes |
2015-10-08 |
https://transterm.cbcb.umd.edu |
|
transtermhp |
2.09 |
To update |
Sequence Analysis |
Transcriptional regulatory element prediction |
Transcriptional regulatory element prediction |
Transcription factors and regulatory sites |
Transcription factors and regulatory sites |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp |
transtermhp |
TransTermHP |
TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
59 |
62 |
467 |
502 |
49 |
55 |
170 |
216 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
718 |
637 |
117 |
108 |
|
|
|
trimal |
trimal |
Tool for automated alignment trimming |
2024-10-02 |
https://trimal.readthedocs.io |
1.5.0 |
trimal |
1.5.0 |
Up-to-date |
Sequence Analysis, Phylogenetics |
Multiple sequence alignment |
Multiple sequence alignment |
Sequence analysis, Sequencing, Sequence sites, features and motifs |
Sequence analysis, Sequencing, Sequence sites, features and motifs |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal |
trimal |
trimAl |
Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
173 |
173 |
2180 |
2180 |
0 |
0 |
0 |
0 |
4 |
4 |
32 |
32 |
115 |
115 |
1230 |
1230 |
3442 |
3442 |
292 |
292 |
https://usegalaxy.fr/published/workflow?id=5ec6d378e60f7ccc, https://usegalaxy.fr/published/workflow?id=63b49f322ec366b5, https://usegalaxy.fr/published/workflow?id=7ebb54181b404733, https://usegalaxy.fr/published/workflow?id=894143d81af8dff0, https://usegalaxy.fr/published/workflow?id=b131218bec7eacb4, https://usegalaxy.fr/published/workflow?id=d425a77157cae2ee, https://usegalaxy.fr/published/workflow?id=e134e9637adfc5b6, https://workflowhub.eu/workflows/1650?version=1 |
sequence-analysis/tapscan-streptophyte-algae |
|
trimmomatic |
trimmomatic |
A flexible read trimming tool for Illumina NGS data |
2024-01-03 |
http://www.usadellab.org/cms/?page=trimmomatic |
0.39 |
trimmomatic |
0.40 |
To update |
Fastq Manipulation |
|
|
|
|
pjbriggs |
https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic |
|
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0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
1 |
1 |
0 |
1 |
1 |
1 |
18851 |
20991 |
437833 |
502595 |
45190 |
60956 |
714562 |
1020864 |
6132 |
7428 |
144168 |
173860 |
1010 |
1011 |
37524 |
37543 |
1734862 |
1334087 |
90386 |
71183 |
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https://usegalaxy.org/published/workflow?id=e6a6223ef5ef85a7, https://usegalaxy.org/published/workflow?id=e6b48a02789d1879, https://usegalaxy.org/published/workflow?id=e6b803c1232cd08e, https://usegalaxy.org/published/workflow?id=e6f57346a02be07f, https://usegalaxy.org/published/workflow?id=e75bd7d392e65209, https://usegalaxy.org/published/workflow?id=e7bfa3c733835b22, https://usegalaxy.org/published/workflow?id=eb01b539d17580c3, https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a, https://usegalaxy.org/published/workflow?id=ebbcdc389aad0eb8, https://usegalaxy.org/published/workflow?id=ebc9aad36017b567, https://usegalaxy.org/published/workflow?id=ec3d8d5d1531f92e, https://usegalaxy.org/published/workflow?id=ec96e3bf30d5f771, https://usegalaxy.org/published/workflow?id=edb299ecbf147618, https://usegalaxy.org/published/workflow?id=ef44d02a79bd28bf, https://usegalaxy.org/published/workflow?id=efb10012b8448b21, https://usegalaxy.org/published/workflow?id=f0feca8af9aeddba, https://usegalaxy.org/published/workflow?id=f1a9667c0b0999f4, https://usegalaxy.org/published/workflow?id=f23e5f333987a89f, https://usegalaxy.org/published/workflow?id=f302d673420a9bdd, https://usegalaxy.org/published/workflow?id=f3aba99a8204081e, https://usegalaxy.org/published/workflow?id=f3ed710e251833a7, https://usegalaxy.org/published/workflow?id=f47f0b25c1405128, https://usegalaxy.org/published/workflow?id=f4ed1c9434ed0445, https://usegalaxy.org/published/workflow?id=f60818a405f1bbbd, https://usegalaxy.org/published/workflow?id=f63f7a0a33a83841, https://usegalaxy.org/published/workflow?id=f88f186bc851e954, https://usegalaxy.org/published/workflow?id=f961fc46d4fddecc, https://usegalaxy.org/published/workflow?id=f9d546aae406cf15, https://usegalaxy.org/published/workflow?id=fae519dcba6bfc72, https://usegalaxy.org/published/workflow?id=fb01e1a49793c8be, https://usegalaxy.org/published/workflow?id=fc09d17e0bce18f8, https://usegalaxy.org/published/workflow?id=fd30cdfe7e38b508, https://usegalaxy.org/published/workflow?id=fe2c0e4694c56b6b, https://usegalaxy.org/published/workflow?id=ff137b61d4ef1b86, https://workflowhub.eu/workflows/1271?version=3, https://workflowhub.eu/workflows/1272?version=2, https://workflowhub.eu/workflows/1573?version=1, https://workflowhub.eu/workflows/1606?version=1, https://workflowhub.eu/workflows/1651?version=1, https://workflowhub.eu/workflows/1653?version=1, https://workflowhub.eu/workflows/1678?version=1, https://workflowhub.eu/workflows/1685?version=1, https://workflowhub.eu/workflows/1716?version=1, https://workflowhub.eu/workflows/1767?version=1, https://workflowhub.eu/workflows/1850?version=1, https://workflowhub.eu/workflows/1854?version=1, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1, https://workflowhub.eu/workflows/628?version=1, https://workflowhub.eu/workflows/676?version=1, https://workflowhub.eu/workflows/876?version=1 |
epigenetics/tal1-binding-site-identification, evolution/mtb_transmission, microbiome/mgnify-amplicon, sequence-analysis/human-reads-removal, transcriptomics/de-novo, transcriptomics/full-de-novo, variant-analysis/exome-seq, variant-analysis/somatic-variant-discovery, variant-analysis/somatic-variants |
|
trimns |
trimns |
TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline |
2021-01-29 |
https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs |
0.1.0 |
trimns_vgp |
1.0 |
To update |
Assembly |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
25 |
25 |
49 |
49 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
49 |
49 |
25 |
25 |
|
|
|
trinity |
trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats |
Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq |
2015-11-09 |
https://github.com/trinityrnaseq/trinityrnaseq |
2.15.1 |
trinity |
2.15.2 |
To update |
Transcriptomics, RNA |
Transcriptome assembly |
Transcriptome assembly |
Transcriptomics, Gene expression, Gene transcripts |
Transcriptomics, Gene transcripts |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity |
trinity |
Trinity |
Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. |
|
0 |
13 |
13 |
13 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
2 |
1 |
0 |
0 |
0 |
0 |
0 |
11 |
0 |
0 |
1 |
0 |
0 |
0 |
11 |
13 |
12 |
2033 |
2319 |
42409 |
52163 |
3769 |
4091 |
48710 |
53240 |
809 |
933 |
22208 |
30291 |
155 |
159 |
3279 |
3411 |
139105 |
116606 |
7502 |
6766 |
https://workflowhub.eu/workflows/1716?version=1 |
transcriptomics/full-de-novo |
|
trinotate |
trinotate |
Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. |
2016-11-15 |
https://trinotate.github.io/ |
3.2.2 |
trinotate |
4.0.2 |
To update |
Transcriptomics, RNA |
Gene functional annotation |
Gene functional annotation |
Gene expression, Transcriptomics |
Transcriptomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate |
trinotate |
Trinotate |
Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
458 |
517 |
2157 |
2558 |
549 |
598 |
2012 |
2211 |
170 |
224 |
950 |
1284 |
0 |
1 |
0 |
10 |
6063 |
5119 |
1340 |
1177 |
https://workflowhub.eu/workflows/1716?version=1 |
transcriptomics/full-de-novo |
|
trycycler |
trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample |
Trycycler toolkit wrappers |
2021-02-11 |
https://github.com/rrwick/Trycycler |
0.5.5 |
trycycler |
0.5.5 |
Up-to-date |
Assembly |
Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation |
Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation |
Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics |
Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler |
trycycler |
Trycycler |
Trycycler: consensus long-read assemblies for bacterial genomes |
|
0 |
5 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
122 |
122 |
15743 |
15743 |
0 |
0 |
0 |
0 |
57 |
57 |
6233 |
6233 |
3 |
3 |
27 |
27 |
22003 |
22003 |
182 |
182 |
|
|
|
tsebra |
tsebra |
This tool has been developed to combine BRAKER predictions. |
2023-10-19 |
https://github.com/Gaius-Augustus/TSEBRA |
1.1.2.5 |
tsebra |
1.1.2.5 |
Up-to-date |
Genome annotation |
Homology-based gene prediction, Alternative splicing prediction |
Homology-based gene prediction, Alternative splicing prediction |
Gene expression, RNA-Seq, Gene transcripts, Model organisms |
Gene expression, RNA-Seq, Gene transcripts, Model organisms |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra |
tsebra |
TSEBRA |
TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
16 |
51 |
51 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
51 |
51 |
16 |
16 |
|
|
|
tsne |
tsne |
T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation |
2017-05-26 |
https://cran.r-project.org/web/packages/Rtsne/ |
0.0.2 |
r-rtsne |
0.13 |
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
25 |
39 |
163 |
382 |
60 |
69 |
275 |
305 |
0 |
0 |
0 |
0 |
2 |
2 |
4 |
4 |
691 |
442 |
110 |
87 |
|
|
|
tximport |
tximport |
Wrapper for the Bioconductor package tximport |
2019-10-15 |
http://bioconductor.org/packages/tximport/ |
1.30.0 |
bioconductor-tximport |
1.34.0 |
To update |
Transcriptomics |
Pathway or network analysis, Formatting, RNA-Seq analysis |
Pathway or network analysis, Formatting, RNA-Seq analysis |
Transcriptomics, Gene transcripts, Workflows |
Transcriptomics, Gene transcripts, Workflows |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport |
tximport |
tximport |
An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
297 |
314 |
2388 |
2576 |
994 |
1081 |
7694 |
8341 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10917 |
10082 |
1395 |
1291 |
https://usegalaxy.eu/published/workflow?id=65aed668233d5f73 |
|
|
ucsc_axtchain |
ucsc_axtchain |
Chain together genome alignments |
2024-08-26 |
http://hgdownload.cse.ucsc.edu/admin/exe/ |
482 |
ucsc-axtchain |
482 |
Up-to-date |
Sequence Analysis |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
57 |
57 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
57 |
57 |
4 |
4 |
|
|
|
ucsc_axttomaf |
ucsc_axtomaf |
Convert dataset from axt to MAF format. |
2024-08-27 |
http://hgdownload.cse.ucsc.edu/admin/exe/ |
482 |
ucsc-axttomaf |
482 |
Up-to-date |
Convert Formats |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
59 |
59 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
59 |
59 |
4 |
4 |
|
|
|
ucsc_blat |
ucsc_blat |
Standalone blat sequence search command line tool |
2017-05-17 |
http://genome.ucsc.edu/goldenPath/help/blatSpec.html |
482 |
ucsc-blat |
482 |
Up-to-date |
Sequence Analysis |
Sequence alignment |
Sequence alignment |
Sequence analysis |
Sequence analysis |
yating-l |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat |
blat |
BLAT |
Fast, accurate spliced alignment of DNA sequences. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
ucsc_chainantirepeat |
ucsc_chainantirepeat |
Remove repeated chains |
2025-03-07 |
http://hgdownload.cse.ucsc.edu/admin/exe/ |
482 |
ucsc-chainantirepeat |
482 |
Up-to-date |
Sequence Analysis |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainantirepeat |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainantirepeat |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
42 |
42 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
42 |
42 |
3 |
3 |
|
|
|
ucsc_chainnet |
ucsc_chainnet |
Make alignment nets out of chains |
2024-08-30 |
http://hgdownload.cse.ucsc.edu/admin/exe/ |
482 |
ucsc-chainnet |
482 |
Up-to-date |
Sequence Analysis |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
61 |
61 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
61 |
61 |
4 |
4 |
|
|
|
ucsc_chainprenet |
ucsc_chainprenet |
Remove chains that don't have a chance of being netted |
2024-08-27 |
http://hgdownload.cse.ucsc.edu/admin/exe/ |
482 |
ucsc-chainprenet |
482 |
Up-to-date |
Sequence Analysis |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
60 |
60 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
60 |
60 |
4 |
4 |
|
|
|
ucsc_chainsort |
ucsc_chainsort |
Sort chains. By default sorts by score. |
2024-08-26 |
http://hgdownload.cse.ucsc.edu/admin/exe/ |
482 |
ucsc-chainsort |
482 |
Up-to-date |
Sequence Analysis |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
60 |
60 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
60 |
60 |
4 |
4 |
|
|
|
ucsc_fasplit |
fasplit |
faSplit is a tool to split a single FASTA file into several files |
2017-09-08 |
http://hgdownload.cse.ucsc.edu/admin/exe/ |
482 |
ucsc-fasplit |
482 |
Up-to-date |
Fasta Manipulation |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
554 |
602 |
3994 |
4315 |
689 |
777 |
6770 |
7638 |
212 |
218 |
1497 |
1540 |
8 |
8 |
38 |
38 |
13531 |
12299 |
1605 |
1463 |
https://usegalaxy.eu/published/workflow?id=02631612a43a4d9b, https://usegalaxy.eu/published/workflow?id=3eaa913306c16146, https://usegalaxy.eu/published/workflow?id=4d32b1b3ac0a7161, https://usegalaxy.eu/published/workflow?id=6158c3b5fc12044e, https://usegalaxy.eu/published/workflow?id=6416cfdbd5273063, https://usegalaxy.eu/published/workflow?id=667bac8d7453e5f1, https://usegalaxy.eu/published/workflow?id=8deb08d4f228e198, https://usegalaxy.eu/published/workflow?id=9a97c6eb4fe015e7, https://usegalaxy.eu/published/workflow?id=d57d41e306241396, https://usegalaxy.eu/published/workflow?id=e423c80058601e78, https://usegalaxy.org.au/published/workflow?id=8ae08ac9e73c8241 |
|
|
ucsc_fatovcf |
fatovcf |
Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs |
2023-01-11 |
http://hgdownload.cse.ucsc.edu/admin/exe/ |
482 |
ucsc-fatovcf |
482 |
Up-to-date |
Convert Formats |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
72 |
72 |
515 |
515 |
205 |
205 |
1868 |
1868 |
13 |
13 |
226 |
226 |
0 |
0 |
0 |
0 |
2609 |
2609 |
290 |
290 |
https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4 |
variant-analysis/pox-tiled-amplicon |
|
ucsc_maftoaxt |
maftoaxt |
Convert dataset from MAF to axt format |
2024-07-30 |
http://hgdownload.cse.ucsc.edu/admin/exe/ |
482 |
ucsc-maftoaxt |
482 |
Up-to-date |
Convert Formats |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
11 |
11 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
11 |
3 |
3 |
|
|
|
ucsc_netfilter |
ucsc_netfilter |
Filter out parts of net |
2024-09-18 |
http://hgdownload.cse.ucsc.edu/admin/exe/ |
482 |
ucsc-netfilter |
482 |
Up-to-date |
Sequence Analysis |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
56 |
56 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
56 |
56 |
4 |
4 |
|
|
|
ucsc_netsyntenic |
ucsc_netsyntenic |
Add synteny info to a net dataset |
2024-09-04 |
http://hgdownload.cse.ucsc.edu/admin/exe/ |
482 |
ucsc-netsyntenic |
482 |
Up-to-date |
Sequence Analysis |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
72 |
72 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
72 |
72 |
6 |
6 |
|
|
|
ucsc_nettoaxt |
ucsc_nettoaxt |
Convert net (and chain) to axt format. |
2024-09-19 |
http://hgdownload.cse.ucsc.edu/admin/exe/ |
482 |
ucsc-nettoaxt |
482 |
Up-to-date |
Convert Formats |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
55 |
55 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
55 |
55 |
4 |
4 |
|
|
|
ucsc_twobittofa |
ucsc-twobittofa |
twoBitToFa is a tool to convert all or part of .2bit file to FASTA |
2016-08-19 |
https://genome.ucsc.edu/goldenpath/help/twoBit.html |
482 |
ucsc-twobittofa |
482 |
Up-to-date |
Convert Formats |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
85 |
126 |
430 |
570 |
131 |
159 |
803 |
861 |
3 |
3 |
73 |
73 |
0 |
0 |
0 |
0 |
1504 |
1306 |
288 |
219 |
|
|
|
ucsc_wigtobigwig |
ucsc_wigtobigwig |
converts bedGraph (wig) files into binary bigwig |
2024-01-14 |
https://genome.ucsc.edu/goldenPath/help/bigWig.html |
482 |
ucsc-wigtobigwig |
482 |
Up-to-date |
Convert Formats |
|
|
Sequence analysis |
Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig |
UCSC_Genome_Browser_Utilities |
UCSC Genome Browser Utilities |
Utilities for handling sequences and assemblies from the UCSC Genome Browser project. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
345 |
345 |
4562 |
4562 |
759 |
759 |
9257 |
9257 |
58 |
58 |
1088 |
1088 |
0 |
0 |
0 |
0 |
14907 |
14907 |
1162 |
1162 |
https://usegalaxy.eu/published/workflow?id=489926f9299594fe, https://usegalaxy.eu/published/workflow?id=4ca06bc64bf896a3, https://usegalaxy.eu/published/workflow?id=bffeb3cd0c708441, https://usegalaxy.eu/published/workflow?id=c46345ba876d5bfe, https://usegalaxy.org/published/workflow?id=28e4871410288cb8, https://usegalaxy.org/published/workflow?id=e20e1371e50bdcee |
|
|
umi-tools |
umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist |
UMI-tools extract - Extract UMIs from fastq |
2017-08-09 |
https://github.com/CGATOxford/UMI-tools |
1.1.6 |
umi_tools |
1.1.6 |
Up-to-date |
Sequence Analysis, Transcriptomics, Single Cell |
Sequencing quality control |
Sequencing quality control |
NGS, Sequence sites, features and motifs, Quality affairs |
Sequence sites, features and motifs, Quality affairs |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools |
umi-tools |
UMI-tools |
Tools for handling Unique Molecular Identifiers in NGS data sets. |
|
0 |
5 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
5 |
5 |
568 |
710 |
48490 |
74207 |
637 |
637 |
12544 |
12796 |
109 |
118 |
17752 |
18006 |
5 |
5 |
48 |
48 |
105057 |
78834 |
1470 |
1319 |
https://usegalaxy.eu/published/workflow?id=06fe33c4420906bf, https://usegalaxy.eu/published/workflow?id=0821ec1cb4d6f30b, https://usegalaxy.eu/published/workflow?id=08cfb9b21c1ec808, https://usegalaxy.eu/published/workflow?id=0c619b25c1394a09, https://usegalaxy.eu/published/workflow?id=153ba1581743d31f, https://usegalaxy.eu/published/workflow?id=24ddd188da35b061, https://usegalaxy.eu/published/workflow?id=26185e8fa5a9b988, https://usegalaxy.eu/published/workflow?id=44c5999436da5f1e, https://usegalaxy.eu/published/workflow?id=49073a24429d93d6, https://usegalaxy.eu/published/workflow?id=6514e610c79df72c, https://usegalaxy.eu/published/workflow?id=8fb156020285e049, https://usegalaxy.eu/published/workflow?id=a1e09c648d8f1fc7, https://usegalaxy.eu/published/workflow?id=af7c349497a75314, https://usegalaxy.eu/published/workflow?id=b619339f4e1c6fdf, https://usegalaxy.eu/published/workflow?id=c64b219b4031fabd, https://usegalaxy.eu/published/workflow?id=c6b22fc33b569c8f, https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765, https://usegalaxy.eu/published/workflow?id=d4b3da4cc5a50044, https://usegalaxy.eu/published/workflow?id=d7aa4c258e2edc95, https://usegalaxy.eu/published/workflow?id=edbdbe7aa21ceba0, https://usegalaxy.eu/published/workflow?id=f5be5bcf9b9f171c, https://usegalaxy.eu/published/workflow?id=f841e1207611f28f, https://usegalaxy.org.au/published/workflow?id=7ae06a27188b9438, https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a, https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33, https://usegalaxy.org/published/workflow?id=b1b75a9323d25085, https://workflowhub.eu/workflows/1494?version=1, https://workflowhub.eu/workflows/1507?version=1, https://workflowhub.eu/workflows/1706?version=1 |
single-cell/scrna-preprocessing, single-cell/scrna-umis, transcriptomics/clipseq |
|
unicycler |
unicycler |
Unicycler is a hybrid assembly pipeline for bacterial genomes. |
2017-05-08 |
https://github.com/rrwick/Unicycler |
0.5.1 |
unicycler |
0.5.1 |
Up-to-date |
Assembly |
Genome assembly, Aggregation |
Genome assembly, Aggregation |
Microbiology, Genomics, Sequencing, Sequence assembly |
Microbiology, Genomics, Sequencing, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler |
unicycler |
Unicycler |
A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
4697 |
5202 |
83521 |
96874 |
5770 |
8769 |
65067 |
104850 |
2392 |
2613 |
22717 |
26831 |
272 |
276 |
2160 |
2183 |
230738 |
173465 |
16860 |
13131 |
https://usegalaxy.eu/published/workflow?id=165089132248a0b0, https://usegalaxy.eu/published/workflow?id=249c115413f17f28, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=2e0075791f7fa384, https://usegalaxy.eu/published/workflow?id=346b46e6316c6950, https://usegalaxy.eu/published/workflow?id=374797e58377c40f, https://usegalaxy.eu/published/workflow?id=39837ca09374598b, https://usegalaxy.eu/published/workflow?id=44e53ea319e07daa, https://usegalaxy.eu/published/workflow?id=69be516a48761365, https://usegalaxy.eu/published/workflow?id=7b755497d168cb13, https://usegalaxy.eu/published/workflow?id=842e0ea7b1eb56af, https://usegalaxy.eu/published/workflow?id=8f3ce55d44d9f369, https://usegalaxy.eu/published/workflow?id=9219557de92e0203, https://usegalaxy.eu/published/workflow?id=b2b46e71046b1999, https://usegalaxy.eu/published/workflow?id=b2dfa74f55a73409, https://usegalaxy.eu/published/workflow?id=c48807045e258dd8, https://usegalaxy.eu/published/workflow?id=c702c76cadebac30, https://usegalaxy.eu/published/workflow?id=dc7107896a3f2964, https://usegalaxy.eu/published/workflow?id=e8eb80ee09159bac, https://usegalaxy.eu/published/workflow?id=ea485dbabc76488d, https://usegalaxy.eu/published/workflow?id=ecf48fa50af560a0, https://usegalaxy.eu/published/workflow?id=fe43cf59e48bf556, https://usegalaxy.fr/published/workflow?id=5bb882218afda132, https://usegalaxy.org.au/published/workflow?id=38d992baf9a2a2bc, https://usegalaxy.org.au/published/workflow?id=8a40059343cf4b87, https://usegalaxy.org.au/published/workflow?id=8f7d5ebead46a6d0, https://usegalaxy.org.au/published/workflow?id=9c60b83feaa22415, https://usegalaxy.org.au/published/workflow?id=b59fada651043735, https://usegalaxy.org.au/published/workflow?id=b7aa22291322e505, https://usegalaxy.org.au/published/workflow?id=c9b7de574fb2f2d5, https://usegalaxy.org.au/published/workflow?id=d9571b3dfef34e5e, https://usegalaxy.org.au/published/workflow?id=f01be6a7685ac476, https://usegalaxy.org.au/published/workflow?id=fc3c83b11f527977, https://usegalaxy.org/published/workflow?id=5039ae2c81d0aba8, https://usegalaxy.org/published/workflow?id=69514a75e4c9af08, https://usegalaxy.org/published/workflow?id=8111bb9bb26bb665, https://usegalaxy.org/published/workflow?id=a67afbea4b2eb26b, https://usegalaxy.org/published/workflow?id=b43b72dcf5f7694d, https://usegalaxy.org/published/workflow?id=bc72dcbca89ca35d, https://usegalaxy.org/published/workflow?id=c65bec6c332bf740, https://usegalaxy.org/published/workflow?id=db0671862a57968d, https://workflowhub.eu/workflows/1477?version=1, https://workflowhub.eu/workflows/1598?version=1, https://workflowhub.eu/workflows/1612?version=1, https://workflowhub.eu/workflows/1616?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/406?version=1, https://workflowhub.eu/workflows/52?version=1, https://workflowhub.eu/workflows/68?version=1 |
assembly/assembly-with-preprocessing, assembly/unicycler-assembly, microbiome/plasmid-metagenomics-nanopore |
|
upsetplot |
rcx_upsetplot |
Upset plot visualization tool using UpSetR |
2025-04-17 |
https://github.com/galaxyproject/tools-iuc |
1.4.0 |
r-upsetr |
1.0.3 |
To update |
Visualization |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/upsetr |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/upsetr |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
usher |
usher_matutils, usher |
UShER toolkit wrappers |
2021-05-11 |
https://github.com/yatisht/usher |
0.2.1 |
usher |
0.6.6 |
To update |
Phylogenetics |
Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) |
Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) |
Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics |
Cladistics, Genotype and phenotype, Phylogenomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher |
usher |
usher |
The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. |
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
5 |
5 |
1060 |
1060 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1060 |
1060 |
5 |
5 |
|
|
|
valet |
valet |
A pipeline for detecting mis-assemblies in metagenomic assemblies. |
2017-11-16 |
https://github.com/marbl/VALET |
|
valet |
1.0 |
To update |
Metagenomics |
Sequence assembly, Sequence assembly visualisation |
Sequence assembly, Sequence assembly visualisation |
Metagenomics, Sequence assembly |
Metagenomics, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet |
valet |
VALET |
VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
74 |
101 |
449 |
711 |
67 |
76 |
160 |
249 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
960 |
609 |
177 |
141 |
https://usegalaxy.eu/published/workflow?id=1524b189069b42a5, https://usegalaxy.eu/published/workflow?id=579ff83177c5ee09 |
|
|
vapor |
vapor |
Classify Influenza samples from raw short read sequence data |
2022-08-24 |
https://github.com/wm75/vaporup |
1.0.3 |
vapor |
1.0.3 |
Up-to-date |
Sequence Analysis |
Data retrieval, De-novo assembly, Read mapping |
Data retrieval, De-novo assembly, Read mapping |
Whole genome sequencing, Mapping, Sequence assembly |
Whole genome sequencing, Mapping, Sequence assembly |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor |
vapor |
VAPOR |
VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
188 |
188 |
197466 |
197466 |
127 |
127 |
1849 |
1849 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
199315 |
199315 |
315 |
315 |
https://usegalaxy.eu/published/workflow?id=629e57958afed44c, https://usegalaxy.eu/published/workflow?id=7c986f4d14c6a539, https://usegalaxy.eu/published/workflow?id=a15dabcadb63b46d, https://usegalaxy.eu/published/workflow?id=c789ab71876c6ead, https://usegalaxy.eu/published/workflow?id=cd25f70f71683ab6, https://usegalaxy.org/published/workflow?id=1518c8c50747a1c1, https://usegalaxy.org/published/workflow?id=97263f3308077ff0, https://workflowhub.eu/workflows/1260?version=2 |
variant-analysis/aiv-analysis |
|
vardict_java |
vardict_java |
VarDict - calls SNVs and indels for tumour-normal pairs |
2020-08-21 |
https://github.com/AstraZeneca-NGS/VarDictJava |
1.8.3 |
python |
|
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
48 |
49 |
409 |
424 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
424 |
409 |
49 |
48 |
https://workflowhub.eu/workflows/1738?version=1, https://workflowhub.eu/workflows/1739?version=1, https://workflowhub.eu/workflows/1740?version=1, https://workflowhub.eu/workflows/1741?version=1, https://workflowhub.eu/workflows/517?version=1, https://workflowhub.eu/workflows/518?version=1 |
|
|
variant_analyzer |
mut2read, mut2sscs, read2mut |
Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data |
2019-11-20 |
|
2.0.0 |
matplotlib |
|
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer |
|
|
|
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
5 |
6 |
54 |
99 |
26 |
29 |
221 |
557 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
656 |
275 |
35 |
31 |
|
|
|
varscan |
varscan_copynumber, varscan_mpileup, varscan_somatic |
VarScan is a variant caller for high-throughput sequencing data |
2018-07-10 |
https://dkoboldt.github.io/varscan/ |
2.4.3 |
varscan |
2.4.6 |
To update |
Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/iuc/tree/master/tools/varscan |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan |
|
|
|
|
0 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
813 |
965 |
13818 |
16510 |
2269 |
2508 |
18111 |
19895 |
101 |
101 |
1552 |
1552 |
288 |
288 |
1010 |
1010 |
38967 |
34491 |
3862 |
3471 |
https://usegalaxy.eu/published/workflow?id=220961d803697f54, https://usegalaxy.eu/published/workflow?id=231a2dc7412d250b, https://usegalaxy.eu/published/workflow?id=2c3d05023c02113e, https://usegalaxy.eu/published/workflow?id=462582bbc236cb7b, https://usegalaxy.eu/published/workflow?id=4f62794453f65cba, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=6ed1016dfdf9f928, https://usegalaxy.eu/published/workflow?id=83049910e2cd5128, https://usegalaxy.eu/published/workflow?id=88064e2231165fd2, https://usegalaxy.eu/published/workflow?id=968f0ac2617aa524, https://usegalaxy.eu/published/workflow?id=a4e3667f6879bfaf, https://usegalaxy.eu/published/workflow?id=af30010868c97316, https://usegalaxy.eu/published/workflow?id=c9ef2d2ce92e2dfb, https://usegalaxy.org/published/workflow?id=0ee0493f3168cbb3, https://usegalaxy.org/published/workflow?id=18c6e87a884fb5ed, https://usegalaxy.org/published/workflow?id=3dbe754882a263cd, https://usegalaxy.org/published/workflow?id=4cbb8181cfdf55d9, https://usegalaxy.org/published/workflow?id=7c5e8394ce29288d, https://usegalaxy.org/published/workflow?id=bf90f2bd20fbff21, https://workflowhub.eu/workflows/1678?version=1, https://workflowhub.eu/workflows/36?version=1, https://workflowhub.eu/workflows/628?version=1 |
variant-analysis/somatic-variants |
|
varvamp |
varvamp |
Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses |
2024-01-27 |
https://github.com/jonas-fuchs/varVAMP/ |
1.2.2 |
varvamp |
1.2.2 |
Up-to-date |
Sequence Analysis |
PCR primer design |
PCR primer design |
Virology, Probes and primers |
Virology, Probes and primers |
iuc |
https://github.com/jonas-fuchs/varVAMP |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp |
varvamp |
varVAMP |
variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
55 |
55 |
912 |
912 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
912 |
912 |
55 |
55 |
https://workflowhub.eu/workflows/1627?version=1 |
sequence-analysis/viral_primer_design |
|
vcf2maf |
vcf2maf |
vcf2maf: Convert VCF into MAF |
2022-06-28 |
https://github.com/mskcc/vcf2maf |
1.6.21 |
vcf2maf |
1.6.22 |
To update |
Convert Formats |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
64 |
64 |
1688 |
1688 |
0 |
0 |
0 |
0 |
7 |
7 |
179 |
179 |
0 |
0 |
0 |
0 |
1867 |
1867 |
71 |
71 |
https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e, https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=ce1712139b4a4273, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1 |
|
|
vcf2tsv |
vcf2tsv |
Converts VCF files into tab-delimited format |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis, Convert Formats |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1000 |
1110 |
178652 |
180838 |
1122 |
2888 |
17000 |
45505 |
165 |
203 |
4866 |
5129 |
72 |
73 |
252 |
254 |
231726 |
200770 |
4274 |
2359 |
https://usegalaxy.eu/published/workflow?id=21a39ac4c1becb31, https://usegalaxy.eu/published/workflow?id=291c36e1b18e9deb, https://usegalaxy.eu/published/workflow?id=3d8aa05129e44fdf, https://usegalaxy.eu/published/workflow?id=4d80a87510b2a54e, https://usegalaxy.eu/published/workflow?id=4f9f7065975b3f97, https://usegalaxy.eu/published/workflow?id=5a16af00bf8bf57b, https://usegalaxy.eu/published/workflow?id=61fe08fb3d5e83f8, https://usegalaxy.eu/published/workflow?id=a2d4221ad117c378, https://usegalaxy.eu/published/workflow?id=b556b0a67ad979da, https://usegalaxy.org.au/published/workflow?id=2362ff8880213586, https://usegalaxy.org.au/published/workflow?id=3e6f755ee62f7301, https://usegalaxy.org.au/published/workflow?id=e154a9b605ea0886, https://usegalaxy.org/published/workflow?id=3d5347f1e8ee7db2, https://usegalaxy.org/published/workflow?id=415c7152cb78e86f, https://usegalaxy.org/published/workflow?id=43861b38cf6e927e, https://usegalaxy.org/published/workflow?id=4dbac8374419d29e, https://usegalaxy.org/published/workflow?id=4ed9f54caa932479, https://usegalaxy.org/published/workflow?id=50206b10de958d03, https://usegalaxy.org/published/workflow?id=57cfc1b5d9ea0d72, https://usegalaxy.org/published/workflow?id=5cad854edbbd3b69, https://usegalaxy.org/published/workflow?id=68d41ffbf92b2a8e, https://usegalaxy.org/published/workflow?id=bb16936081b820f6, https://usegalaxy.org/published/workflow?id=fae519dcba6bfc72, https://workflowhub.eu/workflows/1628?version=1, https://workflowhub.eu/workflows/1659?version=1 |
variant-analysis/baculovirus-isolate-variation, variant-analysis/non-dip |
|
vcfaddinfo |
vcfaddinfo |
Adds info fields from the second dataset which are not present in the first dataset. |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
26 |
32 |
858 |
1007 |
36 |
118 |
6132 |
9104 |
7 |
7 |
184 |
237 |
0 |
0 |
0 |
0 |
10348 |
7174 |
157 |
69 |
|
|
|
vcfallelicprimitives |
vcfallelicprimitives |
Splits alleleic primitives (gaps or mismatches) into multiple VCF lines |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
918 |
1372 |
7607 |
21544 |
1134 |
2095 |
6447 |
15257 |
234 |
280 |
3141 |
3515 |
4 |
6 |
4 |
8 |
40324 |
17199 |
3753 |
2290 |
https://usegalaxy.eu/published/workflow?id=2f1ee01aeee2b9f0, https://usegalaxy.eu/published/workflow?id=4a89ddab941c6819, https://usegalaxy.eu/published/workflow?id=a4e3667f6879bfaf, https://usegalaxy.eu/published/workflow?id=ad609d1a3de251f5, https://usegalaxy.eu/published/workflow?id=b02d90c32dc67730, https://usegalaxy.eu/published/workflow?id=ffe93ec81afefd09, https://usegalaxy.org.au/published/workflow?id=738c0e8227519c25, https://usegalaxy.org.au/published/workflow?id=ac89c2d51c32cc9c, https://usegalaxy.org/published/workflow?id=70dacee3da375e2b, https://workflowhub.eu/workflows/1655?version=1, https://workflowhub.eu/workflows/35?version=1, https://workflowhub.eu/workflows/36?version=1 |
variant-analysis/dip |
|
vcfanno |
vcfanno |
Annotate VCF files |
2021-01-17 |
https://github.com/brentp/vcfanno |
0.3.7 |
vcfanno |
0.3.7 |
Up-to-date |
Variant Analysis |
SNP annotation |
SNP annotation |
Genetic variation, Data submission, annotation and curation |
Genetic variation, Data submission, annotation and curation |
iuc |
https://github.com/galaxyproject/tools-iuc/vcfanno/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno |
vcfanno |
vcfanno |
Fast, flexible annotation of genetic variants. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
239 |
239 |
1308 |
1308 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1308 |
1308 |
239 |
239 |
https://usegalaxy.eu/published/workflow?id=1da86d74f8535f4e, https://usegalaxy.eu/published/workflow?id=2424282f793f0f1b, https://usegalaxy.eu/published/workflow?id=5ed38d8114bcd6f7, https://usegalaxy.eu/published/workflow?id=ce1712139b4a4273, https://workflowhub.eu/workflows/607?version=1, https://workflowhub.eu/workflows/629?version=1 |
|
|
vcfannotate |
vcfannotate |
Intersect VCF records with BED annotations |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
161 |
206 |
2810 |
3070 |
627 |
1507 |
3510 |
14904 |
61 |
69 |
604 |
730 |
5 |
6 |
13 |
14 |
18718 |
6937 |
1788 |
854 |
https://usegalaxy.org.au/published/workflow?id=142e5f7c1f340838, https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org/published/workflow?id=3e2bbafb8c6580af |
|
|
vcfannotategenotypes |
vcfannotategenotypes |
Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
57 |
73 |
114 |
218 |
133 |
403 |
404 |
1863 |
13 |
13 |
199 |
253 |
1 |
1 |
3 |
3 |
2337 |
720 |
490 |
204 |
|
|
|
vcfbedintersect |
vcfbedintersect |
Intersect VCF and BED datasets |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
208 |
251 |
3039 |
4433 |
423 |
1241 |
4483 |
21130 |
42 |
47 |
546 |
658 |
2 |
3 |
17 |
22 |
26243 |
8085 |
1542 |
675 |
https://usegalaxy.org/published/workflow?id=6da54816b436dc58, https://usegalaxy.org/published/workflow?id=9b81d47a468d6f99 |
|
|
vcfbreakcreatemulti |
vcfbreakcreatemulti |
Break multiple alleles into multiple records, or combine overallpoing alleles into a single record |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
29 |
40 |
265 |
478 |
61 |
320 |
3591 |
10654 |
7 |
8 |
386 |
485 |
0 |
1 |
0 |
1 |
11618 |
4242 |
369 |
97 |
https://usegalaxy.org/published/workflow?id=df6c398b2d4f1e99 |
|
|
vcfcheck |
vcfcheck |
Verify that the reference allele matches the reference genome |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
109 |
128 |
1560 |
1680 |
207 |
669 |
754 |
2025 |
18 |
19 |
401 |
461 |
1 |
1 |
1 |
1 |
4167 |
2716 |
817 |
335 |
https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a |
|
|
vcfcombine |
vcfcombine |
Combine multiple VCF datasets |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
337 |
585 |
1639 |
2560 |
996 |
2856 |
4286 |
20198 |
59 |
74 |
481 |
585 |
6 |
6 |
13 |
13 |
23356 |
6419 |
3521 |
1398 |
https://usegalaxy.eu/published/workflow?id=a2d4221ad117c378, https://usegalaxy.eu/published/workflow?id=ddd604341afd9cf7, https://usegalaxy.org/published/workflow?id=2478426a119d9d93, https://usegalaxy.org/published/workflow?id=2d44e2b020bf94f8, https://usegalaxy.org/published/workflow?id=865d2cc4d14ec7e1, https://usegalaxy.org/published/workflow?id=c4a1246974f279c5, https://usegalaxy.org/published/workflow?id=d3e656ab45f40c11, https://usegalaxy.org/published/workflow?id=d43b771d93f0f609, https://usegalaxy.org/published/workflow?id=e2432c4d2b61705a |
|
|
vcfcommonsamples |
vcfcommonsamples |
Output records belonging to samples commong between two datasets. |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
36 |
49 |
81 |
270 |
78 |
297 |
211 |
1889 |
10 |
13 |
217 |
282 |
3 |
3 |
15 |
15 |
2456 |
524 |
362 |
127 |
|
|
|
vcfdistance |
vcfdistance |
Calculate distance to the nearest variant. |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
96 |
106 |
520 |
648 |
135 |
322 |
1960 |
2480 |
21 |
24 |
303 |
368 |
2 |
2 |
2 |
2 |
3498 |
2785 |
454 |
254 |
|
|
|
vcffilter |
vcffilter2 |
Tool for filtering VCF files |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
2682 |
2972 |
41687 |
54337 |
5382 |
11813 |
62117 |
173095 |
319 |
406 |
3130 |
3934 |
53 |
53 |
266 |
266 |
231632 |
107200 |
15244 |
8436 |
https://usegalaxy.eu/published/workflow?id=22454322d370b3ff, https://usegalaxy.eu/published/workflow?id=291c36e1b18e9deb, https://usegalaxy.eu/published/workflow?id=2a13eb981d6ee36e, https://usegalaxy.eu/published/workflow?id=3b7c0b64033f38ac, https://usegalaxy.eu/published/workflow?id=533819bcb5aa78c5, https://usegalaxy.eu/published/workflow?id=591ebf913450f49e, https://usegalaxy.eu/published/workflow?id=5a16af00bf8bf57b, https://usegalaxy.eu/published/workflow?id=5e3c352233aa7a52, https://usegalaxy.eu/published/workflow?id=6a5c39c1d38a10c2, https://usegalaxy.eu/published/workflow?id=865f470be3c18b08, https://usegalaxy.eu/published/workflow?id=88064e2231165fd2, https://usegalaxy.eu/published/workflow?id=8ab6a554cdea5195, https://usegalaxy.eu/published/workflow?id=99799eec4497f977, https://usegalaxy.eu/published/workflow?id=a62f21701ff37788, https://usegalaxy.eu/published/workflow?id=ea0524e0b5eab8b9, https://usegalaxy.eu/published/workflow?id=f560e06d23818b4c, 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https://usegalaxy.org/published/workflow?id=c828990fb009e318, https://usegalaxy.org/published/workflow?id=c95fc8692a886a59, https://usegalaxy.org/published/workflow?id=c9e442a395fc1a58, https://usegalaxy.org/published/workflow?id=cb03300161109123, https://usegalaxy.org/published/workflow?id=cc6ee582a6e5cae2, https://usegalaxy.org/published/workflow?id=ced446bf2428497b, https://usegalaxy.org/published/workflow?id=cfd37af9d6e4cbdb, https://usegalaxy.org/published/workflow?id=d0981820adf9c7d2, https://usegalaxy.org/published/workflow?id=d196c3bde666eccb, https://usegalaxy.org/published/workflow?id=d2edc47cc7963885, https://usegalaxy.org/published/workflow?id=d314df52f2f51502, https://usegalaxy.org/published/workflow?id=d3eae9943ce2a62b, https://usegalaxy.org/published/workflow?id=d43b771d93f0f609, https://usegalaxy.org/published/workflow?id=d50b2df115706adb, https://usegalaxy.org/published/workflow?id=d7049965ca7d8ea9, https://usegalaxy.org/published/workflow?id=d7d65ee5c5ca951f, https://usegalaxy.org/published/workflow?id=d7e14ff032a6ac4f, https://usegalaxy.org/published/workflow?id=d85f8ef78040fbb1, https://usegalaxy.org/published/workflow?id=db8443163482a2e0, https://usegalaxy.org/published/workflow?id=dbcf0fbf5329b3fb, https://usegalaxy.org/published/workflow?id=dbdc894ad54675a8, https://usegalaxy.org/published/workflow?id=dddd23119443b85e, https://usegalaxy.org/published/workflow?id=de2861cdbd4e29ce, https://usegalaxy.org/published/workflow?id=df1fa0b73f741a9c, https://usegalaxy.org/published/workflow?id=e2c77aeabb8053b4, https://usegalaxy.org/published/workflow?id=e2d7b8a4e6c422a3, https://usegalaxy.org/published/workflow?id=e51aaf4d6b16b4d4, https://usegalaxy.org/published/workflow?id=e67db5dc8eab60f3, https://usegalaxy.org/published/workflow?id=e6a6223ef5ef85a7, https://usegalaxy.org/published/workflow?id=e6b803c1232cd08e, https://usegalaxy.org/published/workflow?id=e6f57346a02be07f, https://usegalaxy.org/published/workflow?id=e7030b62a3335bd7, https://usegalaxy.org/published/workflow?id=eb33df15225b8aa0, https://usegalaxy.org/published/workflow?id=ebbcdc389aad0eb8, https://usegalaxy.org/published/workflow?id=ebc9aad36017b567, https://usegalaxy.org/published/workflow?id=ec3d8d5d1531f92e, https://usegalaxy.org/published/workflow?id=ec96e3bf30d5f771, https://usegalaxy.org/published/workflow?id=edb299ecbf147618, https://usegalaxy.org/published/workflow?id=eed1aadf2fb83f6c, https://usegalaxy.org/published/workflow?id=ef44d02a79bd28bf, https://usegalaxy.org/published/workflow?id=f0feca8af9aeddba, https://usegalaxy.org/published/workflow?id=f23e5f333987a89f, https://usegalaxy.org/published/workflow?id=f302d673420a9bdd, https://usegalaxy.org/published/workflow?id=f39603063febba82, https://usegalaxy.org/published/workflow?id=f3ed710e251833a7, https://usegalaxy.org/published/workflow?id=f4ed1c9434ed0445, https://usegalaxy.org/published/workflow?id=f60818a405f1bbbd, https://usegalaxy.org/published/workflow?id=f63f7a0a33a83841, https://usegalaxy.org/published/workflow?id=f88f186bc851e954, https://usegalaxy.org/published/workflow?id=f9d546aae406cf15, https://usegalaxy.org/published/workflow?id=fae519dcba6bfc72, https://usegalaxy.org/published/workflow?id=feeec17310351914, https://workflowhub.eu/workflows/1659?version=1 |
variant-analysis/non-dip |
|
vcffixup |
vcffixup |
Count the allele frequencies across alleles present in each record in the VCF file. |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
177 |
208 |
1003 |
1179 |
282 |
1037 |
2113 |
5539 |
26 |
34 |
252 |
322 |
1 |
1 |
1 |
1 |
7041 |
3369 |
1280 |
486 |
|
|
|
vcfflatten |
vcfflatten2 |
Removes multi-allelic sites by picking the most common alternate |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
24 |
32 |
67 |
194 |
68 |
218 |
360 |
988 |
12 |
16 |
193 |
393 |
1 |
1 |
50 |
50 |
1625 |
670 |
267 |
105 |
|
|
|
vcfgeno2haplo |
vcfgeno2haplo |
Convert genotype-based phased alleles into haplotype alleles |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
117 |
134 |
791 |
900 |
192 |
549 |
2408 |
3817 |
22 |
26 |
243 |
308 |
2 |
2 |
4 |
4 |
5029 |
3446 |
711 |
333 |
https://usegalaxy.org/published/workflow?id=eb4b32fcf4a9f64a |
|
|
vcfgenotypes |
vcfgenotypes |
Convert numerical representation of genotypes to allelic. |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
142 |
171 |
1337 |
1568 |
246 |
900 |
3621 |
6730 |
23 |
26 |
231 |
291 |
1 |
1 |
6 |
6 |
8595 |
5195 |
1098 |
412 |
https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4 |
|
|
vcfhethom |
vcfhethom |
Count the number of heterozygotes and alleles, compute het/hom ratio. |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
261 |
279 |
2002 |
2396 |
183 |
682 |
1967 |
4292 |
19 |
27 |
584 |
754 |
3 |
3 |
12 |
12 |
7454 |
4565 |
991 |
466 |
https://usegalaxy.org/published/workflow?id=7d005f30cd4853c4 |
|
|
vcfleftalign |
vcfleftalign |
Left-align indels and complex variants in VCF dataset |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
42 |
52 |
616 |
740 |
85 |
301 |
345 |
1145 |
9 |
16 |
188 |
270 |
1 |
2 |
1 |
2 |
2157 |
1150 |
371 |
137 |
https://usegalaxy.org/published/workflow?id=2478426a119d9d93 |
|
|
vcfprimers |
vcfprimers |
Extract flanking sequences for each VCF record |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
29 |
39 |
450 |
722 |
68 |
215 |
324 |
880 |
10 |
13 |
197 |
267 |
1 |
1 |
3 |
3 |
1872 |
974 |
268 |
108 |
|
|
|
vcfrandomsample |
vcfrandomsample |
Randomly sample sites from VCF dataset |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
17 |
20 |
89 |
186 |
27 |
81 |
111 |
361 |
6 |
6 |
194 |
243 |
0 |
0 |
0 |
0 |
790 |
394 |
107 |
50 |
|
|
|
vcfselectsamples |
vcfselectsamples |
Select samples from a VCF file |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
77 |
102 |
786 |
973 |
179 |
989 |
923 |
6360 |
22 |
24 |
349 |
427 |
0 |
0 |
0 |
0 |
7760 |
2058 |
1115 |
278 |
https://usegalaxy.org/published/workflow?id=63e0dcf18794dbc1, https://usegalaxy.org/published/workflow?id=67e56a9919ed84f7, https://usegalaxy.org/published/workflow?id=9b4323b68f609e06, https://usegalaxy.org/published/workflow?id=ad6143e2f74e1e94, https://usegalaxy.org/published/workflow?id=db8443163482a2e0, https://usegalaxy.org/published/workflow?id=df6c398b2d4f1e99 |
|
|
vcfsort |
vcfsort |
Sort VCF dataset by coordinate |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
209 |
236 |
1958 |
2132 |
413 |
1369 |
12476 |
25718 |
79 |
89 |
597 |
785 |
4 |
4 |
74 |
74 |
28709 |
15105 |
1698 |
705 |
https://usegalaxy.org.au/published/workflow?id=4871f853090e8be8, https://usegalaxy.org.au/published/workflow?id=d69a765cfc82a399, https://usegalaxy.org/published/workflow?id=50206b10de958d03, https://usegalaxy.org/published/workflow?id=bb16936081b820f6, https://usegalaxy.org/published/workflow?id=fae519dcba6bfc72 |
|
|
vcfvcfintersect |
vcfvcfintersect |
Intersect two VCF datasets |
2017-01-24 |
https://github.com/ekg/vcflib |
|
vcflib |
1.0.14 |
To update |
Variant Analysis |
|
|
|
|
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect |
https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
768 |
874 |
977198 |
979857 |
916 |
2249 |
64595 |
84741 |
232 |
244 |
18029 |
21296 |
15 |
16 |
1681 |
1682 |
1087576 |
1061503 |
3383 |
1931 |
https://usegalaxy.eu/published/workflow?id=0882300f7b399587, https://usegalaxy.eu/published/workflow?id=0be293debca8fb9b, https://usegalaxy.eu/published/workflow?id=2573209308aaad23, https://usegalaxy.eu/published/workflow?id=4b4bfc79205d83f1, https://usegalaxy.eu/published/workflow?id=4f9f7065975b3f97, https://usegalaxy.eu/published/workflow?id=52bdf400f97c5770, https://usegalaxy.eu/published/workflow?id=53de0e742573e588, https://usegalaxy.eu/published/workflow?id=579dd1e95e76402f, https://usegalaxy.eu/published/workflow?id=6dbac47941a804da, https://usegalaxy.eu/published/workflow?id=a6f4371ef9bc1aab, https://usegalaxy.eu/published/workflow?id=b556b0a67ad979da, https://usegalaxy.eu/published/workflow?id=ed20bd120064bab0, https://usegalaxy.eu/published/workflow?id=ee6dc47660540ba6, https://usegalaxy.eu/published/workflow?id=fc216dfb0ec9ed41, https://usegalaxy.eu/published/workflow?id=fcf745185d6e0ea4, https://usegalaxy.fr/published/workflow?id=7d27dd394b921846, https://usegalaxy.fr/published/workflow?id=98529cff0ef36b91, https://usegalaxy.fr/published/workflow?id=d0d12c0b80c286f9, https://usegalaxy.fr/published/workflow?id=e0b225d4b2556365, https://usegalaxy.org.au/published/workflow?id=094a545d44ce28cc, https://usegalaxy.org.au/published/workflow?id=2b2ce7e1206d177d, https://usegalaxy.org.au/published/workflow?id=3223ceaa2b58d940, https://usegalaxy.org.au/published/workflow?id=3c657dd766d02f6a, https://usegalaxy.org.au/published/workflow?id=52b6fe5af4911b1a, https://usegalaxy.org.au/published/workflow?id=7fd58f5fc93f414e, https://usegalaxy.org.au/published/workflow?id=810242a3dc4f6170, https://usegalaxy.org.au/published/workflow?id=888eb87b62c4e6dd, https://usegalaxy.org.au/published/workflow?id=baa763dbdf6afb71, https://usegalaxy.org.au/published/workflow?id=bcf230e526632064, https://usegalaxy.org.au/published/workflow?id=be9213411c520096, https://usegalaxy.org.au/published/workflow?id=c1ce3f2ae7c81c3e, https://usegalaxy.org.au/published/workflow?id=c9156ca3df2b595c, https://usegalaxy.org.au/published/workflow?id=d35d05be576e8b13, https://usegalaxy.org.au/published/workflow?id=e439a0e17a90d24c, https://usegalaxy.org.au/published/workflow?id=fe5542c99cdc57ce, https://usegalaxy.org/published/workflow?id=21a047a4e068860f, https://usegalaxy.org/published/workflow?id=262ab42118016c41, https://usegalaxy.org/published/workflow?id=4cf8cc42e97b2da6, https://usegalaxy.org/published/workflow?id=6b11d738ee57f245, https://usegalaxy.org/published/workflow?id=7dde0721a382ea3e, https://usegalaxy.org/published/workflow?id=7e2651e5ed17e3db, https://usegalaxy.org/published/workflow?id=98b2ac8fc75781f8, https://usegalaxy.org/published/workflow?id=9b81d47a468d6f99, https://usegalaxy.org/published/workflow?id=9e487f763daa66c0, https://usegalaxy.org/published/workflow?id=9fc9f1db50019929, https://usegalaxy.org/published/workflow?id=a98a3ac1a41752bc, https://usegalaxy.org/published/workflow?id=b34ba9b2e4d8f050, https://usegalaxy.org/published/workflow?id=b461ac6f18e0c9cf, https://usegalaxy.org/published/workflow?id=bd355e8ce58a139e, https://usegalaxy.org/published/workflow?id=bf3ccae8d5b6ef58, https://usegalaxy.org/published/workflow?id=d196c3bde666eccb, https://usegalaxy.org/published/workflow?id=d4ea6cdd40522eb1, https://usegalaxy.org/published/workflow?id=e282f505ba9f729f, https://usegalaxy.org/published/workflow?id=e2c77aeabb8053b4, https://usegalaxy.org/published/workflow?id=f9d546aae406cf15, https://workflowhub.eu/workflows/110?version=11 |
|
|
vegan |
vegan_diversity, vegan_fisher_alpha, vegan_rarefaction |
an R package fo community ecologist |
2015-08-27 |
https://cran.r-project.org/package=vegan |
2.4-3 |
r-vegan |
2.3_4 |
To update |
Metagenomics |
Standardisation and normalisation, Analysis |
Standardisation and normalisation, Analysis |
Ecology, Phylogenetics, Environmental science |
Ecology, Phylogenetics, Environmental science |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan |
vegan |
vegan |
Ordination methods, diversity analysis and other functions for community and vegetation ecologists |
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
101 |
116 |
2314 |
2547 |
167 |
318 |
3493 |
5788 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8335 |
5807 |
434 |
268 |
|
|
|
velocyto |
velocyto_cli |
Velocyto is a library for the analysis of RNA velocity. |
2021-04-30 |
http://velocyto.org/ |
0.17.17 |
velocyto.py |
0.17.17 |
Up-to-date |
Transcriptomics, Single Cell |
RNA-Seq analysis, Splicing analysis |
RNA-Seq analysis, Splicing analysis |
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto |
velocyto |
Velocyto |
Estimating RNA velocity in single cell RNA sequencing datasets |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
14 |
14 |
131 |
131 |
12 |
12 |
75 |
75 |
1 |
1 |
192 |
192 |
0 |
0 |
0 |
0 |
398 |
398 |
27 |
27 |
https://usegalaxy.eu/published/workflow?id=c5841e0458a4ebf7, https://usegalaxy.eu/published/workflow?id=c58bb47e04157ee6, https://usegalaxy.org.au/published/workflow?id=1e5a77d9e9630115, https://usegalaxy.org.au/published/workflow?id=77e0ca6492f40c9c, https://usegalaxy.org/published/workflow?id=29d51c37d66deeeb, https://usegalaxy.org/published/workflow?id=6592430b80345167 |
|
|
velvet |
velvetg, velveth |
de novo genomic assembler specially designed for short read sequencing technologies |
2020-06-09 |
https://www.ebi.ac.uk/~zerbino/velvet/ |
|
velvet |
1.2.10 |
To update |
Assembly |
Formatting, De-novo assembly |
Formatting, De-novo assembly |
Sequence assembly |
Sequence assembly |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet |
velvet |
Velvet |
A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
0 |
2567 |
2888 |
27621 |
32158 |
4951 |
5263 |
52855 |
57273 |
2097 |
2221 |
30746 |
33121 |
109 |
109 |
1097 |
1097 |
123649 |
112319 |
10481 |
9724 |
https://usegalaxy.eu/published/workflow?id=01dc0619e050dc91, https://usegalaxy.eu/published/workflow?id=56edd22d14392691, https://usegalaxy.eu/published/workflow?id=6d87481be47902e1, https://usegalaxy.eu/published/workflow?id=842e0ea7b1eb56af, https://usegalaxy.eu/published/workflow?id=b7c2440621968526, https://usegalaxy.eu/published/workflow?id=ef83f7fd2176a244, https://usegalaxy.org.au/published/workflow?id=30430b75d05f54eb, https://usegalaxy.org.au/published/workflow?id=533dbb3242ee4255, https://usegalaxy.org.au/published/workflow?id=7fa13ccbf044edc5, https://usegalaxy.org.au/published/workflow?id=83e3ceceb1a92493, https://usegalaxy.org.au/published/workflow?id=874492eb776ba813, https://usegalaxy.org.au/published/workflow?id=8b6739a000780d99, https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a, https://usegalaxy.org.au/published/workflow?id=9b75924c483b5f6b, https://usegalaxy.org.au/published/workflow?id=aee5b5645c51cac3, https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33, https://usegalaxy.org.au/published/workflow?id=ee7a1615f187391d, https://usegalaxy.org.au/published/workflow?id=f25a05070bf97ded, https://usegalaxy.org.au/published/workflow?id=fb0986a952c35e0a, https://usegalaxy.org/published/workflow?id=4e1ae78405034ad3, https://usegalaxy.org/published/workflow?id=51c485af11d90700, https://usegalaxy.org/published/workflow?id=7a33bc2d0970b502, https://usegalaxy.org/published/workflow?id=c30f6ca171896908, https://usegalaxy.org/published/workflow?id=e745c45651d829b8, https://usegalaxy.org/published/workflow?id=f6bd33dedc7c6c12, https://usegalaxy.org/published/workflow?id=f926e70bee242785, https://workflowhub.eu/workflows/1622?version=1 |
assembly/general-introduction |
|
velvetoptimiser |
velvetoptimiser |
Automatically optimize Velvet assemblies |
2017-12-19 |
|
2.2.6+galaxy2 |
velvet |
1.2.10 |
To update |
Assembly |
Optimisation and refinement, Sequence assembly |
Optimisation and refinement, Sequence assembly |
Genomics, Sequence assembly |
Genomics, Sequence assembly |
simon-gladman |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser |
velvetoptimiser |
VelvetOptimiser |
This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
968 |
1161 |
4741 |
6009 |
2238 |
2532 |
9434 |
10734 |
849 |
1433 |
2848 |
5743 |
0 |
0 |
0 |
0 |
22486 |
17023 |
5126 |
4055 |
https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=ef83f7fd2176a244, https://usegalaxy.org.au/published/workflow?id=8abcfe166f1a6cd8, https://usegalaxy.org.au/published/workflow?id=8d47811c6154d347, https://usegalaxy.org.au/published/workflow?id=fa76b66785ce38b8, https://workflowhub.eu/workflows/1626?version=1 |
assembly/debruijn-graph-assembly |
|
verkko |
verkko |
Telomere-to-telomere assembly pipeline |
2023-01-24 |
https://github.com/marbl/verkko |
1.3.1 |
verkko |
2.2.1 |
To update |
Assembly |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
43 |
43 |
105 |
105 |
0 |
0 |
0 |
0 |
13 |
13 |
136 |
136 |
0 |
0 |
0 |
0 |
241 |
241 |
56 |
56 |
|
|
|
vg |
vg_convert, vg_deconstruct, vg_view |
Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods |
2020-04-08 |
https://github.com/vgteam/vg |
1.23.0 |
vg |
1.67.0 |
To update |
Sequence Analysis, Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg |
|
|
|
|
0 |
0 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
12 |
15 |
15 |
480 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
480 |
15 |
15 |
12 |
https://usegalaxy.eu/published/workflow?id=9ba580ba8b01db40 |
|
|
viralverify |
viralverify |
Contigs prediction as viral, chromosomal, plasmidic or uncertain. |
2025-07-04 |
https://github.com/ablab/viralVerify |
1.1 |
viralverify |
1.1 |
Up-to-date |
Sequence Analysis, Metagenomics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
virannot |
virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv |
virAnnot wrappers |
2025-08-04 |
https://github.com/marieBvr/virAnnot |
1.2.0 |
biopython |
1.70 |
To update |
Metagenomics |
Sequence annotation, Sequence clustering, Sequence cluster visualisation |
Sequence annotation, Sequence clustering, Sequence cluster visualisation |
Metagenomics, Virology, Microbial ecology |
Metagenomics, Virology, Microbial ecology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/virannot |
virannot |
virAnnot |
VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project "Plant Health Bioinformatics Network". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy. |
|
0 |
0 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
16 |
336 |
336 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
14 |
14 |
350 |
350 |
18 |
18 |
https://usegalaxy.eu/published/workflow?id=17f73aba442315e6, https://usegalaxy.eu/published/workflow?id=86465932556bc96c |
|
|
virheat |
virheat |
generates a heatmap of allele frequencies from vcf files |
2024-05-15 |
https://github.com/jonas-fuchs/virHEAT |
0.7.1 |
virheat |
0.7.6 |
To update |
Visualization, Variant Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat |
virheat |
virHEAT |
VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists. The tool provides a condensed look at variant frequencies after mapping raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
29 |
29 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
29 |
29 |
7 |
7 |
|
|
|
virhunter |
virhunter |
Deep Learning method for novel virus detection in sequencing data |
2022-09-13 |
https://github.com/cbib/virhunter |
1.0.0 |
numpy |
|
To update |
Machine Learning |
Sequence classification |
Sequence classification |
Virology |
Virology |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter |
virhunter |
VirHunter |
VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
121 |
121 |
1700 |
1700 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1700 |
1700 |
121 |
121 |
|
|
|
virulign |
virulign |
A tool for codon-correct pairwise alignments, with an augmented functionality to annotate the alignment according the positions of the proteins. |
2025-08-14 |
https://github.com/rega-cev/virulign |
1.1.1 |
virulign |
1.1.1 |
Up-to-date |
RNA, Sequence Analysis, Fasta Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/virulign/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/virulign |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
volcanoplot |
volcanoplot |
Tool to create a Volcano Plot |
2018-10-01 |
https://ggplot2.tidyverse.org/ |
4.0.0 |
r-ggplot2 |
2.2.1 |
To update |
Visualization, Transcriptomics, Statistics |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
4591 |
5038 |
38589 |
45177 |
6962 |
7279 |
66385 |
70667 |
1001 |
1068 |
8606 |
9348 |
266 |
267 |
1555 |
1558 |
126750 |
115135 |
13652 |
12820 |
https://usegalaxy.eu/published/workflow?id=04df470a38b10e94, https://usegalaxy.eu/published/workflow?id=17ad465d9515cd25, https://usegalaxy.eu/published/workflow?id=20ada53472782c9b, https://usegalaxy.eu/published/workflow?id=350d7e6976e15d30, https://usegalaxy.eu/published/workflow?id=3ac10b9887fd0fb2, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=4ddf2ec5c460d622, https://usegalaxy.eu/published/workflow?id=68e8042f11d5a3fd, https://usegalaxy.eu/published/workflow?id=7136ce9f18c74853, https://usegalaxy.eu/published/workflow?id=81f1927bfe3ffea1, https://usegalaxy.eu/published/workflow?id=82ef590b5821805d, https://usegalaxy.eu/published/workflow?id=8b1e2fe9f4a07de0, https://usegalaxy.eu/published/workflow?id=95c4d5549e820d88, https://usegalaxy.eu/published/workflow?id=a9469155eee12ff1, https://usegalaxy.eu/published/workflow?id=bc79a9f797334b01, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=c7b9fb6872444809, https://usegalaxy.eu/published/workflow?id=d1b3b62e7f91e217, https://usegalaxy.eu/published/workflow?id=d41b52a15ba56f54, https://usegalaxy.eu/published/workflow?id=e04be1ab5a16eb9f, https://usegalaxy.eu/published/workflow?id=e7e26967cf6cb8d8, https://usegalaxy.eu/published/workflow?id=f58526da1fd68108, https://usegalaxy.eu/published/workflow?id=fd156028b09d213a, https://usegalaxy.org.au/published/workflow?id=04ab43fb3e7840ef, https://usegalaxy.org.au/published/workflow?id=28705b86e0595ded, https://usegalaxy.org.au/published/workflow?id=5fe66b29dcfb22ab, https://usegalaxy.org.au/published/workflow?id=897e9d7432d231e9, https://usegalaxy.org.au/published/workflow?id=8eab5e2b2c683076, https://usegalaxy.org.au/published/workflow?id=9988bc2402f32dc1, https://usegalaxy.org.au/published/workflow?id=a8d9a16eea69b812, https://usegalaxy.org.au/published/workflow?id=a9e59d38c6c710bc, https://usegalaxy.org/published/workflow?id=0930f955bdac93e8, https://usegalaxy.org/published/workflow?id=13a3954b8894e1b1, https://usegalaxy.org/published/workflow?id=25cdc47baba556c5, https://usegalaxy.org/published/workflow?id=40a65b5bc1dcc0b4, https://usegalaxy.org/published/workflow?id=420a332da24fb9e9, https://usegalaxy.org/published/workflow?id=4c840284d2984fa0, https://usegalaxy.org/published/workflow?id=5944c5effd56b0d6, https://usegalaxy.org/published/workflow?id=667493d318b86b7d, https://usegalaxy.org/published/workflow?id=68832752b883c226, https://usegalaxy.org/published/workflow?id=7497bfdd2085b6e0, https://usegalaxy.org/published/workflow?id=b0e19e7315b64c87, https://usegalaxy.org/published/workflow?id=e40c2e7f6b73fb11, https://workflowhub.eu/workflows/1201?version=4, https://workflowhub.eu/workflows/1207?version=2, https://workflowhub.eu/workflows/1556?version=1, https://workflowhub.eu/workflows/1708?version=1, https://workflowhub.eu/workflows/1709?version=1 |
genome-annotation/crispr-screen, single-cell/pseudobulk-analysis, transcriptomics/rna-seq-analysis-clustering-viz, transcriptomics/rna-seq-viz-with-volcanoplot, transcriptomics/rna-seq-viz-with-volcanoplot-r |
|
vsearch |
vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting |
VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. |
2014-11-30 |
https://github.com/torognes/vsearch |
2.8.3 |
vsearch |
2.30.0 |
To update |
Sequence Analysis |
DNA mapping, Chimera detection |
DNA mapping, Chimera detection |
Metagenomics, Sequence analysis |
Metagenomics, Sequence analysis |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch |
vsearch |
VSEARCH |
High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. |
|
0 |
8 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
8 |
226 |
259 |
13600 |
15795 |
323 |
642 |
14828 |
59476 |
82 |
97 |
6641 |
7811 |
11 |
12 |
285 |
286 |
83368 |
35354 |
1010 |
642 |
https://usegalaxy.eu/published/workflow?id=401746888e8b3aa8, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=9382f9bbbdddb5ad, https://usegalaxy.eu/published/workflow?id=9cbba5de2cbeeb0f, https://usegalaxy.eu/published/workflow?id=a8417c63e9e22afb, https://usegalaxy.eu/published/workflow?id=c3aa516e78ca4191, https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://workflowhub.eu/workflows/232?version=1, https://workflowhub.eu/workflows/233?version=1 |
|
|
vsnp |
vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics |
The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. |
2020-04-26 |
https://github.com/USDA-VS/vSNP |
3.0.6 |
pysam |
0.23.3 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
weblogo3 |
rgweblogo3 |
Sequence Logo generator for fasta |
2017-11-17 |
|
3.5.0 |
weblogo |
3.7.9 |
To update |
Graphics |
Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition |
Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition |
Nucleic acid sites, features and motifs, Sequence analysis |
Nucleic acid sites, features and motifs, Sequence analysis |
devteam |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 |
weblogo |
WebLogo |
Web-based application designed to make generate sequence logos. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
305 |
344 |
3638 |
3856 |
1198 |
3777 |
8383 |
31758 |
52 |
69 |
577 |
1423 |
10 |
10 |
40 |
40 |
37077 |
12638 |
4200 |
1565 |
https://usegalaxy.eu/published/workflow?id=974cc681d07ec788, https://usegalaxy.org/published/workflow?id=042758b8a8c5ac80, https://usegalaxy.org/published/workflow?id=18e7a954c0b6e4bc, https://usegalaxy.org/published/workflow?id=b2fb90873471f4e7 |
|
|
windowmasker |
windowmasker_mkcounts, windowmasker_ustat |
Identify repetitive regions using WindowMasker |
2023-12-14 |
https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ |
1.0 |
blast |
2.17.0 |
To update |
Sequence Analysis |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker |
|
|
|
|
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
23 |
23 |
856 |
856 |
14 |
14 |
609 |
609 |
3 |
3 |
807 |
807 |
0 |
0 |
0 |
0 |
2272 |
2272 |
40 |
40 |
https://usegalaxy.eu/published/workflow?id=1ce406de61de8492, https://usegalaxy.eu/published/workflow?id=2880a32a52d27743, https://usegalaxy.eu/published/workflow?id=2e93613c688ea52e, https://usegalaxy.eu/published/workflow?id=309969a261189b5f, https://usegalaxy.eu/published/workflow?id=38f12705279b5dfa, https://usegalaxy.eu/published/workflow?id=3cf3dd9727b7ac92, https://usegalaxy.eu/published/workflow?id=5f29105e842716db, https://usegalaxy.eu/published/workflow?id=aada0111f835ce49, https://usegalaxy.eu/published/workflow?id=cc2bc81352d2e2cd, https://usegalaxy.eu/published/workflow?id=efb58bba65393347 |
|
|
winnowmap |
winnowmap |
A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. |
2021-04-29 |
https://github.com/marbl/Winnowmap |
2.03 |
winnowmap |
2.03 |
Up-to-date |
Next Gen Mappers |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
54 |
54 |
317 |
317 |
19 |
19 |
90 |
90 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
407 |
407 |
73 |
73 |
https://usegalaxy.eu/published/workflow?id=2cd5670f075704ab, https://usegalaxy.eu/published/workflow?id=e522be58f0bac656 |
|
|
xpath |
xpath |
XPath XML querying tool |
2015-04-14 |
http://search.cpan.org/dist/XML-XPath/ |
|
perl-xml-xpath |
1.47 |
To update |
Text Manipulation |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
8 |
10 |
30 |
248 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
249 |
30 |
11 |
8 |
https://usegalaxy.eu/published/workflow?id=1f3f6757de60d3cf |
|
|
yahs |
yahs |
Yet Another Hi-C scaffolding tool |
2022-06-28 |
https://github.com/c-zhou/yahs |
1.2a.2 |
yahs |
1.2.2 |
To update |
Assembly |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
291 |
291 |
2516 |
2516 |
107 |
107 |
750 |
750 |
41 |
41 |
1062 |
1062 |
0 |
0 |
0 |
0 |
4328 |
4328 |
439 |
439 |
https://usegalaxy.eu/published/workflow?id=069d99391a69baf4, https://usegalaxy.eu/published/workflow?id=082bfd9b36e921e8, https://usegalaxy.eu/published/workflow?id=0c3ce9feb83f7920, https://usegalaxy.eu/published/workflow?id=0cf3c2114ab65858, https://usegalaxy.eu/published/workflow?id=3010ecad1a342331, https://usegalaxy.eu/published/workflow?id=31f8c7c46207432f, https://usegalaxy.eu/published/workflow?id=3b57fc81001667b5, https://usegalaxy.eu/published/workflow?id=44c92c04f1d14631, https://usegalaxy.eu/published/workflow?id=4949751217c0e211, https://usegalaxy.eu/published/workflow?id=5395e76fa828c343, https://usegalaxy.eu/published/workflow?id=652433160b04b232, https://usegalaxy.eu/published/workflow?id=792b24fc23bd3071, https://usegalaxy.eu/published/workflow?id=7b4a9aebb09b51ca, https://usegalaxy.eu/published/workflow?id=7e383fe34031a9d0, https://usegalaxy.eu/published/workflow?id=7e68cf8a67efa8e9, https://usegalaxy.eu/published/workflow?id=84236d781f7dd2ad, https://usegalaxy.eu/published/workflow?id=a2daeb488bee0152, https://usegalaxy.eu/published/workflow?id=a37d1e0db16cfb67, https://usegalaxy.eu/published/workflow?id=a53f78aa6866b811, https://usegalaxy.eu/published/workflow?id=b287bb779cf686ef, https://usegalaxy.eu/published/workflow?id=bc8ccd13a07bd9ec, https://usegalaxy.eu/published/workflow?id=c8f94a2e838fc0f1, https://usegalaxy.eu/published/workflow?id=cab2aa791a814d55, https://usegalaxy.eu/published/workflow?id=d649ec485c4b3994, https://usegalaxy.eu/published/workflow?id=f1e2577699125607, https://usegalaxy.eu/published/workflow?id=f63127675a07e00a, https://usegalaxy.eu/published/workflow?id=feeb1fa358ccf328, https://usegalaxy.org.au/published/workflow?id=0aa316f8c6cff444, https://usegalaxy.org.au/published/workflow?id=0dbb85f727302a72, https://usegalaxy.org.au/published/workflow?id=29f0c07c8a24b542, https://usegalaxy.org.au/published/workflow?id=3b6e9f03b088bf01, https://usegalaxy.org.au/published/workflow?id=455e68f185fec41b, https://usegalaxy.org.au/published/workflow?id=466809eb3392f7fb, https://usegalaxy.org.au/published/workflow?id=4ea1049371de111c, https://usegalaxy.org.au/published/workflow?id=6c1c11a81a2ab1b8, https://usegalaxy.org.au/published/workflow?id=6de8899c40a90b98, https://usegalaxy.org.au/published/workflow?id=6ec5728eec9c26d7, https://usegalaxy.org.au/published/workflow?id=7028436ef03171cc, https://usegalaxy.org.au/published/workflow?id=77b2fcf8c805ad5d, https://usegalaxy.org.au/published/workflow?id=7a97e8ccc332c1e8, https://usegalaxy.org.au/published/workflow?id=868775ef66d174a5, https://usegalaxy.org.au/published/workflow?id=86eb0ea9dc230f04, https://usegalaxy.org.au/published/workflow?id=ae2a397837b232b1, https://usegalaxy.org.au/published/workflow?id=ae6a03240680712a, https://usegalaxy.org.au/published/workflow?id=b53f82aaf32fbaa9, https://usegalaxy.org.au/published/workflow?id=b9e89401313a0cca, https://usegalaxy.org.au/published/workflow?id=be35847680078c90, https://usegalaxy.org.au/published/workflow?id=cac0b8a09d59044b, https://usegalaxy.org.au/published/workflow?id=ea98be0f99aaceb9, https://usegalaxy.org.au/published/workflow?id=f53d8ade897b3f46, https://usegalaxy.org.au/published/workflow?id=fdec6e2fcd5e2cf5, https://usegalaxy.org/published/workflow?id=155839aeb6340f54, https://usegalaxy.org/published/workflow?id=1ea88ca80a7f0038, https://usegalaxy.org/published/workflow?id=23eeee48217654d4, https://usegalaxy.org/published/workflow?id=28dbbfb3d480f4b1, https://usegalaxy.org/published/workflow?id=28ddea356ae57da1, https://usegalaxy.org/published/workflow?id=325783f21bc5fef6, https://usegalaxy.org/published/workflow?id=349f1bcdbc84045f, https://usegalaxy.org/published/workflow?id=3b0d42747f598f82, https://usegalaxy.org/published/workflow?id=3d805d7e0f34c727, https://usegalaxy.org/published/workflow?id=3db51822f04f4ff7, https://usegalaxy.org/published/workflow?id=49a07807fcea8158, https://usegalaxy.org/published/workflow?id=6341c384ceaf47ed, https://usegalaxy.org/published/workflow?id=74049914e4a6c791, https://usegalaxy.org/published/workflow?id=7b8ee08ba291d231, https://usegalaxy.org/published/workflow?id=88327cb2e0fe3c25, https://usegalaxy.org/published/workflow?id=903e35b62946ed76, https://usegalaxy.org/published/workflow?id=91a4daecbb97d03e, https://usegalaxy.org/published/workflow?id=9f4c4038d1c519e2, https://usegalaxy.org/published/workflow?id=a4a6d6846c1692f9, https://usegalaxy.org/published/workflow?id=afa89bb0e8966753, https://usegalaxy.org/published/workflow?id=c03ada2070e9ca8a, https://usegalaxy.org/published/workflow?id=c95e9116e4b7982b, https://usegalaxy.org/published/workflow?id=f09033420c6267ab, https://usegalaxy.org/published/workflow?id=fa36d9b50e956917, https://usegalaxy.org/published/workflow?id=fb98ef955b3dbd4b, https://workflowhub.eu/workflows/1054?version=1, https://workflowhub.eu/workflows/1164?version=2, https://workflowhub.eu/workflows/608?version=1, https://workflowhub.eu/workflows/625?version=26, https://workflowhub.eu/workflows/702?version=1 |
assembly/vgp_genome_assembly |
|
zerone |
zerone |
ChIP-seq discretization and quality control |
2018-09-05 |
https://github.com/nanakiksc/zerone |
1.0 |
zerone |
1.0 |
Up-to-date |
ChIP-seq |
|
|
|
|
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
7 |
12 |
14 |
96 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
96 |
14 |
12 |
7 |
|
|
|
CRSConverter |
crsconverter |
Tools to transforms geographical vector data to a specified coordinate reference system. |
2025-05-20 |
https://github.com/Morphy427/phylodiversity_workflow/CRSConverter |
1.1 |
r-sf |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/CRSConverter |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
47 |
47 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
47 |
47 |
3 |
3 |
https://usegalaxy.eu/published/workflow?id=89525918b2a32023 |
ecology/phylodiversity_workflow |
|
EstimEndem |
estimate_endem |
Tools to estimates the endemism of each cell in a spatial grid. |
2025-05-20 |
https://github.com/Morphy427/phylodiversity_workflow/EstimEndem |
0.1.1+galaxy0 |
r-phyloregion |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/EstimEndem |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
40 |
40 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
40 |
40 |
3 |
3 |
https://usegalaxy.eu/published/workflow?id=89525918b2a32023 |
ecology/phylodiversity_workflow |
|
Geometric means (Dead wood) |
Map_shp, Mean_geom, bar_plot |
Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). |
2023-11-10 |
https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom |
0.1.0+galaxy0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow |
|
|
|
|
0 |
0 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
60 |
60 |
163 |
163 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
20 |
20 |
183 |
183 |
62 |
62 |
|
|
|
MALDIquant |
maldi_quant_peak_detection, maldi_quant_preprocessing |
MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. |
2018-08-22 |
http://strimmerlab.org/software/maldiquant/ |
1.22.0 |
r-base |
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant |
|
|
|
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
31 |
37 |
985 |
3848 |
0 |
0 |
0 |
0 |
21 |
21 |
1215 |
1362 |
0 |
0 |
0 |
0 |
5210 |
2200 |
58 |
52 |
https://usegalaxy.eu/published/workflow?id=7ee6976f69131683, https://usegalaxy.eu/published/workflow?id=a5ca8b9807ed3f73, https://usegalaxy.org.au/published/workflow?id=3678781bf7619a89, https://workflowhub.eu/workflows/1587?version=1 |
metabolomics/msi-finding-nglycans |
|
MFAssignR |
mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot |
The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements |
2024-08-02 |
https://github.com/RECETOX/MFAssignR |
1.1.2 |
r-mfassignr |
1.1.2 |
Up-to-date |
Metabolomics |
Visualisation |
Visualisation |
Proteomics experiment, Molecular interactions, pathways and networks, Workflows |
Proteomics experiment, Molecular interactions, pathways and networks, Workflows |
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr |
https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr |
mfassignr |
MFAssignR |
Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements. |
|
0 |
0 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
80 |
80 |
2 |
2 |
13 |
13 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
93 |
93 |
7 |
7 |
https://workflowhub.eu/workflows/1351?version=1, https://workflowhub.eu/workflows/1591?version=1 |
metabolomics/mfassignr |
|
Make data paper sketches from EML |
data_paper_from_EML |
This tool derived from the R Shiny App MetaShRIMPS <https://github.com/TanguyGen/metaCure> is made to produce draft of data paper from Ecological Metadata Language (EML) based metadata documents. |
2024-10-15 |
https://github.com/TanguyGen/emldown |
0.1.0+galaxy0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/make_data_paper_sketches |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
28 |
28 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
28 |
28 |
3 |
3 |
|
|
|
PylOccuMatcher |
phylogenetic_occupancy_matcher |
Tools to matches phylogenetic data with occupancy data. |
2025-05-20 |
https://github.com/Morphy427/phylodiversity_workflow/PhylOccuMatcher |
1.0 |
r-phyloregion |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/PhylOccuMatcher |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
22 |
22 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
22 |
22 |
4 |
4 |
https://usegalaxy.eu/published/workflow?id=89525918b2a32023 |
ecology/phylodiversity_workflow |
|
PyloIndex |
phylo_index |
Tools to computes the phylodiversity index. |
2025-05-20 |
https://github.com/Morphy427/phylodiversity_workflow/PyloIndex |
1.0 |
r-phyloregion |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/PhyloIndex |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
18 |
18 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
18 |
18 |
5 |
5 |
https://usegalaxy.eu/published/workflow?id=89525918b2a32023 |
ecology/phylodiversity_workflow |
|
QCxMS |
qcxms_getres, qcxms_neutral_run, qcxms_production_run |
QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). |
2023-08-24 |
https://github.com/grimme-lab/QCxMS |
5.2.1 |
|
|
To update |
Computational chemistry, Molecular Dynamics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms |
https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms |
|
|
|
|
0 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
45445 |
45445 |
2 |
2 |
155 |
155 |
2 |
2 |
780 |
780 |
0 |
0 |
0 |
0 |
46380 |
46380 |
16 |
16 |
https://usegalaxy.eu/published/workflow?id=4e9a2e12467bc02e, https://usegalaxy.eu/published/workflow?id=5465916d9b51f411, https://workflowhub.eu/workflows/1350?version=1, https://workflowhub.eu/workflows/1597?version=1, https://workflowhub.eu/workflows/897?version=3 |
metabolomics/qcxms-predictions |
|
SCCAF |
run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out |
SCCAF: Single Cell Clustering Assessment Framework. |
2019-10-20 |
https://github.com/sccaf/sccaf |
0.0.9 |
sccaf |
0.0.10 |
To update |
Transcriptomics |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf |
|
|
|
|
0 |
3 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
8 |
87 |
110 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
111 |
88 |
9 |
7 |
|
|
|
WormsMeasurements |
WormsMeasurements |
This tool uses WoRMS (World Register of Marine Species) to add measurement values to a dataset based on scientific names. |
2025-05-07 |
https://github.com/jeanlecras/tools-ecology |
0.1.2 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/WormsMeasurements |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
97 |
97 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
97 |
97 |
4 |
4 |
https://usegalaxy.eu/published/workflow?id=749bb05ec8674bec |
ecology/ecoregiolifetraits |
|
ab1fastq |
ab1_fastq_converter |
Tool to convert ab1 files into FASTQ files |
2021-10-08 |
|
1.20.0 |
bioconductor-sangerseqr |
1.42.0 |
To update |
Convert Formats |
|
|
|
|
ecology |
https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
503 |
503 |
65003 |
65003 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
20 |
20 |
6753 |
6753 |
71756 |
71756 |
523 |
523 |
https://usegalaxy.eu/published/workflow?id=52cb9bacc26b013e, https://usegalaxy.eu/published/workflow?id=c7f34c67c9054234, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1 |
ecology/ENA_Biodiv_submission, sequence-analysis/Manage_AB1_Sanger |
|
ambertools |
ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap |
Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. |
2019-06-13 |
http://ambermd.org/AmberTools.php |
21.10 |
ambertools |
|
To update |
Molecular Dynamics, Computational chemistry |
|
|
|
|
chemteam |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools |
|
|
|
|
0 |
2 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
7 |
5 |
429 |
458 |
45081 |
45818 |
158 |
158 |
1806 |
1806 |
115 |
115 |
2251 |
2251 |
0 |
0 |
0 |
0 |
49875 |
49138 |
731 |
702 |
https://usegalaxy.eu/published/workflow?id=07e1478df88a17cc, https://usegalaxy.eu/published/workflow?id=2a1b21d39ebb6e49, https://usegalaxy.eu/published/workflow?id=3729015f676693c8, https://usegalaxy.eu/published/workflow?id=3c6ff60d1d3ceb3d, https://usegalaxy.eu/published/workflow?id=5d793801998146bc, https://usegalaxy.eu/published/workflow?id=843c10c447496280, https://usegalaxy.eu/published/workflow?id=84c95f31896213fd, https://usegalaxy.eu/published/workflow?id=abd1cb3457338eb5, https://usegalaxy.eu/published/workflow?id=adc6d049e9283789, https://usegalaxy.eu/published/workflow?id=bf99d06567288766, https://usegalaxy.eu/published/workflow?id=c39a79bb45b2566e, https://usegalaxy.eu/published/workflow?id=d4d8e907e26c8587, https://usegalaxy.eu/published/workflow?id=e0dddc2579c3614e, https://usegalaxy.eu/published/workflow?id=e73beff62f35d677, https://usegalaxy.org.au/published/workflow?id=28cf646b95e4d3ab, https://usegalaxy.org/published/workflow?id=00a4dbc9329c638b, https://usegalaxy.org/published/workflow?id=0fb89e9c397c8938, https://usegalaxy.org/published/workflow?id=183254b3565bcb04, https://usegalaxy.org/published/workflow?id=3c1e2bbb1a77cc30, https://usegalaxy.org/published/workflow?id=442a2868873e7f77, https://usegalaxy.org/published/workflow?id=a638e12411586555, https://usegalaxy.org/published/workflow?id=aaec757e04605d3a, https://usegalaxy.org/published/workflow?id=ad19db6504b6dc33, https://workflowhub.eu/workflows/1686?version=1, https://workflowhub.eu/workflows/247?version=2, https://workflowhub.eu/workflows/248?version=4, https://workflowhub.eu/workflows/761?version=1, https://workflowhub.eu/workflows/762?version=1, https://workflowhub.eu/workflows/763?version=1, https://workflowhub.eu/workflows/764?version=1 |
computational-chemistry/htmd-analysis |
|
analyse_short_astro_text_astro_tool |
analyse_short_astro_text_astro_tool |
Tool to analyse short astrophysics texts |
2024-06-04 |
|
0.0.1+galaxy0 |
astroquery |
|
To update |
Astronomy |
|
|
|
|
astroteam |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/analyse-short-astro-text |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
https://usegalaxy.eu/published/workflow?id=f9ae5a312e84cf0a, https://workflowhub.eu/workflows/1353?version=2 |
|
|
appendfdr |
append_fdr |
|
2015-01-24 |
|
0.2.0 |
|
|
To update |
|
|
|
|
|
galaxyp |
|
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
aquainfra_importer |
aquainfra_importer |
A data source tool for downloading datasets via the AquaINFRA Interaction Platform. |
2024-05-14 |
https://github.com/AquaINFRA/galaxy |
1.0 |
|
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
50 |
50 |
497 |
497 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
497 |
497 |
50 |
50 |
|
|
|
aquainfra_ogc_api_processes |
aquainfra_ogc_api_processes |
Wrapper for OGC API Processes developed in the AquaINFRA project. |
2024-10-10 |
https://github.com/AquaINFRA/galaxy |
0.7.0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/AquaINFRA/tools-ecology/tree/master |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_ogc_api_processes |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
43 |
43 |
1826 |
1826 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1826 |
1826 |
43 |
43 |
https://usegalaxy.eu/published/workflow?id=140b2882fc32d49f |
|
|
artbio_bam_cleaning |
artbio_bam_cleaning |
filter bam files before somatic-varscan or lumpy-smoove analysis |
2020-10-02 |
http://artbio.fr |
1.10+galaxy0 |
samtools |
1.22.1 |
To update |
SAM, Variant Analysis |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning |
https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
astronomicalarchivestool |
astronomical_archives |
Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy |
2023-07-17 |
|
0.10.21 |
astropy |
|
To update |
Data Source |
|
|
|
|
astroteam |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/ |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
8 |
8 |
78 |
78 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
78 |
78 |
8 |
8 |
|
|
|
astropytools |
astropy_csv2fits, astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo |
AstropyTools library contains Galaxy tools for elementary Astrophysical operations |
2023-04-11 |
https://github.com/astropy/astropy |
0.1.0+galaxy1 |
astropy |
|
To update |
Astronomy |
|
|
|
|
astroteam |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools |
|
|
|
|
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
5 |
5 |
30 |
30 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
30 |
30 |
5 |
5 |
https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=d9535e4afec8866b, https://usegalaxy.eu/published/workflow?id=f9ae5a312e84cf0a, https://workflowhub.eu/workflows/1267?version=1, https://workflowhub.eu/workflows/1353?version=2, https://workflowhub.eu/workflows/1369?version=1, https://workflowhub.eu/workflows/1730?version=1 |
|
|
atlas_fastq_provider |
fastq_provider |
Retrieval and download of FASTQ files from ENA and other repositories such as HCA. |
2022-03-09 |
https://github.com/ebi-gene-expression-group/atlas-fastq-provider |
0.4.4 |
atlas-fastq-provider |
0.4.7 |
To update |
Data Source, RNA, Transcriptomics |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
bamparse |
bamparse |
Generates hit count lists from bam alignments. |
2017-10-12 |
http://artbio.fr |
4.1.1 |
pysam |
0.23.3 |
To update |
RNA, Transcriptomics |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse |
https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
baseline_toxicity_calculator |
tt_baseline |
Toxicity prediction using QSAR models |
2024-03-25 |
https://github.com/bernt-matthias/mb-galaxy-tools |
0.1.0+galaxy0 |
pandas |
|
To update |
Ecology, Text Manipulation |
|
|
|
|
mbernt |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
bed_to_protein_map |
bed_to_protein_map |
Converts a BED file to a tabular list of exon locations |
2018-01-04 |
|
0.2.0 |
python |
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
177 |
195 |
555 |
634 |
118 |
118 |
398 |
398 |
21 |
22 |
219 |
225 |
0 |
0 |
0 |
0 |
1257 |
1172 |
335 |
316 |
https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2, https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=e336bca259abd474, https://workflowhub.eu/workflows/1407?version=1, https://workflowhub.eu/workflows/1437?version=1, https://workflowhub.eu/workflows/1788?version=1 |
proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation |
|
bgc_ocean |
harmonize_insitu_to_netcdf |
Process in-situ and biogechemical oceanographic Argo or Glider data for the Earth System |
2024-12-05 |
https://github.com/Marie59/FE-ft-ESG/tree/main/ocean |
3.0 |
|
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
75 |
75 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
75 |
75 |
5 |
5 |
https://usegalaxy.eu/published/workflow?id=44827462c065bae3, https://usegalaxy.eu/published/workflow?id=d3d9d1f173fd7bfe, https://workflowhub.eu/workflows/1961?version=1 |
climate/ocean_qcv_analysis |
|
bigwig_to_bedgraph |
bigwig_to_bedgraph |
Converts a bigWig file to bedGraph format |
2021-10-06 |
http://artbio.fr |
377+galaxy1 |
ucsc-bigwigtobedgraph |
482 |
To update |
Convert Formats |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph |
https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
715 |
873 |
7732 |
9584 |
1 |
1 |
1 |
1 |
1 |
2 |
4 |
7 |
0 |
0 |
0 |
0 |
9592 |
7737 |
876 |
717 |
|
|
|
bigwig_to_wig |
bigwig_to_wig |
Converts a bigWig file to Wiggle (WIG) format |
2018-09-25 |
https://artbio.fr |
3+galaxy0 |
ucsc-bigwiginfo |
482 |
To update |
Convert Formats |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig |
https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
bio3d |
bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize |
Bio3d is a program that can be used to analyse molecular dynamics trajectories. |
2018-10-03 |
http://thegrantlab.org/bio3d/index.php |
2.4_1 |
r-bio3d |
2.3_3 |
To update |
Computational chemistry |
|
|
|
|
chemteam |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d |
|
|
|
|
0 |
4 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
5 |
5 |
368 |
408 |
12210 |
13386 |
109 |
109 |
1423 |
1423 |
119 |
122 |
3385 |
3449 |
0 |
0 |
0 |
0 |
18258 |
17018 |
639 |
596 |
https://usegalaxy.eu/published/workflow?id=092d01f759659e6b, https://usegalaxy.eu/published/workflow?id=9858fdf13a522ea8, https://usegalaxy.org.au/published/workflow?id=5add59b908662af0, https://usegalaxy.org.au/published/workflow?id=c2f25a1bf07e8ab1, https://workflowhub.eu/workflows/1689?version=1, https://workflowhub.eu/workflows/1697?version=1 |
computational-chemistry/analysis-md-simulations, computational-chemistry/htmd-analysis |
|
biobb_pytorch |
biobb_pytorch_apply_mdae, biobb_pytorch_train_mdae |
biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular [PyTorch](https://pytorch.org/) Python library. |
2024-06-26 |
https://github.com/bioexcel/biobb_pytorch |
4.2.1 |
biobb_pytorch |
5.1.0 |
To update |
Molecular Dynamics, Computational chemistry |
|
|
|
|
chemteam |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biobb_pytorch |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biobb_pytorch |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
bioconductor-msnbase |
bioconductor_msnbase_centroid, bioconductor_msnbase_smooth_chromatogram, bioconductor_msnbase_smooth_mz |
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. |
2025-01-22 |
https://bioconductor.org/packages/release/bioc/html/MSnbase.html |
2.32.0 |
bioconductor-msnbase |
2.32.0 |
Up-to-date |
Metabolomics, Proteomics |
Data handling, Visualisation |
Data handling, Visualisation |
Proteomics, Proteomics experiment, Data management, Data visualisation |
Proteomics, Proteomics experiment, Data visualisation |
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-msnbase |
https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-msnbase |
msnbase |
MSnbase |
Basic plotting, data manipulation and processing of MS-based Proteomics data. |
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
bioconductor_mzr |
bioconductor_mzr_convert |
Galaxy wrapper for the Bioconductor mzR package, enabling conversion between common mass spectrometry data formats (mzML, mzXML, netCDF) within Galaxy workflows. |
2025-06-19 |
https://bioconductor.org/packages/mzR |
2.40.0 |
bioconductor-mzr |
2.40.0 |
Up-to-date |
Proteomics, Metabolomics |
Formatting |
Formatting |
Proteomics, Proteomics experiment, Data management |
Proteomics, Proteomics experiment |
recetox |
https://github.com/RECETOX/galaxytools/tree/main/tools/bioconductor-mzR |
https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-mzR |
mzr |
mzR |
Provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
bioconductor_scp |
bioconductor_scp |
scp is a package for the single cell proteomics data processing. |
2025-01-21 |
https://uclouvain-cbio.github.io/scp/index.html |
1.16.0 |
bioconductor-scp |
1.16.0 |
Up-to-date |
Proteomics, Single Cell |
Visualisation, Expression analysis |
Visualisation, Expression analysis |
Proteomics experiment, Proteomics |
Proteomics experiment, Proteomics |
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp |
https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp |
scp |
scp |
Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the 'QFeatures' package and relies on 'SingleCellExpirement' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
4 |
4 |
0 |
0 |
0 |
0 |
1 |
1 |
88 |
88 |
0 |
0 |
0 |
0 |
92 |
92 |
3 |
3 |
|
proteomics/bioconductor-scp |
|
biomoldyn |
biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering |
Tools for MD analysis |
2020-01-30 |
https://github.com/moldyn/ |
1.5.2 |
scipy |
|
To update |
Molecular Dynamics, Computational chemistry |
|
|
|
|
chemteam |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn |
|
|
|
|
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
3 |
98 |
99 |
539 |
600 |
119 |
119 |
638 |
638 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1238 |
1177 |
218 |
217 |
https://usegalaxy.eu/published/workflow?id=1b10ece62e745125, https://usegalaxy.eu/published/workflow?id=d1357759d0962144, https://usegalaxy.eu/published/workflow?id=e3b0b521ee8f2aef, https://usegalaxy.org/published/workflow?id=195a608c481040de, https://usegalaxy.org/published/workflow?id=28c7e8269d478244, https://usegalaxy.org/published/workflow?id=634bbef1f67a0e30, https://workflowhub.eu/workflows/249?version=4 |
|
|
biotransformer |
biotransformer |
BioTransformer is a tool for prediction of small molecule metabolism in mammals. |
2020-08-26 |
https://bitbucket.org/djoumbou/biotransformerjar/src/master/ |
3.0.20230403 |
biotransformer |
3.0.20230403 |
Up-to-date |
Metabolomics |
Metabolic pathway prediction, PTM site prediction, Natural product identification |
Metabolic pathway prediction, PTM site prediction, Natural product identification |
Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR |
Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR |
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer |
https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer |
biotransformer |
BioTransformer |
BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
1 |
1 |
92 |
92 |
1 |
1 |
2 |
2 |
95 |
95 |
3 |
3 |
|
|
|
blast2go |
blast2go |
Maps BLAST results to GO annotation terms |
2013-09-23 |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go |
0.0.11 |
b2g4pipe |
|
To update |
Ontology Manipulation, Sequence Analysis |
Gene functional annotation |
Gene functional annotation |
Nucleic acid sites, features and motifs |
Nucleic acid sites, features and motifs |
peterjc |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go |
Blast2GO |
Blast2GO |
Bioinformatics platform for high-quality functional annotation and analysis of genomic datasets. It allows analyzing and visualizing newly sequenced genomes by combining state-of-the-art methodologies, standard resources and algorithms. It allows to gain biological insights fast and easy even for completely novel genomes. Perform out-of-the-box the entire workflow of functional annotation of your transcriptomic datasets including its analysis and biological interpretation. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
205 |
303 |
851 |
1255 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
10 |
1265 |
851 |
304 |
205 |
https://usegalaxy.eu/published/workflow?id=33312e5643279e8a |
|
|
blast_plus_remote_blastp |
blast_plus_remote_blastp |
NCBI BLAST+ with -remote option |
2015-01-24 |
https://blast.ncbi.nlm.nih.gov/ |
2.6.0 |
blast |
2.17.0 |
To update |
Sequence Analysis |
|
|
|
|
galaxyp |
https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
blast_rbh |
blast_reciprocal_best_hits |
BLAST Reciprocal Best Hits (RBH) from two FASTA files |
2014-05-15 |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh |
0.3.0 |
biopython |
1.70 |
To update |
Fasta Manipulation, Sequence Analysis |
Gene functional annotation, Nucleic acid sequence analysis |
Gene functional annotation, Nucleic acid sequence analysis |
Nucleic acid sites, features and motifs |
Nucleic acid sites, features and motifs |
peterjc |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh |
blast_rbh |
blast_rbh |
This tool is a short Python script to run reciprocal BLAST searches on a pair of sequence files, and extract the reciprocal best hits. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
413 |
502 |
25833 |
37031 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
37031 |
25833 |
502 |
413 |
https://usegalaxy.eu/published/workflow?id=7f6950394a8c9c4a |
|
|
blast_to_scaffold |
blast2scaffold |
Generate DNA scaffold from blastn or tblastx alignments of Contigs |
2016-01-05 |
http://artbio.fr |
1.1.0 |
python |
|
To update |
RNA, Sequence Analysis, Assembly |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold |
https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
0 |
1 |
0 |
|
|
|
blast_unmatched |
blast_unmatched |
Extract unmatched query sequences from blast |
2017-10-03 |
http://artbio.fr |
1.0.1 |
python |
|
To update |
Fasta Manipulation |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched |
https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
blastparser_and_hits |
BlastParser_and_hits |
Parse blast outputs and compile hits |
2017-10-15 |
http://artbio.fr |
2.7.1 |
python |
|
To update |
Assembly, RNA |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits |
https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
0 |
1 |
0 |
|
|
|
blastx_to_scaffold |
blastx2scaffold |
Generate DNA scaffold from blastx alignment of Contigs |
2015-06-17 |
http://artbio.fr |
1.1.1 |
python |
|
To update |
RNA, Sequence Analysis, Assembly |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold |
https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
blastxml_to_top_descr |
blastxml_to_top_descr |
Make table of top BLAST match descriptions |
2013-09-23 |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr |
0.1.2 |
python |
|
To update |
Convert Formats, Sequence Analysis, Text Manipulation |
Sequence alignment, Sequence annotation |
Sequence alignment, Sequence annotation |
Sequence analysis |
Sequence analysis |
peterjc |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr |
https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr |
blastxml_to_top_descr |
blastxml_to_top_descr |
This tool is a short Python script to parse a BLAST XML file, and extract the identifiers with description for the top matches (by default the top 3), and output these as a simple tabular file along with the query identifiers. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
530 |
653 |
263613 |
265902 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
265902 |
263613 |
653 |
530 |
https://usegalaxy.eu/published/workflow?id=33312e5643279e8a, https://usegalaxy.eu/published/workflow?id=8f747dbff3216993, https://usegalaxy.eu/published/workflow?id=bebcbd6f0ffa55c5, https://usegalaxy.eu/published/workflow?id=e14b81a8c0b1b7a4 |
|
|
bumbershoot |
idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch |
|
2015-08-28 |
http://proteowizard.sourceforge.net/ |
3.0.21142 |
bumbershoot |
3_0_21142_0e4f4a4 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot |
|
|
|
|
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
14 |
22 |
158 |
1474 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1474 |
158 |
22 |
14 |
|
|
|
c3s |
c3s |
Copernicus Climate Change Service (C3S) |
2021-04-13 |
https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset |
0.3.0 |
python |
|
To update |
Climate Analysis |
|
|
|
|
climate |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
17 |
17 |
422 |
422 |
7 |
7 |
10 |
10 |
3 |
3 |
139 |
139 |
0 |
0 |
0 |
0 |
571 |
571 |
27 |
27 |
https://usegalaxy.eu/published/workflow?id=21363a774a7575f0, https://usegalaxy.eu/published/workflow?id=ac5b66c42681e7a8, https://usegalaxy.eu/published/workflow?id=b610849d70c1e225, https://usegalaxy.eu/published/workflow?id=ddb21f7793eff83d, https://workflowhub.eu/workflows/1625?version=1 |
climate/earth_system, contributing/create-new-tutorial |
|
cads |
cads |
Copernicus Atmosphere Data Store (ADS) |
2021-06-19 |
https://ads.atmosphere.copernicus.eu/#!/home |
0.1.0 |
python |
|
To update |
Climate Analysis |
|
|
|
|
climate |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
1 |
52 |
52 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
52 |
52 |
1 |
1 |
|
|
|
calisp |
calisp |
Calgary approach to isotopes in proteomics |
2023-06-01 |
https://github.com/kinestetika/Calisp/ |
3.0.13 |
calisp |
3.1.4 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
4 |
4 |
507 |
507 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
507 |
507 |
4 |
4 |
|
|
|
cap3 |
cap3 |
cap3 wrapper |
2017-09-02 |
http://artbio.fr |
2.0.1 |
cap3 |
10.2011 |
To update |
Assembly |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 |
https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
301 |
301 |
12523 |
12523 |
0 |
0 |
0 |
0 |
173 |
173 |
7922 |
7922 |
0 |
0 |
0 |
0 |
20445 |
20445 |
474 |
474 |
https://usegalaxy.eu/published/workflow?id=98bfad0c684011e9, https://usegalaxy.eu/published/workflow?id=ab646c6ab6de7061, https://usegalaxy.org.au/published/workflow?id=94c7fdcbbc7b428a, https://usegalaxy.org.au/published/workflow?id=dccc8fb49d61ac33 |
|
|
cardinal |
cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots |
Statistical and computational tools for analyzing mass spectrometry imaging datasets |
2018-10-01 |
http://cardinalmsi.org |
3.4.3 |
bioconductor-cardinal |
3.8.0 |
To update |
Proteomics, Metabolomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal |
|
|
|
|
0 |
9 |
11 |
11 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
11 |
9 |
156 |
193 |
30686 |
51576 |
1 |
1 |
12 |
12 |
67 |
69 |
8886 |
9794 |
26 |
26 |
132 |
132 |
61514 |
39716 |
289 |
250 |
https://usegalaxy.eu/published/workflow?id=03e8b0d3dcedc092, https://usegalaxy.eu/published/workflow?id=785433e42d82be65, https://usegalaxy.eu/published/workflow?id=7ee6976f69131683, https://usegalaxy.eu/published/workflow?id=9e497c5c9e64d9b3, https://usegalaxy.eu/published/workflow?id=a5ca8b9807ed3f73, https://usegalaxy.eu/published/workflow?id=f4a55ef0d4c2cd97, https://usegalaxy.eu/published/workflow?id=fb233e418d015649, https://usegalaxy.org.au/published/workflow?id=04f6ad62f34313ea, https://usegalaxy.org.au/published/workflow?id=3678781bf7619a89, https://usegalaxy.org.au/published/workflow?id=80cf8be8c8bf384a, https://workflowhub.eu/workflows/1455?version=1, https://workflowhub.eu/workflows/1587?version=1, https://workflowhub.eu/workflows/1593?version=1 |
metabolomics/msi-analyte-distribution, metabolomics/msi-finding-nglycans, proteomics/mass-spectrometry-imaging-loading-exploring-data |
|
cdo |
cdo_info, cdo_operations |
CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available. |
2021-09-01 |
https://code.mpimet.mpg.de/projects/cdo/ |
2.0.0 |
|
|
To update |
Climate Analysis |
|
|
|
|
climate |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
14 |
14 |
228 |
228 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
228 |
228 |
14 |
14 |
https://usegalaxy.eu/published/workflow?id=4f0f3b911b4e4921, https://usegalaxy.eu/published/workflow?id=6afc245029ce5008, https://usegalaxy.eu/published/workflow?id=b4bfcbf8acee9cc3, https://usegalaxy.eu/published/workflow?id=d94460f342b70eb3, https://workflowhub.eu/workflows/1652?version=1 |
ecology/x-array-map-plot |
|
cds_essential_variability |
cds_essential_variability |
Get Copernicus Essential Climate Variables for assessing climate variability |
2019-05-03 |
https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview |
0.2.0 |
python |
|
To update |
Climate Analysis, Data Source |
|
|
|
|
climate |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
33 |
45 |
126 |
355 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
355 |
126 |
45 |
33 |
https://usegalaxy.eu/published/workflow?id=392a5d91ac221104, https://usegalaxy.eu/published/workflow?id=f774cf05ddff3612, https://workflowhub.eu/workflows/1441?version=1 |
climate/climate-101 |
|
cesm |
cesm |
Community Earth System Model (CESM) |
2021-06-15 |
https://www.cesm.ucar.edu/ |
2.1.3 |
cesm |
2.1.3 |
Up-to-date |
Climate Analysis |
|
|
|
|
climate |
https://github.com/ESCOMP/CESM |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
2 |
2 |
14 |
14 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
14 |
14 |
2 |
2 |
https://usegalaxy.eu/published/workflow?id=46b4ad3ce0b7bc0b |
|
|
champ_blocs |
cb_dissim, cb_ivr, cb_div |
Compute indicators for turnover boulders fields |
2022-10-28 |
|
0.0.0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/Marie59/champ_blocs |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs |
|
|
|
|
0 |
0 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
9 |
9 |
216 |
216 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
11 |
11 |
227 |
227 |
11 |
11 |
https://usegalaxy.eu/published/workflow?id=a3ad27817f77061b, https://workflowhub.eu/workflows/1690?version=1, https://workflowhub.eu/workflows/661?version=1 |
ecology/champs-blocs |
|
checkv |
checkv_end_to_end |
Assess quality of single-contig viral genomes |
2024-09-13 |
https://bitbucket.org/berkeleylab/checkv/ |
1.0.3 |
checkv |
1.0.3 |
Up-to-date |
Metagenomics |
Sequence assembly, Validation, Read mapping |
Sequence assembly, Validation, Read mapping |
Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping |
Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping |
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv |
checkv |
CheckV |
CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
83 |
83 |
4527 |
4527 |
1 |
1 |
21 |
21 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4548 |
4548 |
84 |
84 |
https://usegalaxy.eu/published/workflow?id=36de05d50c703164, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95 |
|
|
cherry_pick_fasta |
cherry_pick_fasta |
Pick fasta sequence with specific header content |
2015-06-17 |
http://artbio.fr |
4.1 |
python |
|
To update |
Fasta Manipulation |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta |
https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
1 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
climate_stripes |
climate_stripes |
Create climate stripes from a tabular input file |
2019-10-05 |
https://www.climate-lab-book.ac.uk/2018/warming-stripes/ |
1.0.2 |
python |
|
To update |
Climate Analysis, Visualization |
|
|
|
|
climate |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
31 |
40 |
183 |
278 |
5 |
5 |
22 |
22 |
3 |
3 |
276 |
276 |
0 |
0 |
0 |
0 |
576 |
481 |
48 |
39 |
https://usegalaxy.eu/published/workflow?id=0c6dd9e75d9a2130, https://usegalaxy.eu/published/workflow?id=392a5d91ac221104, https://workflowhub.eu/workflows/123?version=1, https://workflowhub.eu/workflows/1432?version=1, https://workflowhub.eu/workflows/1441?version=1 |
climate/climate-101, climate/pangeo |
|
concatenate_multiple_datasets |
cat_multi_datasets |
Concatenate multiple datasets tail-to-head, including collection datasets. |
2018-03-11 |
http://artbio.fr |
1.4.3 |
|
|
To update |
Text Manipulation |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets |
https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
995 |
996 |
11863 |
11865 |
511 |
512 |
3329 |
3331 |
246 |
332 |
2968 |
4431 |
1 |
1 |
3 |
3 |
19630 |
18163 |
1841 |
1753 |
https://usegalaxy.eu/published/workflow?id=00f15824c7a9b196, https://usegalaxy.eu/published/workflow?id=03ef267ff7634a4b, https://usegalaxy.eu/published/workflow?id=18af9bbae833f8fe, https://usegalaxy.eu/published/workflow?id=373d861ef4b0081a, https://usegalaxy.eu/published/workflow?id=43098b8afe78b071, https://usegalaxy.eu/published/workflow?id=6aaf2b342d57f78d, https://usegalaxy.eu/published/workflow?id=7bda7ae31c427347, https://usegalaxy.eu/published/workflow?id=7cbda24fd0767899, https://usegalaxy.eu/published/workflow?id=82879b0eb4a71ad0, https://usegalaxy.eu/published/workflow?id=841367f185aaade4, https://usegalaxy.eu/published/workflow?id=8c6371b360217f72, https://usegalaxy.eu/published/workflow?id=b6457cb04bf31613, https://usegalaxy.eu/published/workflow?id=ce5c9287a67e6085, https://usegalaxy.eu/published/workflow?id=cf0159c14418525e, https://usegalaxy.eu/published/workflow?id=e4dabaf57668dbd1, https://usegalaxy.eu/published/workflow?id=e8a8c0b59ba9d593, https://usegalaxy.eu/published/workflow?id=ea3b120f105434ec, https://usegalaxy.org.au/published/workflow?id=869440d35a618836, https://usegalaxy.org.au/published/workflow?id=92fcdd490831c6c5, https://usegalaxy.org/published/workflow?id=2a4823c060dd216e, https://usegalaxy.org/published/workflow?id=31186e478383465b, https://usegalaxy.org/published/workflow?id=3511da8b41b1fb5d, https://usegalaxy.org/published/workflow?id=412da1489d6aed45, https://usegalaxy.org/published/workflow?id=46207bf9ce5ee26a, https://usegalaxy.org/published/workflow?id=4680511d4daad5d7, https://usegalaxy.org/published/workflow?id=4c996921fb6a2334, https://usegalaxy.org/published/workflow?id=696b2efc589afd6f, https://usegalaxy.org/published/workflow?id=7454015793c4adc9, https://usegalaxy.org/published/workflow?id=8b4945a0fb49e03e, https://usegalaxy.org/published/workflow?id=a97c694b3298ae44, https://usegalaxy.org/published/workflow?id=ac3755c1ae5f7f16, https://usegalaxy.org/published/workflow?id=af85a2ae187409f4, https://usegalaxy.org/published/workflow?id=b7c67632a6eabda5, https://usegalaxy.org/published/workflow?id=c7693951c6215e19, https://usegalaxy.org/published/workflow?id=d1ca40dd7e591025, https://usegalaxy.org/published/workflow?id=d485bf21a5069fe4, https://workflowhub.eu/workflows/1189?version=2, https://workflowhub.eu/workflows/1407?version=1, https://workflowhub.eu/workflows/233?version=1, https://workflowhub.eu/workflows/622?version=11 |
proteomics/proteogenomics-dbcreation |
|
consalign |
aligned_to_consensus |
Tool to compute a consensus sequence from several aligned fasta sequences |
2023-04-11 |
|
1.0.0 |
r-bioseq |
|
To update |
Sequence Analysis |
|
|
|
|
ecology |
https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
283 |
283 |
2617 |
2617 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
16 |
4351 |
4351 |
6968 |
6968 |
299 |
299 |
https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1 |
sequence-analysis/Manage_AB1_Sanger |
|
consolidate_vcfs |
consolidate_vcfs |
Combines freebayes and mpileup files for use by vcf2snvalignment |
2015-11-05 |
https://snvphyl.readthedocs.io/en/latest/ |
1.8.2 |
snvphyl-tools |
1.8.2 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/snvphyl-galaxy |
https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
cooler |
cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify |
cooler different tools to process Hi-C from mirnylab |
2017-07-27 |
https://github.com/open2c/cooler |
0.9.3 |
htslib |
1.22.1 |
To update |
Epigenetics |
|
|
|
|
lldelisle |
https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler |
|
|
|
|
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
32 |
32 |
475 |
475 |
40 |
40 |
276 |
276 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
751 |
751 |
72 |
72 |
https://usegalaxy.eu/published/workflow?id=1214523f54a999fc, https://usegalaxy.eu/published/workflow?id=2a9c812f59b7b36c, https://usegalaxy.eu/published/workflow?id=4464d3b0fc782a1a, https://usegalaxy.eu/published/workflow?id=506a451679fe25b4, https://usegalaxy.eu/published/workflow?id=72201ffaf488f278, https://usegalaxy.eu/published/workflow?id=9843ae66c3b367b7, https://usegalaxy.eu/published/workflow?id=9f8a93cfffb31cd6, https://usegalaxy.eu/published/workflow?id=9fc8b89954c04ee1, https://usegalaxy.eu/published/workflow?id=ceb0a029c6d33ec6, https://usegalaxy.eu/published/workflow?id=d9fc0df2a159e542, https://usegalaxy.eu/published/workflow?id=f394d1b12779ba41, https://usegalaxy.eu/published/workflow?id=fc4e3479d86f9a26, https://usegalaxy.org/published/workflow?id=06eaa5b141fe7a08, https://usegalaxy.org/published/workflow?id=0bc1b8888d8b20c4, https://usegalaxy.org/published/workflow?id=1dc312e3fba9f810, https://usegalaxy.org/published/workflow?id=1e4eb6ccb47d9fc7, https://usegalaxy.org/published/workflow?id=4998f171ec922c7d, https://usegalaxy.org/published/workflow?id=7353afb9301780e5, https://usegalaxy.org/published/workflow?id=a93eb877596ce0ef, https://usegalaxy.org/published/workflow?id=b31ab9e76409a9b7, https://usegalaxy.org/published/workflow?id=c8a92318855d85a5, https://usegalaxy.org/published/workflow?id=f13432eef7ac28e9, https://usegalaxy.org/published/workflow?id=f21d576695f9fe77, https://usegalaxy.org/published/workflow?id=f80b80aa7fb196ba, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/420?version=3 |
|
|
cpm_tpm_rpk |
cpm_tpm_rpk |
Generate CPM,TPM or RPK from raw counts |
2018-07-11 |
http://artbio.fr |
0.6.0 |
r-optparse |
1.3.2 |
To update |
Transcriptomics |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk |
https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
crbeam_astro_tool |
crbeam_astro_tool |
CRbeam |
2024-01-31 |
|
0.0.2+galaxy0 |
crbeam |
|
To update |
Astronomy |
|
|
|
|
astroteam |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/crbeam |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
https://workflowhub.eu/workflows/1369?version=1 |
|
|
cta_astro_tool |
cta_astro_tool |
Basic simulation of CTA telescope observations using gammapy package |
2024-04-19 |
|
0.0.1+galaxy0 |
unzip |
|
To update |
Astronomy |
|
|
|
|
astroteam |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
1 |
1 |
|
|
|
ctsm_fates |
ctsm_fates |
EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model |
2020-10-21 |
https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api |
2.0 |
fates-emerald |
|
To update |
Climate Analysis |
|
|
|
|
climate |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
71 |
71 |
275 |
275 |
12 |
12 |
35 |
35 |
1 |
1 |
150 |
150 |
0 |
0 |
0 |
0 |
460 |
460 |
84 |
84 |
https://usegalaxy.eu/published/workflow?id=7b50e72deb46c6e8, https://workflowhub.eu/workflows/1427?version=1 |
climate/fates |
|
custom_pro_db |
custom_pro_db |
CustomProDB |
2017-10-06 |
https://bioconductor.org/packages/release/bioc/html/customProDB.html |
1.22.0 |
bioconductor-rgalaxy |
1.37.1 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
196 |
208 |
1876 |
1998 |
88 |
88 |
493 |
493 |
23 |
23 |
530 |
530 |
1 |
1 |
1 |
1 |
3022 |
2900 |
320 |
308 |
https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2, https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d, https://usegalaxy.eu/published/workflow?id=c3f2350f0be2d9c9, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=e336bca259abd474, https://workflowhub.eu/workflows/1407?version=1, https://workflowhub.eu/workflows/1437?version=1, https://workflowhub.eu/workflows/1788?version=1 |
proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation |
|
custom_pro_db_annotation_data_manager |
|
CustomProDB Annotation |
2017-10-06 |
https://bioconductor.org/packages/release/bioc/html/customProDB.html |
|
|
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
data_exploration |
tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs |
Explore data through multiple statistical tools |
2021-06-23 |
|
0.0.0 |
r-tangles |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/Marie59/Data_explo_tools |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration |
|
|
|
|
0 |
0 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
0 |
122 |
122 |
1286 |
1286 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
44 |
44 |
1330 |
1330 |
128 |
128 |
https://usegalaxy.eu/published/workflow?id=7b576a562031ff7e, https://usegalaxy.eu/published/workflow?id=a0404f6291874c01, https://workflowhub.eu/workflows/1693?version=1, https://workflowhub.eu/workflows/656?version=1 |
ecology/biodiversity-data-exploration |
|
data_manager_eggnog_mapper |
|
downloads eggnog data for eggnog-mapper |
2019-11-11 |
|
|
|
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
data_manager_eggnog_mapper_abspath |
|
download eggnog data for eggnog-mapper |
2019-11-11 |
|
|
|
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
dbbuilder |
dbbuilder |
Protein Database Downloader |
2015-01-24 |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder |
0.3.4 |
wget |
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
997 |
1171 |
6303 |
7599 |
38 |
38 |
180 |
180 |
104 |
109 |
1413 |
1423 |
12 |
13 |
25 |
27 |
9229 |
7921 |
1331 |
1151 |
https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=5374daf356516a40, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=71816adecac46e74, https://usegalaxy.eu/published/workflow?id=73dc2384535bf6af, https://usegalaxy.eu/published/workflow?id=7dd7908f4c8d722a, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=9e0d784860d6cc91, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=afb138fc03ca61a8, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f, https://usegalaxy.eu/published/workflow?id=cb9a26ea53ce7a27, https://usegalaxy.eu/published/workflow?id=d2a9d4eb5b3c72a2, https://usegalaxy.eu/published/workflow?id=d55df785d4c71876, https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=eeb6cff210cac091, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.eu/published/workflow?id=f2b45a7ff4f449e6, https://usegalaxy.org.au/published/workflow?id=65a659982f955743, https://usegalaxy.org.au/published/workflow?id=7cddb345877f08bf, https://usegalaxy.org.au/published/workflow?id=9281258aefd17c0c, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org/published/workflow?id=42331381df05b956, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1218?version=1, https://workflowhub.eu/workflows/1225?version=1, https://workflowhub.eu/workflows/1396?version=1, https://workflowhub.eu/workflows/1425?version=1, https://workflowhub.eu/workflows/1434?version=1, https://workflowhub.eu/workflows/1435?version=1, https://workflowhub.eu/workflows/1438?version=1, https://workflowhub.eu/workflows/1464?version=1 |
microbiome/clinical-mp-1-database-generation, microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-3-verification, proteomics/clinical-mp-1-database-generation, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-3-verification, proteomics/database-handling |
|
decoyfasta |
|
Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool. |
2015-01-24 |
|
|
|
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
deseq2_normalization |
deseq2_normalization |
Normalizes gene hitlists |
2018-01-05 |
http://artbio.fr |
1.40.2+galaxy1 |
bioconductor-deseq2 |
1.46.0 |
To update |
Transcriptomics, Statistics, Single Cell |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization |
https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
desi_legacy_survey_astro_tool |
desi_legacy_survey_astro_tool |
Tool to query Legacy Survey data |
2024-11-14 |
|
0.0.2+galaxy0 |
astropy |
|
To update |
Astronomy |
|
|
|
|
astroteam |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/desi-legacy-survey |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
2 |
2 |
https://usegalaxy.eu/published/workflow?id=bc78c184fabcff1d, https://usegalaxy.eu/published/workflow?id=f9ae5a312e84cf0a, https://workflowhub.eu/workflows/1353?version=2, https://workflowhub.eu/workflows/1730?version=1 |
|
|
dfast |
dfast |
Prokaryotic genome annotation |
2025-04-16 |
https://github.com/nigyta/dfast_core/ |
1.3.6 |
dfast |
1.3.7 |
To update |
Genome annotation |
Genome annotation |
Genome annotation |
Nucleic acid structure analysis, Genomics, Sequence analysis |
Nucleic acid structure analysis, Genomics, Sequence analysis |
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/dfast/ |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/dfast |
dfast |
DFAST |
Flexible prokaryotic genome annotation pipeline for faster genome publication. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
dfpl |
dfpl_predict, dfpl_train |
Galaxy wrapper for deepFPlearn. |
2024-12-18 |
https://github.com/yigbt/deepFPlearn |
2.1 |
deepfplearn |
2.1 |
Up-to-date |
Computational chemistry, Machine Learning |
|
|
|
|
ufz |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/dfpl |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/dfpl |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
dia_umpire |
dia_umpire_se |
DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics |
2015-08-26 |
http://diaumpire.sourceforge.net/ |
2.1.3 |
dia_umpire |
2.1.6 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
4 |
7 |
33 |
0 |
0 |
0 |
0 |
5 |
5 |
177 |
187 |
0 |
0 |
0 |
0 |
220 |
184 |
9 |
7 |
|
|
|
dialignr |
dialignr |
DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. |
2020-12-23 |
https://github.com/shubham1637/DIAlignR |
1.2.0 |
bioconductor-dialignr |
2.10.0 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
2 |
2 |
40 |
40 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
40 |
40 |
2 |
2 |
|
|
|
diann |
diann |
DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. |
2023-06-26 |
https://github.com/vdemichev/DiaNN |
1.8.1 |
|
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/vdemichev/DiaNN |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
31 |
31 |
181 |
181 |
0 |
0 |
0 |
0 |
29 |
29 |
333 |
333 |
0 |
0 |
0 |
0 |
514 |
514 |
60 |
60 |
|
|
|
diapysef |
diapysef |
diapysef is a convenience package for working with DIA-PASEF data |
2020-02-27 |
https://pypi.org/project/diapysef/ |
0.3.5.0 |
diapysef |
1.0.10 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
47 |
49 |
175 |
284 |
0 |
0 |
0 |
0 |
6 |
6 |
391 |
391 |
0 |
0 |
0 |
0 |
675 |
566 |
55 |
53 |
https://workflowhub.eu/workflows/1421?version=1 |
proteomics/DIA_lib_OSW |
|
diffacto |
diffacto |
Diffacto comparative protein abundance estimation |
2021-06-20 |
https://github.com/statisticalbiotechnology/diffacto |
1.0.6 |
diffacto |
1.0.7 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
9 |
9 |
13 |
13 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
13 |
13 |
9 |
9 |
|
|
|
digestdb |
digestdb |
|
2015-01-24 |
|
0.1.0 |
trans_proteomic_pipeline |
|
To update |
|
|
|
|
|
galaxyp |
|
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
directag_and_tagrecon |
|
|
2015-01-24 |
|
|
|
|
To update |
|
|
|
|
|
galaxyp |
|
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
dose_response_analysis_tool |
dr_curve |
A tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses |
2024-04-06 |
https://github.com/bernt-matthias/mb-galaxy-tools |
3.0.1 |
r-drc |
3.0_1 |
To update |
Ecology |
|
|
|
|
ufz |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
droplet_barcode_plot |
_dropletBarcodePlot |
Make a cell barcode plot for droplet single-cell RNA-seq QC |
2019-11-07 |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary |
1.6.1+galaxy2 |
scxa-plots |
0.0.1 |
To update |
Sequence Analysis |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
236 |
247 |
1326 |
1440 |
88 |
89 |
379 |
383 |
3 |
3 |
51 |
51 |
1 |
1 |
4 |
4 |
1878 |
1760 |
340 |
328 |
https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=9a9bbd8046da7b19, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d, https://workflowhub.eu/workflows/1533?version=1, https://workflowhub.eu/workflows/1537?version=1 |
single-cell/scrna-case_alevin |
|
earth |
landcover_subindicator |
Access, process, visualise oceanographic data for the Earth System |
2024-10-21 |
https://github.com/Marie59/FE-ft-ESG/tree/main/earth |
0.1.0 |
numpy |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
1 |
1 |
|
|
|
ecoregionalization |
ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ClaraGuess, ecoregion_clara_cluster, ecoregion_eco_map, indicspecies, ecoregion_taxa_seeker |
Tools to compute ecoregionalization with BRT model predictions and clustering. |
2023-07-26 |
https://github.com/PaulineSGN/Workflow_Galaxy |
0.1.2+galaxy0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow |
|
|
|
|
0 |
0 |
8 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
0 |
13 |
13 |
987 |
987 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
987 |
987 |
13 |
13 |
https://usegalaxy.eu/published/workflow?id=749bb05ec8674bec, https://usegalaxy.eu/published/workflow?id=89ff2a1143954d83, https://usegalaxy.eu/published/workflow?id=b727b64f37238fff, https://usegalaxy.eu/published/workflow?id=c5de0b794849e1b1, https://workflowhub.eu/workflows/1208?version=1, https://workflowhub.eu/workflows/1209?version=1, https://workflowhub.eu/workflows/1680?version=1, https://workflowhub.eu/workflows/658?version=1 |
ecology/Ecoregionalization_tutorial, ecology/ecoregiolifetraits |
|
eggnog_mapper |
eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search |
eggnog-mapper fast functional annotation of novel sequences |
2019-11-11 |
|
2.1.8 |
eggnog-mapper |
2.1.13 |
To update |
Proteomics |
Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval |
Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval |
Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis |
Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper |
eggnog-mapper-v2 |
eggNOG-mapper v2 |
EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. |
|
0 |
3 |
3 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
1 |
3 |
3 |
1977 |
2018 |
64994 |
65580 |
518 |
518 |
9634 |
9634 |
541 |
541 |
25986 |
25986 |
144 |
144 |
66224 |
66224 |
167424 |
166838 |
3221 |
3180 |
https://usegalaxy.cz/published/workflow?id=932f4901960a595a, https://usegalaxy.eu/published/workflow?id=2d2862b48918b22f, https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=c5e6047b3b256b06, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://usegalaxy.org.au/published/workflow?id=35f39173f0ac9179, https://usegalaxy.org.au/published/workflow?id=4e161a8f5098cc49, https://usegalaxy.org.au/published/workflow?id=876163677f1cccc4, https://usegalaxy.org/published/workflow?id=92613e1e0b13aa0a, https://workflowhub.eu/workflows/1262?version=1, https://workflowhub.eu/workflows/1521?version=1, https://workflowhub.eu/workflows/1525?version=1, https://workflowhub.eu/workflows/754?version=1, https://workflowhub.eu/workflows/755?version=1 |
genome-annotation/funannotate, genome-annotation/functional |
|
embl2fa |
embl2fa |
Converts EMBL flat format to fasta format |
2022-11-12 |
http://artbio.fr |
0.2 |
|
|
To update |
Text Manipulation |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa |
https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
emlassemblyline |
annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template |
Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa |
2023-07-21 |
https://github.com/EDIorg/EMLassemblyline |
0.1.0+galaxy0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline |
|
|
|
|
0 |
0 |
11 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
40 |
40 |
646 |
646 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
648 |
648 |
41 |
41 |
https://usegalaxy.eu/published/workflow?id=a30d511e3dda0895, https://usegalaxy.eu/published/workflow?id=ab89c61db3d7abbb |
|
|
encyclopedia |
encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut |
Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis |
2020-09-11 |
https://bitbucket.org/searleb/encyclopedia/wiki/Home |
1.12.34 |
encyclopedia |
2.12.30 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia |
|
|
|
|
0 |
4 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
0 |
34 |
34 |
893 |
893 |
3 |
3 |
42 |
42 |
7 |
7 |
58 |
58 |
0 |
0 |
0 |
0 |
993 |
993 |
44 |
44 |
https://usegalaxy.eu/published/workflow?id=14f9c2099db30570, https://usegalaxy.eu/published/workflow?id=3676aafc35dc2fe7, https://usegalaxy.eu/published/workflow?id=5d4e4b9f07a1ec20, https://usegalaxy.eu/published/workflow?id=5dec0e5a2d75cdc1, https://usegalaxy.eu/published/workflow?id=6d494e2f634eba70, https://usegalaxy.eu/published/workflow?id=87c21b682af78ec9, https://usegalaxy.eu/published/workflow?id=9ac15b644c805a2b, https://usegalaxy.eu/published/workflow?id=f1309010689eb98a, https://workflowhub.eu/workflows/1471?version=1 |
proteomics/encyclopedia |
|
eodie |
eodie |
Earth Observation Data Information Extractor |
2021-12-30 |
https://eodie.readthedocs.io/ |
1.0.2 |
eodie |
|
To update |
Climate Analysis |
|
|
|
|
climate |
https://gitlab.com/eetun-tiimi/EODIE |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
4 |
4 |
45 |
45 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
45 |
45 |
4 |
4 |
|
|
|
eukcc |
eukcc_single |
Galaxy wrapper for EukCC |
2025-07-25 |
https://github.com/EBI-Metagenomics/EukCC |
2.1.3 |
eukcc |
2.1.3 |
Up-to-date |
Metagenomics |
Sequence assembly validation |
Sequence assembly validation |
Metagenomics |
Metagenomics |
ufz |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/eukcc |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/eukcc |
eukcc |
EukCC |
EukCC is a completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
ez_histograms |
ez_histograms |
ggplot2 histograms and density plots |
2024-02-07 |
https://github.com/tidyverse/ggplot2 |
3.4.4 |
r-ggplot2 |
2.2.1 |
To update |
Visualization, Statistics |
Data analysis, Statistical calculation, Visualisation |
Statistical calculation, Visualisation |
Ecology |
Ecology |
artbio |
https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms |
https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms |
ez_histograms |
ez_histograms |
This tool produces histograms or density plots from any tabular datasets, using ggplot2.You may provide headerless tables as well as tables with column headers. Any non-numeric columns will be filtered out. Your first column may contains row names, but it will also work if your first column already corresponds to the numeric values of a variable. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
fasta_merge_files_and_filter_unique_sequences |
fasta_merge_files_and_filter_unique_sequences |
Concatenate FASTA database files together |
2015-01-24 |
https://github.com/galaxyproteomics/tools-galaxyp/ |
1.2.0 |
python |
|
To update |
Fasta Manipulation |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1552 |
1771 |
35725 |
38519 |
1724 |
1724 |
42712 |
42712 |
289 |
306 |
5517 |
6718 |
32 |
33 |
400 |
402 |
88351 |
84354 |
3834 |
3597 |
https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=1809fcaec264eac9, https://usegalaxy.eu/published/workflow?id=1860e02bcb894a64, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=2f7e13eb26c8cd18, https://usegalaxy.eu/published/workflow?id=3081569659a45b9e, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=3fe4aa24e80e35c1, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=4c81726bde25c36a, https://usegalaxy.eu/published/workflow?id=5374daf356516a40, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=71816adecac46e74, https://usegalaxy.eu/published/workflow?id=73dc2384535bf6af, https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3, https://usegalaxy.eu/published/workflow?id=7dd7908f4c8d722a, https://usegalaxy.eu/published/workflow?id=7e05f46acdfb81c4, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=8ef3379dded2490a, https://usegalaxy.eu/published/workflow?id=90f993a1b245eb68, 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https://usegalaxy.eu/published/workflow?id=d55df785d4c71876, https://usegalaxy.eu/published/workflow?id=d5756e3ebfa285ef, https://usegalaxy.eu/published/workflow?id=d7c7a4d6c8072167, https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=eeb6cff210cac091, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.eu/published/workflow?id=f2b45a7ff4f449e6, https://usegalaxy.eu/published/workflow?id=f6a763951d815944, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=3242ec69dec6e13f, https://usegalaxy.org.au/published/workflow?id=351f3fab960c013b, https://usegalaxy.org.au/published/workflow?id=65a659982f955743, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org.au/published/workflow?id=7cddb345877f08bf, https://usegalaxy.org.au/published/workflow?id=9281258aefd17c0c, https://usegalaxy.org.au/published/workflow?id=9365a7de314c9f85, https://usegalaxy.org.au/published/workflow?id=b60922a253df6654, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org.au/published/workflow?id=eda40b58616a0fe4, https://usegalaxy.org/published/workflow?id=2be8ecd5922d23d1, https://usegalaxy.org/published/workflow?id=2d3063882d8239ff, https://usegalaxy.org/published/workflow?id=3ef08553982f6ffc, https://usegalaxy.org/published/workflow?id=42331381df05b956, https://usegalaxy.org/published/workflow?id=48dafc35989f13b1, https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95, https://usegalaxy.org/published/workflow?id=63adc811e3ae529d, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=93810012f2610de4, https://usegalaxy.org/published/workflow?id=e336bca259abd474, https://usegalaxy.org/published/workflow?id=e3a30c0583183c1e, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/100?version=1, https://workflowhub.eu/workflows/102?version=1, https://workflowhub.eu/workflows/1060?version=1, https://workflowhub.eu/workflows/1216?version=1, https://workflowhub.eu/workflows/1218?version=1, https://workflowhub.eu/workflows/1225?version=1, https://workflowhub.eu/workflows/1396?version=1, https://workflowhub.eu/workflows/1407?version=1, https://workflowhub.eu/workflows/1410?version=1, https://workflowhub.eu/workflows/1425?version=1, https://workflowhub.eu/workflows/1434?version=1, https://workflowhub.eu/workflows/1435?version=1, https://workflowhub.eu/workflows/1437?version=1, https://workflowhub.eu/workflows/1438?version=1, https://workflowhub.eu/workflows/1461?version=1, https://workflowhub.eu/workflows/1464?version=1, https://workflowhub.eu/workflows/1474?version=1, https://workflowhub.eu/workflows/1487?version=2, https://workflowhub.eu/workflows/1788?version=1, https://workflowhub.eu/workflows/1793?version=1, https://workflowhub.eu/workflows/1839?version=1 |
microbiome/clinical-mp-1-database-generation, microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-3-verification, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/clinical-mp-1-database-generation, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-3-verification, proteomics/database-handling, proteomics/neoantigen-fragpipe-discovery, proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation |
|
fastg2protlib |
fastg2protlib-peptides, fastg2protlib-validate |
Generate FASTA from FASTG |
2020-07-23 |
https://github.com/galaxyproteomics/fastg2protlib.git |
1.0.2 |
|
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
7 |
7 |
31 |
31 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
31 |
31 |
7 |
7 |
|
|
|
fastq_pair |
fastq_pair |
Paired-end fastq pairer |
2022-03-17 |
https://github.com/linsalrob/fastq-pair |
1.0+galaxy0 |
fastq-pair |
1.0 |
To update |
Fastq Manipulation |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
fastq_quality_trimmer |
cshl_fastq_quality_trimmer |
FASTQ trimmer based on quality |
2022-03-11 |
https://github.com/agordon/fastx_toolkit |
0.0.14+galaxy0 |
fastx_toolkit |
0.0.14 |
To update |
Fastq Manipulation |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
fastq_utils |
fastq_filter_n, fastq_trim_poly_at |
Set of tools for handling fastq files |
2022-02-15 |
https://github.com/nunofonseca/fastq_utils |
0.25.1+galaxy0 |
fastq_utils |
0.25.3 |
To update |
Transcriptomics, RNA |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
feature_alignment |
feature_alignment |
TRIC integrates information from all available runs via a graph-based alignment strategy |
2015-02-06 |
|
0.11.0 |
msproteomicstools |
0.11.0 |
Up-to-date |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
2 |
2 |
19 |
19 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
19 |
19 |
2 |
2 |
|
|
|
fetch_fasta_from_ncbi |
retrieve_fasta_from_NCBI |
Fetch fasta sequences from NCBI using eutils wrappers |
2015-06-17 |
http://artbio.fr |
3.1.0 |
urllib3 |
1.12 |
To update |
Fasta Manipulation, Data Source |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi |
https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
4 |
5 |
0 |
2 |
0 |
|
|
|
filter_by_fasta_ids |
filter_by_fasta_ids |
Filter FASTA on the headers and/or the sequences |
2015-01-24 |
|
2.3 |
python |
|
To update |
Fasta Manipulation, Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1293 |
1457 |
109310 |
115300 |
1547 |
1547 |
53560 |
53560 |
301 |
301 |
12056 |
12056 |
54 |
54 |
483 |
483 |
181399 |
175409 |
3359 |
3195 |
https://usegalaxy.eu/published/workflow?id=02f240f6cf72080a, https://usegalaxy.eu/published/workflow?id=04a4dcac3fd922c5, https://usegalaxy.eu/published/workflow?id=1b38e0d69e366be1, https://usegalaxy.eu/published/workflow?id=21fc597d983f1194, https://usegalaxy.eu/published/workflow?id=2cec6a39cd496f09, https://usegalaxy.eu/published/workflow?id=2d2d0c2231babc50, https://usegalaxy.eu/published/workflow?id=4eb9dfe91fc2dc67, https://usegalaxy.eu/published/workflow?id=69e603a2da979c93, https://usegalaxy.eu/published/workflow?id=7dd7908f4c8d722a, https://usegalaxy.eu/published/workflow?id=82a60d94d699efbf, https://usegalaxy.eu/published/workflow?id=93d1035a307fe63d, https://usegalaxy.eu/published/workflow?id=972db4abc51bb3ab, https://usegalaxy.eu/published/workflow?id=afb138fc03ca61a8, https://usegalaxy.eu/published/workflow?id=b51559006f86db9e, https://usegalaxy.eu/published/workflow?id=b681f7b677b23168, https://usegalaxy.eu/published/workflow?id=d2a9d4eb5b3c72a2, https://usegalaxy.eu/published/workflow?id=d55df785d4c71876, https://usegalaxy.eu/published/workflow?id=df08e520ec3dbcb7, https://usegalaxy.fr/published/workflow?id=41264142d3c00016, https://usegalaxy.fr/published/workflow?id=8b1678200a1d157a, https://usegalaxy.org.au/published/workflow?id=fba0eb562a710733, https://usegalaxy.org/published/workflow?id=386d3b300cf05305, https://usegalaxy.org/published/workflow?id=3c7349268d74c576, https://usegalaxy.org/published/workflow?id=4884918895db9af0, https://usegalaxy.org/published/workflow?id=4b7e73bb7ac93c95, https://usegalaxy.org/published/workflow?id=505c826e8c99d7bf, https://usegalaxy.org/published/workflow?id=89d3c800d3be6050, https://usegalaxy.org/published/workflow?id=94da3d448bb8a137, https://usegalaxy.org/published/workflow?id=ec3cc032a90c44f1, https://workflowhub.eu/workflows/1630?version=1, https://workflowhub.eu/workflows/1635?version=1, https://workflowhub.eu/workflows/1650?version=1, https://workflowhub.eu/workflows/1717?version=2 |
sequence-analysis/Manage_AB1_Sanger, sequence-analysis/tapscan-streptophyte-algae, transcriptomics/mirna-target-finder |
|
filter_compounds |
filter_orgmet_anorg |
Tool for filtering organometallics/anorganic compounds from a list of compounds. |
2021-01-06 |
https://github.com/RECETOX/galaxytools/ |
3.1.1 |
openbabel |
2.3.90dev7d621d9 |
To update |
Metabolomics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds |
https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
filter_density |
filterdensity |
Filter out position based on distance between SNVs |
2015-11-19 |
https://snvphyl.readthedocs.io/en/latest/ |
1.8.2 |
snvphyl-tools |
1.8.2 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/snvphyl-galaxy |
https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
filter_stats |
filterstat |
SNVPhyl filter_stats |
2015-07-31 |
https://snvphyl.readthedocs.io/en/latest/ |
1.8.2 |
snvphyl-tools |
1.8.2 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/snvphyl-galaxy |
https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
filter_vcf |
filtervcf |
SNVPhyl filter_vcf |
2015-08-04 |
https://snvphyl.readthedocs.io/en/latest/ |
1.8.2 |
snvphyl-tools |
1.8.2 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/snvphyl-galaxy |
https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
find_repeats |
findrepeat |
Find repetitive regions on a reference genome using MUMMer |
2015-07-31 |
https://snvphyl.readthedocs.io/en/latest/ |
1.8.2 |
snvphyl-tools |
1.8.2 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/snvphyl-galaxy |
https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
fishertest |
fishertest |
Fisher's exact test on two-column hit lists. |
2015-06-17 |
http://artbio.fr |
2.32.0+galaxy0 |
bioconductor-qvalue |
2.38.0 |
To update |
RNA, Statistics |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test |
https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
fits2tiff_astro_tool |
fits2tiff_astro_tool |
Tool to convert FITS files to TIFF |
2025-07-18 |
|
0.0.1+galaxy0 |
astropy |
|
To update |
Astronomy |
|
|
|
|
astroteam |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/fits2tiff |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
1 |
1 |
|
|
|
flashlfq |
flashlfq |
FlashLFQ mass-spectrometry proteomics label-free quantification |
2017-12-06 |
https://github.com/smith-chem-wisc/FlashLFQ |
1.0.3.1 |
flashlfq |
2.1.4 |
To update |
Proteomics |
Label-free quantification |
Label-free quantification |
Proteomics experiment, Proteomics |
Proteomics experiment, Proteomics |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq |
flashlfq |
FlashLFQ |
FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
47 |
59 |
516 |
760 |
0 |
0 |
0 |
0 |
16 |
16 |
216 |
226 |
0 |
0 |
0 |
0 |
986 |
732 |
75 |
63 |
https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d, https://workflowhub.eu/workflows/1450?version=1 |
proteomics/metaquantome-data-creation |
|
fragpipe |
fragpipe |
Data analysis for mass spectrometry-based proteomics. |
2022-07-21 |
https://fragpipe.nesvilab.org/ |
20.0 |
fragpipe |
23.1 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
41 |
41 |
435 |
435 |
23 |
23 |
70 |
70 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
505 |
505 |
64 |
64 |
https://usegalaxy.eu/published/workflow?id=8ef3379dded2490a, https://usegalaxy.eu/published/workflow?id=bee2a7669a7dea5b, https://usegalaxy.org.au/published/workflow?id=9365a7de314c9f85, https://usegalaxy.org/published/workflow?id=e3a30c0583183c1e, https://workflowhub.eu/workflows/1410?version=1, https://workflowhub.eu/workflows/1793?version=1 |
proteomics/neoantigen-fragpipe-discovery |
|
freeenergy |
|
Free energy tools of BRIDGE. |
2019-10-24 |
|
|
|
|
To update |
Molecular Dynamics, Computational chemistry |
|
|
|
|
chemteam |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
freqsap |
freqsap |
Get frequencies of single amino-acid polymorphisms based on nucleid-acid polymorphism for different populations from UniProt and DbSNP. |
2025-07-18 |
https://github.com/RECETOX/galaxytools |
1.0.0+galaxy0 |
pandas |
|
To update |
Proteomics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/main/tools/freqsap |
https://github.com/RECETOX/galaxytools/tree/master/tools/freqsap |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
frogs |
FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom |
Suite for metabarcoding analysis |
2021-08-16 |
http://frogs.toulouse.inrae.fr/ |
4.2.0 |
frogs |
5.0.2 |
To update |
Metagenomics |
|
|
|
|
frogs |
https://github.com/geraldinepascal/FROGS-wrappers/ |
https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs |
|
|
|
|
0 |
0 |
0 |
28 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
18 |
18 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1271 |
1272 |
73623 |
73661 |
73661 |
73623 |
1272 |
1271 |
https://usegalaxy.fr/published/workflow?id=048cb90ec1ac7120, https://usegalaxy.fr/published/workflow?id=2ac84b2bd45876cf, https://usegalaxy.fr/published/workflow?id=b46954345641a3b8, https://usegalaxy.fr/published/workflow?id=d68b4aa5337f016b |
|
|
from_hicup_to_juicebox |
fromHicupToJuicebox |
Convert the output of hicup (as sam or bam) to the input of juicebox. |
2018-06-05 |
|
0.0.2 |
pysam |
0.23.3 |
To update |
Epigenetics |
|
|
|
|
lldelisle |
|
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
fromgtftobed12 |
fromgtfTobed12 |
Convert GTF files to BED12 format |
2019-07-31 |
https://pythonhosted.org/gffutils/contents.html |
0.11.1+galaxy1 |
gffutils |
0.13 |
To update |
Convert Formats |
|
|
|
|
lldelisle |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gatk4 |
filtermutectcalls, mergemutectstats, mutect2 |
Find somatic variations |
2021-12-29 |
http://artbio.fr |
4.1.7.0 |
gatk4 |
4.6.2.0 |
To update |
Variant Analysis |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gc_derivatization |
gc_derivatization |
In silico derivatization for GC. |
2024-03-15 |
https://github.com/RECETOX/gc-meox-tms |
1.0.1 |
gc-meox-tms |
1.0.1 |
Up-to-date |
Metabolomics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization |
https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
6 |
6 |
0 |
0 |
0 |
0 |
1 |
1 |
45 |
45 |
0 |
0 |
0 |
0 |
51 |
51 |
3 |
3 |
|
|
|
gdal |
gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo |
Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. |
2019-02-25 |
https://www.gdal.org |
3.0.0 |
|
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal |
|
|
|
|
0 |
0 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
11 |
15 |
724 |
1525 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
3 |
3 |
1528 |
727 |
17 |
13 |
https://usegalaxy.eu/published/workflow?id=3b0803542deff026, https://usegalaxy.eu/published/workflow?id=b0b6c8756070650b, https://workflowhub.eu/workflows/1670?version=1, https://workflowhub.eu/workflows/404?version=1 |
ecology/gbif_cleaning |
|
genomad |
genomad_end_to_end |
Identify virus and plasmid genomes from nucleotide sequences |
2024-06-17 |
https://github.com/apcamargo/genomad/ |
1.11.1 |
genomad |
1.11.1 |
Up-to-date |
Metagenomics |
Sequence annotation, Taxonomic classification |
Sequence annotation, Taxonomic classification |
Sequence analysis |
Sequence analysis |
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad |
genomad |
geNomad |
geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
119 |
119 |
2576 |
2576 |
20 |
20 |
71 |
71 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2647 |
2647 |
139 |
139 |
https://usegalaxy.eu/published/workflow?id=36de05d50c703164 |
|
|
get_reference_fasta |
get_fasta_reference |
Obtain reference genome sequence. |
2015-06-17 |
http://artbio.fr |
0.3.2 |
|
|
To update |
Data Source, Fasta Manipulation |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta |
https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gettn5extendedcoverage |
getTn5ExtendedCoverage |
Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension |
2018-06-13 |
|
0.0.2 |
pysam |
0.23.3 |
To update |
Epigenetics |
|
|
|
|
lldelisle |
|
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gffcompare_to_bed |
gffcompare_to_bed |
Filter and convert a gffCompare GTF to BED |
2018-01-10 |
https://github.com/gpertea/gffcompare/ |
0.2.1 |
python |
|
To update |
Convert Formats |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
381 |
435 |
1352 |
2561 |
460 |
460 |
1295 |
1295 |
79 |
81 |
657 |
677 |
0 |
0 |
0 |
0 |
4533 |
3304 |
976 |
920 |
https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2, https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=e336bca259abd474, https://workflowhub.eu/workflows/1407?version=1, https://workflowhub.eu/workflows/1437?version=1, https://workflowhub.eu/workflows/1788?version=1 |
proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation |
|
grb_detection_astro_tool |
grb_detection_astro_tool |
SPI-ACS GRB detection |
2025-08-13 |
|
0.0.1+galaxy0 |
numpy |
|
To update |
Astronomy |
|
|
|
|
astroteam |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/grb-detection |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gromacs |
gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj |
GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. |
2018-10-03 |
https://github.com/gromacs |
2022 |
gromacs |
2021.3 |
To update |
Molecular Dynamics, Computational chemistry |
|
|
|
|
chemteam |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs |
|
|
|
|
0 |
8 |
15 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
13 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
15 |
9 |
800 |
895 |
211260 |
221677 |
520 |
520 |
42336 |
42336 |
171 |
177 |
13561 |
13803 |
0 |
0 |
0 |
0 |
277816 |
267157 |
1592 |
1491 |
https://usegalaxy.eu/published/workflow?id=07e1478df88a17cc, https://usegalaxy.eu/published/workflow?id=092d01f759659e6b, https://usegalaxy.eu/published/workflow?id=1b10ece62e745125, https://usegalaxy.eu/published/workflow?id=2a1b21d39ebb6e49, https://usegalaxy.eu/published/workflow?id=3729015f676693c8, https://usegalaxy.eu/published/workflow?id=3c6ff60d1d3ceb3d, https://usegalaxy.eu/published/workflow?id=5d793801998146bc, https://usegalaxy.eu/published/workflow?id=7969bdac8adb8810, https://usegalaxy.eu/published/workflow?id=843c10c447496280, https://usegalaxy.eu/published/workflow?id=84c95f31896213fd, https://usegalaxy.eu/published/workflow?id=abd1cb3457338eb5, https://usegalaxy.eu/published/workflow?id=ac84daeb82d76e1c, https://usegalaxy.eu/published/workflow?id=adc6d049e9283789, https://usegalaxy.eu/published/workflow?id=b51b2f4950d26b07, https://usegalaxy.eu/published/workflow?id=bf99d06567288766, https://usegalaxy.eu/published/workflow?id=c39a79bb45b2566e, https://usegalaxy.eu/published/workflow?id=d1357759d0962144, https://usegalaxy.eu/published/workflow?id=d4d8e907e26c8587, https://usegalaxy.eu/published/workflow?id=d873ff816f028d4f, https://usegalaxy.eu/published/workflow?id=d91e715b5e3457d3, https://usegalaxy.eu/published/workflow?id=e0dddc2579c3614e, https://usegalaxy.eu/published/workflow?id=e3b0b521ee8f2aef, https://usegalaxy.eu/published/workflow?id=e73beff62f35d677, https://usegalaxy.eu/published/workflow?id=fb425d6accf3ca55, https://usegalaxy.org.au/published/workflow?id=28cf646b95e4d3ab, https://usegalaxy.org.au/published/workflow?id=5add59b908662af0, https://usegalaxy.org.au/published/workflow?id=8a20b3ed4a81263d, https://usegalaxy.org/published/workflow?id=00a4dbc9329c638b, https://usegalaxy.org/published/workflow?id=0fb89e9c397c8938, https://usegalaxy.org/published/workflow?id=183254b3565bcb04, https://usegalaxy.org/published/workflow?id=195a608c481040de, https://usegalaxy.org/published/workflow?id=28c7e8269d478244, https://usegalaxy.org/published/workflow?id=3c1e2bbb1a77cc30, https://usegalaxy.org/published/workflow?id=442a2868873e7f77, https://usegalaxy.org/published/workflow?id=634bbef1f67a0e30, https://usegalaxy.org/published/workflow?id=a638e12411586555, https://usegalaxy.org/published/workflow?id=aaec757e04605d3a, https://usegalaxy.org/published/workflow?id=ad19db6504b6dc33, https://usegalaxy.org/published/workflow?id=d2b994833b79d2cb, https://workflowhub.eu/workflows/1645?version=1, https://workflowhub.eu/workflows/1686?version=1, https://workflowhub.eu/workflows/1689?version=1, https://workflowhub.eu/workflows/247?version=2, https://workflowhub.eu/workflows/248?version=4, https://workflowhub.eu/workflows/249?version=4, https://workflowhub.eu/workflows/761?version=1, https://workflowhub.eu/workflows/762?version=1, https://workflowhub.eu/workflows/763?version=1, https://workflowhub.eu/workflows/764?version=1 |
computational-chemistry/htmd-analysis, computational-chemistry/md-simulation-gromacs |
|
gsc_center_scale |
center_scale |
Center or scale (standardize) data |
2019-07-09 |
http://artbio.fr |
4.3.1+galaxy1 |
r-optparse |
1.3.2 |
To update |
Statistics, Single Cell |
RNA-Seq analysis, Clustering, Visualisation, Expression analysis |
RNA-Seq analysis, Clustering, Visualisation |
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale |
galaxy_single_cell_suite |
Galaxy Single Cell suite |
Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gsc_filter_cells |
filter_cells |
Filter single cell RNAseq data on library depth and number of detected genes |
2019-06-23 |
http://artbio.fr |
4.3.1+galaxy1 |
r-optparse |
1.3.2 |
To update |
Transcriptomics, Single Cell |
RNA-Seq analysis, Clustering, Visualisation, Expression analysis |
RNA-Seq analysis, Clustering, Visualisation |
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells |
galaxy_single_cell_suite |
Galaxy Single Cell suite |
Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gsc_filter_genes |
filter_genes |
Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data |
2019-06-23 |
http://artbio.fr |
4.3.1+galaxy1 |
r-optparse |
1.3.2 |
To update |
Transcriptomics, Single Cell |
RNA-Seq analysis, Clustering, Visualisation, Expression analysis |
RNA-Seq analysis, Clustering, Visualisation |
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes |
galaxy_single_cell_suite |
Galaxy Single Cell suite |
Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gsc_gene_expression_correlations |
single_cell_gene_expression_correlations |
Compute single-cell paire-wise gene expressions correlations |
2019-06-24 |
http://artbio.fr |
4.3.1+galaxy1 |
r-optparse |
1.3.2 |
To update |
Transcriptomics, Single Cell |
RNA-Seq analysis, Clustering, Visualisation, Expression analysis |
RNA-Seq analysis, Clustering, Visualisation |
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations |
galaxy_single_cell_suite |
Galaxy Single Cell suite |
Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gsc_high_dimensions_visualisation |
high_dimensions_visualisation |
Generates PCA, t-SNE and HCPC visualisation |
2019-06-23 |
http://artbio.fr |
4.3+galaxy1 |
r-optparse |
1.3.2 |
To update |
Transcriptomics, Visualization, Single Cell |
RNA-Seq analysis, Clustering, Visualisation, Expression analysis |
RNA-Seq analysis, Clustering, Visualisation |
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation |
galaxy_single_cell_suite |
Galaxy Single Cell suite |
Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gsc_mannwhitney_de |
mannwhitney_de |
Perform a mann-whitney differential testing between two sets of gene expression data |
2019-06-23 |
http://artbio.fr |
4.1.3+galaxy1 |
r-optparse |
1.3.2 |
To update |
Transcriptomics, Single Cell |
RNA-Seq analysis, Clustering, Visualisation, Expression analysis |
RNA-Seq analysis, Clustering, Visualisation |
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de |
galaxy_single_cell_suite |
Galaxy Single Cell suite |
Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gsc_scran_normalize |
scran_normalize |
Normalize raw counts using scran |
2019-09-23 |
http://artbio.fr |
1.28.1+galaxy1 |
bioconductor-scran |
1.34.0 |
To update |
Transcriptomics, Single Cell |
RNA-Seq analysis, Clustering, Visualisation, Expression analysis |
RNA-Seq analysis, Clustering, Visualisation |
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize |
galaxy_single_cell_suite |
Galaxy Single Cell suite |
Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
34 |
34 |
125 |
125 |
18 |
18 |
334 |
334 |
5 |
5 |
157 |
157 |
0 |
0 |
0 |
0 |
616 |
616 |
57 |
57 |
|
|
|
gsc_signature_score |
signature_score |
Compute signature scores from single cell RNAseq data |
2019-06-23 |
http://artbio.fr |
2.3.9+galaxy1 |
r-optparse |
1.3.2 |
To update |
Transcriptomics, Single Cell |
RNA-Seq analysis, Clustering, Visualisation, Expression analysis |
RNA-Seq analysis, Clustering, Visualisation |
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score |
https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score |
galaxy_single_cell_suite |
Galaxy Single Cell suite |
Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
gtf2gene_list |
_ensembl_gtf2gene_list |
Utility to extract annotations from Ensembl GTF files. |
2019-11-07 |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary |
1.52.0+galaxy0 |
atlas-gene-annotation-manipulation |
1.1.1 |
To update |
Sequence Analysis |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
429 |
449 |
2337 |
2550 |
463 |
464 |
1318 |
1322 |
52 |
52 |
292 |
292 |
2 |
2 |
5 |
5 |
4169 |
3952 |
967 |
946 |
https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=50f8693fac7e134b, https://usegalaxy.eu/published/workflow?id=73b41b975da284d5, https://usegalaxy.eu/published/workflow?id=83ae28e23099a3f6, https://usegalaxy.eu/published/workflow?id=9a9bbd8046da7b19, https://usegalaxy.eu/published/workflow?id=aeb0f5b74e51f5c2, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=e97bdba3834ac465, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d, https://workflowhub.eu/workflows/1533?version=1, https://workflowhub.eu/workflows/1537?version=1 |
single-cell/scrna-case_alevin |
|
guppy_basecaller |
guppy-basecaller |
A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies |
2020-11-18 |
http://artbio.fr |
6.5.7+galaxy0 |
|
|
To update |
Nanopore |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy |
https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
7 |
7 |
0 |
0 |
0 |
0 |
7 |
7 |
1 |
1 |
|
|
|
hardklor |
hardklor, kronik |
Hardklör |
2016-04-26 |
|
2.30.1+galaxy1 |
hardklor |
2.3.2 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
3 |
6 |
25 |
111 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
111 |
25 |
6 |
3 |
|
|
|
hess_astro_tool |
hess_astro_tool |
Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope |
2024-02-19 |
|
0.0.2+galaxy0 |
ipython |
|
To update |
Astronomy |
|
|
|
|
astroteam |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
2 |
2 |
https://workflowhub.eu/workflows/766?version=1 |
|
|
high_dim_heatmap |
high_dim_heatmap |
gplot heatmap.2 function adapted for plotting large heatmaps |
2019-07-20 |
https://github.com/cran/gplots |
3.1.3+galaxy0 |
r-gplots |
2.17.0 |
To update |
Visualization |
|
|
|
|
artbio |
https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap |
https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
hirieftools |
calc_delta_pi, pi_db_split, pi_dbspec_align |
HiRIEF tools |
2017-04-11 |
|
1.3 |
python |
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
hirondelle_crim_ogc_api_processes |
hirondelle_crim |
This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. |
2024-06-07 |
https://github.com/AquaINFRA/galaxy |
0.2.0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
237 |
237 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
237 |
237 |
4 |
4 |
https://usegalaxy.eu/published/workflow?id=6173008772bdba09, https://usegalaxy.eu/published/workflow?id=b1fa4a3561988704 |
|
|
hyperstack_to_bleach_corrected_movie |
hyperstack_to_bleach_corrected_movie |
Generate blach corrected movie from hyperstack |
2023-02-27 |
|
20241220 |
Fiji |
20250206 |
To update |
Imaging |
|
|
|
|
lldelisle |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
idconvert |
idconvert |
Convert mass spectrometry identification files on linux or MacOSX |
2019-02-22 |
|
|
proteowizard |
3_0_9992 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
12 |
34 |
55 |
278 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
278 |
55 |
34 |
12 |
|
|
|
iedb_netmhcpan |
iedb_netmhciipan, iedb_netmhcpan |
Predict binding of peptides to any MHC or MHC II molecule of known sequence using artificial neural networks |
2025-07-09 |
http://tools.immuneepitope.org/main/tools-api/ |
4.1+galaxy0 |
|
|
To update |
Data Source, Sequence Analysis |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
19 |
19 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
19 |
19 |
2 |
2 |
|
|
|
incucyte_stack_and_upload_omero |
incucyte_stack_and_upload_omero |
Combine images to stack and upload to the omero server |
2023-02-17 |
|
20231221 |
Fiji |
20250206 |
To update |
Imaging |
|
|
|
|
lldelisle |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
interpolation |
interpolation_run_idw_interpolation |
Run IDW interpolation based on a .csv and .geojson file |
2024-01-05 |
https://github.com/AquaINFRA/galaxy |
1.0 |
r-getopt |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
70 |
70 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
70 |
70 |
7 |
7 |
https://usegalaxy.eu/published/workflow?id=0b2304aa2083bd1a, https://workflowhub.eu/workflows/807?version=1 |
|
|
ipaPy2 |
ipapy2_MS1_annotation, ipapy2_MS2_annotation, ipapy2_clustering, ipapy2_compute_all_adducts, ipapy2_compute_bio, ipapy2_gibbs_sampler, ipapy2_gibbs_sampler_add, ipapy2_map_isotope_patterns |
Mass spectrometry data annotation tool. |
2023-12-04 |
https://github.com/francescodc87/ipaPy2 |
1.3.0 |
ipapy2 |
1.3.0 |
Up-to-date |
Metabolomics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 |
https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
iphop |
iphop_predict |
Integrated Phage Host Prediction |
2024-10-14 |
https://bitbucket.org/srouxjgi/iphop/ |
1.3.3 |
iphop |
1.4.1 |
To update |
Metagenomics |
Sample comparison |
Sample comparison |
|
|
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/iphop/ |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/iphop |
iphop |
iPHoP |
An automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
9 |
26 |
26 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
26 |
26 |
9 |
9 |
|
|
|
isolib |
isolib |
Create an isotopic pattern library for given compounds and adducts. |
2023-10-26 |
https://github.com/RECETOX/galaxytools/ |
2.6+galaxy3 |
bioconductor-metabocoreutils |
1.14.0 |
To update |
Metabolomics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/isolib |
https://github.com/RECETOX/galaxytools/tree/master/tools/isolib |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
6 |
6 |
0 |
0 |
0 |
0 |
1 |
1 |
219 |
219 |
0 |
0 |
0 |
0 |
225 |
225 |
3 |
3 |
|
|
|
justdiff |
justdiff |
Unix diff |
2017-09-27 |
http://artbio.fr |
3.10+galaxy0 |
diffutils |
|
To update |
Text Manipulation |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff |
https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
justgzip |
justgzip |
Compress fastq sequence files |
2018-05-16 |
http://artbio.fr |
2.8+galaxy0 |
pigz |
|
To update |
Convert Formats |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip |
https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
20 |
20 |
20 |
20 |
1 |
1 |
|
|
|
lambdaminer |
lm_get_projects |
Lambda-Miner Tools |
2025-03-06 |
https://lambda-miner-project.pages.ufz.de/lambda-miner-workflows/ |
0.1.0+galaxy0 |
pandas |
|
To update |
Web Services, Data Source |
|
|
|
|
ufz |
https://github.com/jw44lavo/galaxy-tools/blob/bgo/tools/lambdaminer/ |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/lambdaminer |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
lfq_protein_quant |
lfq_protein_quant |
Enable protein summarisation and quantitation |
2018-10-02 |
https://github.com/compomics/LFQ_galaxy_p |
1.0 |
bioconductor-msnbase |
2.32.0 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
9 |
19 |
27 |
117 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
117 |
27 |
19 |
9 |
|
|
|
longorf |
longORF |
obtain longest ORF in six-frame translations |
2018-06-01 |
|
0.3.0 |
|
|
To update |
Sequence Analysis |
|
|
|
|
mbernt |
https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
ltq_iquant_cli |
|
|
2015-01-24 |
|
|
|
|
To update |
|
|
|
|
|
galaxyp |
|
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
lumpy_smoove |
lumpy_smoove, vcf2hrdetect |
Galaxy wrapper of the lumpy-using smoove workflow |
2020-07-12 |
http://artbio.fr |
0.2.8+galaxy1 |
svtyper |
0.7.1 |
To update |
Variant Analysis |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove |
https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
lumpy_sv |
lumpy |
Find structural variations |
2017-07-24 |
http://artbio.fr |
1.3 |
lumpy-sv |
0.3.1 |
To update |
Variant Analysis |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv |
https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
make_nr |
make_nr |
Make a FASTA file non-redundant |
2018-11-06 |
https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr |
0.0.3 |
biopython |
1.70 |
To update |
Fasta Manipulation, Sequence Analysis |
Sequence alignment, Genome annotation |
Sequence alignment, Genome annotation |
Molecular biology, Sequence analysis |
Molecular biology, Sequence analysis |
peterjc |
https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr |
https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr |
make_nr |
make_nr |
Make a FASTA file non-redundant, with a Galaxy wrapperThis tool is copyright 2018 by Peter Cock, The James Hutton Institute, UK. All rights reserved.This tool is a short Python script intended to be run prior to calling the NCBI BLAST+ command line tool makeblastdb or in other settings where you want to collapse duplicated sequences in a FASTA file to a single representative. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
manta |
manta |
Structural variant and indel caller for mapped sequencing data |
2019-10-25 |
http://artbio.fr |
1.6 |
manta |
1.6.0 |
To update |
Variant Analysis |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/manta |
https://github.com/ARTbio/tools-artbio/tree/main/tools/manta |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
88 |
88 |
1118 |
1118 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1118 |
1118 |
88 |
88 |
|
|
|
map_peptides_to_bed |
map_peptides_to_bed |
Map peptides to a reference genome for display by a genome browser |
2016-01-13 |
|
0.2 |
biopython |
1.70 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
5 |
9 |
10 |
46 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
46 |
10 |
9 |
5 |
|
|
|
mapping_quality_stats |
mapqstatistics |
Collects and shows the distribution of MAPQ values in a BAM alignment file |
2022-06-15 |
http://artbio.fr |
0.22.0 |
r-optparse |
1.3.2 |
To update |
Sequence Analysis, Statistics |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats |
https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
marine_omics |
sanntis_marine |
The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data |
2024-07-26 |
https://github.com/Finn-Lab/SanntiS |
0.9.3.5 |
sanntis |
0.9.4.1 |
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
22 |
22 |
198 |
198 |
0 |
0 |
0 |
0 |
5 |
5 |
112 |
112 |
0 |
0 |
0 |
0 |
310 |
310 |
27 |
27 |
https://usegalaxy.eu/published/workflow?id=a448400f69594135, https://usegalaxy.eu/published/workflow?id=b9c938d1af08124b, https://usegalaxy.eu/published/workflow?id=cc59ae1a9878942c, https://workflowhub.eu/workflows/1663?version=1 |
ecology/marine_omics_bgc |
|
matchms |
matchms_add_key, matchms_convert, matchms_matchms_export_skyline_transition_list, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting |
Searching, filtering and converting mass spectral libraries. |
2020-11-16 |
https://github.com/matchms/matchms |
0.30.2 |
matchms |
0.30.2 |
Up-to-date |
Metabolomics |
Spectral library search, Format validation, Filtering |
Spectral library search, Format validation, Filtering |
Metabolomics |
Metabolomics |
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/matchms |
https://github.com/RECETOX/galaxytools/tree/master/tools/matchms |
matchms |
Matchms |
Tool to import, process, clean, and compare mass spectrometry data. |
|
0 |
14 |
14 |
11 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
0 |
28 |
28 |
1904 |
1904 |
5 |
5 |
29 |
29 |
5 |
5 |
4132 |
4132 |
27 |
27 |
399 |
399 |
6464 |
6464 |
65 |
65 |
https://usegalaxy.eu/published/workflow?id=3086366b744e8da9, https://usegalaxy.eu/published/workflow?id=3358c516f5412e92, https://usegalaxy.fr/published/workflow?id=1407c1703f360f07, https://workflowhub.eu/workflows/1582?version=1, https://workflowhub.eu/workflows/888?version=2 |
metabolomics/gc_ms_with_xcms |
|
max_projections_stack_and_upload_omero |
max_projections_stack_and_upload_omero |
Combine images from max projections to stack and upload to the omero server |
2024-12-12 |
|
20241213.2 |
Fiji |
20250206 |
To update |
Imaging |
|
|
|
|
lldelisle |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
maxquant |
maxquant, maxquant_mqpar |
wrapper for MaxQuant |
2015-01-24 |
https://www.maxquant.org/ |
2.0.3.0 |
maxquant |
2.0.3.0 |
Up-to-date |
Proteomics |
Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting |
Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering |
Proteomics experiment, Proteomics, Statistics and probability |
Proteomics experiment, Proteomics, Statistics and probability |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant |
maxquant |
MaxQuant |
Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
1628 |
1682 |
7932 |
8757 |
775 |
775 |
3791 |
3791 |
407 |
416 |
3720 |
3831 |
3 |
3 |
33 |
33 |
16412 |
15476 |
2876 |
2813 |
https://usegalaxy.eu/published/workflow?id=0135ee4b3fa0cbce, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=96d198ed953449fd, https://usegalaxy.eu/published/workflow?id=9e0d784860d6cc91, https://usegalaxy.eu/published/workflow?id=a49275eb8b2b2ecb, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=d789165f4e0c50eb, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c, https://usegalaxy.org.au/published/workflow?id=43a951ec514498f6, https://usegalaxy.org.au/published/workflow?id=781457327e644c7e, https://usegalaxy.org.au/published/workflow?id=b0a79310e0dc3fb4, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org/published/workflow?id=2404d5e5b1817825, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1177?version=1, https://workflowhub.eu/workflows/1225?version=1, https://workflowhub.eu/workflows/1396?version=1, https://workflowhub.eu/workflows/1401?version=1, https://workflowhub.eu/workflows/1420?version=1, https://workflowhub.eu/workflows/1421?version=1, https://workflowhub.eu/workflows/1435?version=1, https://workflowhub.eu/workflows/1448?version=1, https://workflowhub.eu/workflows/1468?version=1 |
microbiome/clinical-mp-2-discovery, microbiome/clinical-mp-4-quantitation, proteomics/DIA_lib_OSW, proteomics/clinical-mp-2-discovery, proteomics/clinical-mp-4-quantitation, proteomics/maxquant-label-free, proteomics/maxquant-msstats-dda-lfq, proteomics/maxquant-msstats-tmt |
|
md_converter |
md_slicer |
A tool for slicing trajectory files using MDTraj. |
2019-10-07 |
|
1.9.9 |
mdtraj |
|
To update |
Molecular Dynamics, Computational chemistry |
|
|
|
|
chemteam |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
16 |
21 |
102 |
179 |
4 |
4 |
6 |
6 |
7 |
7 |
539 |
539 |
0 |
0 |
0 |
0 |
724 |
647 |
32 |
27 |
|
|
|
md_converter |
md_converter |
A tool for interconverting between different MD structure and trajectory file formats. |
2018-10-13 |
|
1.9.7 |
mdtraj |
|
To update |
Molecular Dynamics, Computational chemistry |
|
|
|
|
chemteam |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
309 |
342 |
27397 |
27743 |
75 |
75 |
849 |
849 |
105 |
105 |
1433 |
1433 |
0 |
0 |
0 |
0 |
30025 |
29679 |
522 |
489 |
https://usegalaxy.eu/published/workflow?id=07e1478df88a17cc, https://usegalaxy.eu/published/workflow?id=092d01f759659e6b, https://usegalaxy.eu/published/workflow?id=3c6ff60d1d3ceb3d, https://usegalaxy.eu/published/workflow?id=843c10c447496280, https://usegalaxy.eu/published/workflow?id=abd1cb3457338eb5, https://usegalaxy.org.au/published/workflow?id=5add59b908662af0, https://usegalaxy.org/published/workflow?id=0fb89e9c397c8938, https://usegalaxy.org/published/workflow?id=183254b3565bcb04, https://usegalaxy.org/published/workflow?id=3c1e2bbb1a77cc30, https://usegalaxy.org/published/workflow?id=442a2868873e7f77, https://usegalaxy.org/published/workflow?id=ad19db6504b6dc33, https://workflowhub.eu/workflows/1689?version=1, https://workflowhub.eu/workflows/248?version=4 |
computational-chemistry/htmd-analysis, computational-chemistry/med-chem-data, fair/med-chem-data |
|
mdanalysis |
mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf |
MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations |
2018-10-04 |
https://github.com/MDAnalysis/mdanalysis |
1.0.0 |
mdanalysis |
|
To update |
Computational chemistry |
|
|
|
|
chemteam |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis |
|
|
|
|
0 |
5 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
10 |
10 |
164 |
177 |
2894 |
3569 |
33 |
33 |
238 |
238 |
52 |
52 |
935 |
935 |
0 |
0 |
0 |
0 |
4742 |
4067 |
262 |
249 |
https://usegalaxy.eu/published/workflow?id=092d01f759659e6b, https://usegalaxy.eu/published/workflow?id=b47e415f80941ba0, https://usegalaxy.org.au/published/workflow?id=5add59b908662af0, https://workflowhub.eu/workflows/1689?version=1, https://workflowhub.eu/workflows/1694?version=1 |
computational-chemistry/analysis-md-simulations, computational-chemistry/htmd-analysis |
|
mdtraj |
traj_selections_and_merge |
MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories |
2020-06-24 |
https://github.com/mdtraj/mdtraj |
1.9.7 |
mdtraj |
|
To update |
Computational chemistry |
|
|
|
|
chemteam |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
8 |
8 |
36 |
36 |
4 |
4 |
63 |
63 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
99 |
99 |
12 |
12 |
|
|
|
mean_per_zone |
mean_per_zone |
Creates a png image showing statistic over areas as defined in the vector file |
2019-03-15 |
https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ |
0.2.0 |
python |
|
To update |
Visualization, GIS, Climate Analysis |
|
|
|
|
climate |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
3 |
1 |
25 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
25 |
1 |
3 |
1 |
|
|
|
measure_gastruloids |
measureGastruloids |
Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index |
2022-01-18 |
|
20221216 |
fiji |
20250206 |
To update |
Imaging |
|
|
|
|
lldelisle |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
medenv |
iabiodiv_smartbiodiv_med_environ |
Retrieve environmental data from etopo, cmems and woa |
2023-11-30 |
https://github.com/jeremyfix/medenv |
0.1.0 |
pandas |
|
To update |
Ecology, Data Source |
|
|
|
|
ecology |
https://github.com/jeremyfix/medenv |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
11 |
38 |
38 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
38 |
38 |
11 |
11 |
|
|
|
meta_proteome_analyzer |
meta_proteome_analyzer |
MetaProteomeAnalyzer |
2017-03-03 |
https://github.com/compomics/meta-proteome-analyzer/ |
2.0.0 |
mpa-portable |
2.0.0 |
Up-to-date |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
22 |
22 |
148 |
148 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
148 |
148 |
22 |
22 |
|
|
|
metagene_annotator |
metagene_annotator |
MetaGeneAnnotator gene-finding program for prokaryote and phage |
2018-03-21 |
http://metagene.nig.ac.jp/ |
1.0 |
metagene_annotator |
1.0 |
Up-to-date |
Sequence Analysis |
Sequence annotation |
Sequence annotation |
Genomics, Model organisms, Data submission, annotation and curation |
Genomics, Model organisms, Data submission, annotation and curation |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator |
metageneannotator |
MetaGeneAnnotator |
Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
439 |
457 |
20971 |
21069 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
21069 |
20971 |
457 |
439 |
https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=799b924edd3c401b, https://usegalaxy.eu/published/workflow?id=9b9e1e28f3683f92, https://usegalaxy.eu/published/workflow?id=c0f225536e78a178 |
|
|
metanovo |
metanovo |
Produce targeted databases for mass spectrometry analysis. |
2022-03-29 |
https://github.com/uct-cbio/proteomics-pipelines |
1.9.4 |
metanovo |
1.9.4 |
Up-to-date |
Proteomics |
Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis |
Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis |
Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules |
Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo |
metanovo |
MetaNovo |
An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
40 |
40 |
5000 |
5000 |
5 |
5 |
34 |
34 |
4 |
4 |
92 |
92 |
0 |
0 |
0 |
0 |
5126 |
5126 |
49 |
49 |
https://usegalaxy.eu/published/workflow?id=2f7e13eb26c8cd18, https://usegalaxy.eu/published/workflow?id=7cfbf4b7bd3f30d3, https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f, https://usegalaxy.eu/published/workflow?id=d7c7a4d6c8072167, https://usegalaxy.eu/published/workflow?id=f2b45a7ff4f449e6, https://usegalaxy.org.au/published/workflow?id=351f3fab960c013b, https://usegalaxy.org/published/workflow?id=2be8ecd5922d23d1, https://workflowhub.eu/workflows/1216?version=1, https://workflowhub.eu/workflows/1461?version=1, https://workflowhub.eu/workflows/1474?version=1 |
microbiome/clinical-mp-1-database-generation, proteomics/clinical-mp-1-database-generation |
|
metaquantome |
metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz |
quantitative analysis of microbiome taxonomy and function |
2018-11-27 |
https://github.com/galaxyproteomics/metaquantome/ |
2.0.2 |
metaquantome |
2.0.2 |
Up-to-date |
Proteomics |
Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference |
Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference |
Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics |
Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome |
metaQuantome |
metaQuantome |
metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. |
|
0 |
6 |
6 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
6 |
6 |
80 |
89 |
2277 |
3166 |
0 |
0 |
0 |
0 |
27 |
27 |
2323 |
2323 |
0 |
0 |
0 |
0 |
5489 |
4600 |
116 |
107 |
https://usegalaxy.eu/published/workflow?id=4c364c6be27981ba, https://usegalaxy.eu/published/workflow?id=695f7defb516d80d, https://usegalaxy.eu/published/workflow?id=ce7f7c6eef526d67, https://usegalaxy.eu/published/workflow?id=dc438d4ae1866df8, https://usegalaxy.eu/published/workflow?id=e5a89ef7b5f1c1d9, https://usegalaxy.org.au/published/workflow?id=cada735fa0716570, https://usegalaxy.org.au/published/workflow?id=f8183bba3a1d150d, https://workflowhub.eu/workflows/1453?version=1, https://workflowhub.eu/workflows/1459?version=1 |
proteomics/metaquantome-function, proteomics/metaquantome-taxonomy |
|
mgf_formatter |
mgf_formatter |
|
2014-09-26 |
|
1.0.0 |
mgf-formatter |
1.0.0 |
Up-to-date |
|
|
|
|
|
galaxyp |
|
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
mircounts |
mircounts |
Generates miRNA count lists from read alignments to mirBase. |
2017-06-12 |
http://artbio.fr |
1.6 |
tar |
|
To update |
RNA, Transcriptomics |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts |
https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts |
|
|
|
|
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
30 |
30 |
44 |
44 |
1868 |
1868 |
0 |
0 |
0 |
0 |
1898 |
1898 |
45 |
45 |
|
|
|
misc |
target_screen, use_theoretical_mz_annotations |
|
2024-02-16 |
https://github.com/RECETOX/galaxytools |
1.0.0 |
pandas |
|
To update |
Metabolomics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/misc |
https://github.com/RECETOX/galaxytools/tree/master/tools/misc |
|
|
|
|
0 |
1 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
151 |
151 |
0 |
0 |
0 |
0 |
1 |
1 |
90 |
90 |
0 |
0 |
0 |
0 |
241 |
241 |
5 |
5 |
https://workflowhub.eu/workflows/888?version=2 |
|
|
morpheus |
morpheus |
Morpheus MS Search Application |
2015-10-29 |
https://cwenger.github.io/Morpheus |
288 |
morpheus |
290 |
To update |
Proteomics |
Peptide database search |
Peptide database search |
Proteomics |
Proteomics |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus |
morpheus |
Morpheus |
A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
10 |
20 |
77 |
205 |
0 |
0 |
0 |
0 |
157 |
157 |
1237 |
1273 |
0 |
0 |
0 |
0 |
1478 |
1314 |
177 |
167 |
|
|
|
mqppep |
mqppep_anova, mqppep_preproc |
MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA |
2022-03-31 |
https://github.com/galaxyproteomics/tools-galaxyp/ |
0.1.19 |
bioconductor-preprocesscore |
1.68.0 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
4 |
4 |
15 |
15 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
15 |
15 |
4 |
4 |
|
|
|
ms2deepscore |
ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training |
Mass spectra similarity scoring using a trained ms2deepscore model. |
2024-08-15 |
https://github.com/matchms/ms2deepscore |
2.0.0 |
ms2deepscore |
2.5.4 |
To update |
Metabolomics |
Spectrum calculation, Spectral library search, Network analysis |
Spectrum calculation, Spectral library search, Network analysis |
Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening |
Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening |
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore |
https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore |
ms2deepscore |
MS2DeepScore |
MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra. |
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
|
|
|
msconvert |
msconvert |
msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container |
2015-01-24 |
http://proteowizard.sourceforge.net/tools.shtml |
3.0.20287 |
|
|
To update |
Proteomics |
Filtering, Formatting |
Filtering, Formatting |
Proteomics, Proteomics experiment |
Proteomics, Proteomics experiment |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert |
msconvert |
msConvert |
msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
550 |
604 |
58574 |
66339 |
133 |
133 |
2254 |
2254 |
76 |
76 |
4844 |
4844 |
108 |
113 |
7765 |
7906 |
81343 |
73437 |
926 |
867 |
https://usegalaxy.eu/published/workflow?id=02700454f57eb556, https://usegalaxy.eu/published/workflow?id=14f9c2099db30570, https://usegalaxy.eu/published/workflow?id=1809fcaec264eac9, https://usegalaxy.eu/published/workflow?id=3676aafc35dc2fe7, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=4c81726bde25c36a, https://usegalaxy.eu/published/workflow?id=5d4e4b9f07a1ec20, https://usegalaxy.eu/published/workflow?id=5dec0e5a2d75cdc1, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6b7b86756060659b, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6d3332794ceca465, https://usegalaxy.eu/published/workflow?id=6d494e2f634eba70, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=87c21b682af78ec9, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=9ac15b644c805a2b, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=b73fa5f8c0403454, https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=c750484145c9903b, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=d5756e3ebfa285ef, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d, https://usegalaxy.fr/published/workflow?id=1407c1703f360f07, https://usegalaxy.org.au/published/workflow?id=762791e094457bf2, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org/published/workflow?id=8ecc114eb9097855, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1225?version=1, https://workflowhub.eu/workflows/1396?version=1, https://workflowhub.eu/workflows/1416?version=1, https://workflowhub.eu/workflows/1435?version=1, https://workflowhub.eu/workflows/1450?version=1, https://workflowhub.eu/workflows/1463?version=1, https://workflowhub.eu/workflows/1471?version=1, https://workflowhub.eu/workflows/1582?version=1, https://workflowhub.eu/workflows/1791?version=1 |
metabolomics/gc_ms_with_xcms, microbiome/clinical-mp-2-discovery, proteomics/DIA_Analysis_OSW, proteomics/clinical-mp-2-discovery, proteomics/encyclopedia, proteomics/metaquantome-data-creation, proteomics/neoantigen-peptide-verification, proteomics/protein-id-oms |
|
msgfplus |
msgfplus |
MSGF+ |
2015-11-10 |
|
0.5 |
msgf_plus |
2024.03.26 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
34 |
54 |
762 |
944 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
944 |
762 |
54 |
34 |
|
|
|
msmetaenhancer |
msmetaenhancer |
|
2021-11-22 |
https://github.com/RECETOX/MSMetaEnhancer |
0.4.1 |
msmetaenhancer |
0.4.1 |
Up-to-date |
Metabolomics |
Annotation, Standardisation and normalisation |
Annotation, Standardisation and normalisation |
Metabolomics, Compound libraries and screening, Data submission, annotation and curation |
Metabolomics, Compound libraries and screening, Data submission, annotation and curation |
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer |
https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer |
msmetaenhancer |
MSMetaEnhancer |
Tool for mass spectra metadata annotation. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
12 |
12 |
241 |
241 |
0 |
0 |
0 |
0 |
2 |
2 |
112 |
112 |
3 |
3 |
13 |
13 |
366 |
366 |
17 |
17 |
https://workflowhub.eu/workflows/888?version=2 |
|
|
msms_extractor |
msms_extractor |
Extract MS/MS scans from the mzML file(s) based on PSM report. |
2019-10-23 |
|
1.0.0 |
proteowizard |
3_0_9992 |
To update |
Proteomics |
|
|
|
|
galaxyp |
|
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
7 |
12 |
21 |
113 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
8 |
121 |
21 |
13 |
7 |
https://usegalaxy.eu/published/workflow?id=6b7b86756060659b, https://usegalaxy.eu/published/workflow?id=c750484145c9903b |
|
|
msp_merge |
msp_merge |
|
2022-05-05 |
https://github.com/RECETOX/galaxytools |
0.1.0 |
matchms |
0.30.2 |
To update |
Metabolomics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge |
https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
msstatstmt |
msstats |
MSstats tool for analyzing mass spectrometry proteomic datasets |
2020-07-25 |
https://github.com/MeenaChoi/MSstats |
4.0.0 |
bioconductor-msstats |
4.14.0 |
To update |
Proteomics |
Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling |
Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling |
Proteomics, Proteomics experiment, Protein expression |
Proteomics, Proteomics experiment, Protein expression |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats |
msstatstmt |
MSstatsTMT |
Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
800 |
803 |
2969 |
3004 |
283 |
283 |
1456 |
1456 |
99 |
99 |
1605 |
1605 |
0 |
0 |
0 |
0 |
6065 |
6030 |
1185 |
1182 |
https://usegalaxy.org.au/published/workflow?id=1727d16fa4dec19c, https://workflowhub.eu/workflows/1426?version=1, https://workflowhub.eu/workflows/1458?version=1, https://workflowhub.eu/workflows/1462?version=1 |
proteomics/DIA_Analysis_MSstats, proteomics/maxquant-label-free, proteomics/maxquant-msstats-dda-lfq |
|
msstatstmt |
msstatstmt |
MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling |
2021-01-20 |
http://msstats.org/msstatstmt/ |
2.0.0 |
bioconductor-msstatstmt |
2.10.0 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
113 |
113 |
844 |
844 |
10 |
10 |
47 |
47 |
18 |
18 |
693 |
693 |
0 |
0 |
0 |
0 |
1584 |
1584 |
141 |
141 |
https://usegalaxy.eu/published/workflow?id=755ede37d94dc456, https://usegalaxy.eu/published/workflow?id=8f3cafa3bc59ff82, https://usegalaxy.eu/published/workflow?id=d148459a4d4b91f1, https://usegalaxy.org.au/published/workflow?id=050a66ff6d4c2b53, https://usegalaxy.org/published/workflow?id=3f797bfb67130883, https://workflowhub.eu/workflows/1219?version=1, https://workflowhub.eu/workflows/1401?version=1, https://workflowhub.eu/workflows/1433?version=1, https://workflowhub.eu/workflows/1482?version=1 |
microbiome/clinical-mp-5-data-interpretation, proteomics/clinical-mp-5-data-interpretation, proteomics/maxquant-msstats-tmt |
|
mt2mq |
mt2mq |
Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome |
2020-06-23 |
|
1.1.0 |
r-tidyverse |
|
To update |
Proteomics |
|
|
|
|
galaxyp |
|
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
39 |
43 |
258 |
286 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
286 |
258 |
43 |
39 |
|
|
|
mutational_patterns |
mutational_patterns |
Mutational patterns and signatures in base substitution catalogs |
2020-09-13 |
http://artbio.fr |
3.12.0 |
bioconductor-mutationalpatterns |
3.16.0 |
To update |
Variant Analysis |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns |
https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
mz_to_sqlite |
mz_to_sqlite |
Creates a SQLite database for proteomics data |
2015-06-01 |
https://github.com/galaxyproteomics/mzToSQLite |
2.1.1+galaxy0 |
mztosqlite |
2.1.1 |
To update |
Proteomics |
Conversion, Peptide database search |
Conversion, Peptide database search |
Proteomics, Biological databases |
Proteomics, Biological databases |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite |
mztosqlite |
mzToSQLite |
Convert proteomics data files into a SQLite databaseExtract data from proteomics mzIdentML and mass spec scan files: mzML, MGF, etc and store in a SQLite database.The intended purpose is to provide a Galaxy dataset that can support an interactive Galaxy visualization plugin. |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
136 |
146 |
868 |
959 |
17 |
17 |
83 |
83 |
18 |
18 |
336 |
336 |
0 |
0 |
0 |
0 |
1378 |
1287 |
181 |
171 |
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proteomics/proteogenomics-dbsearch |
|
mzml_validator |
mzml_validator |
mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative. |
2023-01-12 |
https://github.com/RECETOX/galaxytools |
0.1.0+galaxy2 |
lxml |
|
To update |
Metabolomics, Proteomics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator |
https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator |
|
|
|
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
mzspeclib |
mzspeclib_convert, mzspeclib_describe, mzspeclib_validate |
mzspeclib is a library and set of tools for handling, converting, and validating mass spectral libraries in a standardized format. This suite provides Galaxy wrappers for mzspeclib's core functionalities, including conversion and validation of spectral libraries. |
2025-06-12 |
https://github.com/HUPO-PSI/mzspeclib-py |
1.0.7 |
mzspeclib |
1.0.7 |
Up-to-date |
Proteomics, Metabolomics |
Conversion, Format validation |
Conversion, Format validation |
Proteomics, Metabolomics |
Proteomics, Metabolomics |
recetox |
https://github.com/RECETOX/galaxytools/tree/main/tools/mzspeclib |
https://github.com/RECETOX/galaxytools/tree/master/tools/mzspeclib |
mzspeclib |
mzspeclib |
A python reference implementation of the mzSpecLib spectral library format. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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0 |
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0 |
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0 |
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0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
mztabm |
mztabm_validate |
Tools for handling mzTab-M files using various packages. |
2025-07-01 |
https://github.com/lifs-tools/jmzTab-m |
1.0.6 |
jmztab-m |
1.0.6 |
Up-to-date |
Metabolomics |
Loading, Format validation, Formatting |
Format validation, Formatting |
Ontology and terminology, Metabolomics, Data submission, annotation and curation |
Ontology and terminology, Metabolomics, Data submission, annotation and curation |
recetox |
https://github.com/RECETOX/galaxytools/tree/main/tools/mztabm |
https://github.com/RECETOX/galaxytools/tree/master/tools/mztabm |
jmztab-m |
jmztab-m |
Reference implementation for mzTab 2.0 for metabolomics |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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0 |
0 |
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0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
ncbi_blast_plus |
blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper |
NCBI BLAST+ |
2013-09-23 |
https://blast.ncbi.nlm.nih.gov/ |
2.16.0 |
blast |
2.17.0 |
To update |
Sequence Analysis |
|
|
|
|
devteam |
https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus |
https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus |
|
|
|
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0 |
16 |
16 |
16 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
16 |
16 |
16 |
0 |
0 |
0 |
0 |
0 |
16 |
0 |
0 |
0 |
0 |
16 |
15 |
16 |
16 |
15 |
4564 |
5012 |
608297 |
687163 |
5091 |
6262 |
690841 |
770815 |
1316 |
1731 |
262398 |
287817 |
159 |
164 |
12993 |
13154 |
1758949 |
1574529 |
13169 |
11130 |
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assembly/assembly-decontamination, data-science/online-resources-gene, ecology/ENA_Biodiv_submission, ecology/Obitools-metabarcoding, ecology/eDNA-taxonomic-analysis, genome-annotation/functional, proteomics/neoantigen-peptide-verification, proteomics/proteogenomics-novel-peptide-analysis, sequence-analysis/Manage_AB1_Sanger, sequence-analysis/ncbi-blast-against-the-madland, sequence-analysis/viral_primer_design |
|
nfdi4earth_os4a_importer |
nfdi4earth_os4a |
A data source tool for downloading datasets via NFDI4Earth's OneStop4All search user interface. |
2025-09-23 |
https://onestop4all.nfdi4earth.de/ |
1.0 |
|
|
To update |
Ecology |
|
|
|
|
ecology |
https://git.rwth-aachen.de/nfdi4earth/onestop4all/onestop4all-implementation/-/tree/develop |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/nfdi4earth_os4a_importer |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
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0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
oases |
oasesoptimiserv |
Short read assembler |
2017-10-15 |
http://artbio.fr |
1.4.0 |
oases |
0.2.09 |
To update |
Assembly, RNA |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/oases |
https://github.com/ARTbio/tools-artbio/tree/main/tools/oases |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
obisindicators |
obisindicators, obis_data |
Compute biodiveristy indicators for marine data from obis |
2022-11-04 |
https://github.com/Marie59/obisindicators |
0.0.2 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators |
|
|
|
|
0 |
0 |
2 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
29 |
29 |
399 |
399 |
15 |
15 |
25 |
25 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
424 |
424 |
44 |
44 |
https://usegalaxy.eu/published/workflow?id=4f51080ffe7d57e0, https://usegalaxy.eu/published/workflow?id=9e05bd65faf58ab3, https://workflowhub.eu/workflows/1698?version=1, https://workflowhub.eu/workflows/662?version=1, https://workflowhub.eu/workflows/758?version=1 |
climate/earth_system, ecology/obisindicators |
|
ocean |
argo_getdata, copernicusmarine, divand_full_analysis |
Access, process, and visualise oceanographic data for the Earth System |
2023-11-17 |
https://github.com/Marie59/FE-ft-ESG/tree/main/ocean |
0.1.15 |
copernicusmarine |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean |
|
|
|
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
14 |
14 |
189 |
189 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
189 |
189 |
14 |
14 |
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climate/argo_pangeo, climate/earth_system, climate/ocean-variables |
|
ocean_data_view_manager |
tool_biogeochemical_calibration, tool_odv, tool_odv_history |
The tool merges various datasets with a common vocabulary and creates a single generic ODV spreadsheet in an automatic way. |
2025-03-18 |
https://github.com/Marie59/FE-ft-ESG/tree/main/ocean |
2.1 |
|
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager |
|
|
|
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
112 |
112 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
112 |
112 |
4 |
4 |
https://usegalaxy.eu/published/workflow?id=44827462c065bae3, https://usegalaxy.eu/published/workflow?id=d3d9d1f173fd7bfe, https://workflowhub.eu/workflows/1961?version=1 |
climate/ocean_qcv_analysis |
|
ocean_neural_network |
bgc_canyon_b |
Robust Estimation of Open Ocean CO2 Variables and Nutrient Concentrations From T, S, and O2 Data Using Bayesian Neural Networks |
2025-03-18 |
https://github.com/Marie59/FE-ft-ESG/tree/main/ocean |
0.9.3 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_neural_network |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_neural_network |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
ogcProcess_otb_bandmath |
otb_band_math |
Outputs a monoband image which is the result of a mathematical operation on several multi-band images. |
2024-03-12 |
https://github.com/AquaINFRA/galaxy |
1.0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
100 |
100 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
100 |
100 |
8 |
8 |
https://usegalaxy.eu/published/workflow?id=b1fa4a3561988704, https://usegalaxy.eu/published/workflow?id=e8244d1c80ea0470 |
|
|
ogcProcess_otb_meanShiftSmoothing |
otb_mean_shift_smoothing |
This application smooths an image using the MeanShift algorithm. |
2024-03-12 |
https://github.com/AquaINFRA/galaxy |
1.0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
57 |
57 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
57 |
57 |
4 |
4 |
https://usegalaxy.eu/published/workflow?id=e8244d1c80ea0470 |
|
|
omero_clean_rois_tables |
omero_clean_rois_tables |
Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down |
2023-06-23 |
|
20230623 |
fiji |
20250206 |
To update |
Imaging |
|
|
|
|
lldelisle |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
omero_get_children_ids |
omero_get_children_ids |
Get omero id of children of an omero object id |
2023-12-22 |
|
0.2.0 |
omero-py |
5.11.1 |
To update |
Imaging |
|
|
|
|
lldelisle |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
omero_get_full_images |
omero_get_full_images |
Get full images from omero |
2024-05-21 |
|
20240521 |
fiji |
20250206 |
To update |
Imaging |
|
|
|
|
lldelisle |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
omero_hyperstack_to_fluo_measurements_on_gastruloid |
omero_hyperstack_to_fluo_measurements_on_gastruloid |
Analyse Hyperstack on OMERO server to measure fluorescence levels |
2023-03-24 |
|
20230809 |
fiji |
20250206 |
To update |
Imaging |
|
|
|
|
lldelisle |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
omero_hyperstack_to_gastruloid_measurements |
omero_hyperstack_to_gastruloid_measurements |
Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements |
2023-03-24 |
|
20240214 |
fiji |
20250206 |
To update |
Imaging |
|
|
|
|
lldelisle |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
omero_upload |
omero_dataset_to_plate, omero_filter, omero_get_id, omero_get_value, omero_import, omero_metadata_import, omero_roi_import |
Interact with an OMERO.server using omero-py and ezomero. |
2024-02-07 |
https://github.com/ome/omero-py/ |
5.18.0 |
|
|
To update |
Imaging |
Image analysis |
Image analysis |
Imaging, Data visualisation |
Imaging, Data visualisation |
ufz |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero |
omero |
OMERO |
Client-server Java software for visualisation, management and analysis of biological microscope images. |
|
0 |
0 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
2 |
2 |
https://workflowhub.eu/workflows/1258?version=1, https://workflowhub.eu/workflows/1259?version=1 |
imaging/omero-suite |
|
openmm |
pdbfixer |
OpenMM is a toolkit for molecular simulation using high performance GPU code. |
2022-03-25 |
https://github.com/openmm |
1.8.1 |
pdbfixer |
|
To update |
Molecular Dynamics, Computational chemistry |
|
|
|
|
chemteam |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
100 |
100 |
1933 |
1933 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1933 |
1933 |
100 |
100 |
|
|
|
openms |
AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter |
OpenMS Suite for LC/MS data management and analyses |
2017-02-21 |
https://www.openms.de/ |
3.1 |
openms |
3.4.1 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms |
|
|
|
|
0 |
34 |
144 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
18 |
141 |
124 |
583 |
698 |
31371 |
114208 |
10 |
10 |
417 |
417 |
33 |
34 |
1304 |
1308 |
0 |
0 |
0 |
0 |
115933 |
33092 |
742 |
626 |
https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=68edbb8eec38ad00, https://usegalaxy.eu/published/workflow?id=7463b26aab6a965d, https://usegalaxy.eu/published/workflow?id=86d50bbaaa3936dc, https://usegalaxy.eu/published/workflow?id=afb138fc03ca61a8, https://usegalaxy.eu/published/workflow?id=d55df785d4c71876, https://usegalaxy.eu/published/workflow?id=da10c475c83c5469, https://usegalaxy.eu/published/workflow?id=e9e41c23261d4ac5, https://usegalaxy.eu/published/workflow?id=eaf4d8f8fb3e683d, https://usegalaxy.org.au/published/workflow?id=03efeb2948494130, https://usegalaxy.org.au/published/workflow?id=236e0f306916149b, https://usegalaxy.org.au/published/workflow?id=33922db405a97cbb, https://usegalaxy.org.au/published/workflow?id=59c9a6efaf57ce35, https://usegalaxy.org.au/published/workflow?id=65a659982f955743, https://usegalaxy.org.au/published/workflow?id=7cddb345877f08bf, https://usegalaxy.org.au/published/workflow?id=88fa3e250db2d70e, https://usegalaxy.org.au/published/workflow?id=c2f449e69d06ccf5, https://usegalaxy.org.au/published/workflow?id=da79aa2dfd6b34bc, https://usegalaxy.org/published/workflow?id=0775ff66d1bc04b5, https://usegalaxy.org/published/workflow?id=9865fee6c68fc201, https://usegalaxy.org/published/workflow?id=f9048d9678e21f36, https://workflowhub.eu/workflows/1394?version=1, https://workflowhub.eu/workflows/1399?version=1, https://workflowhub.eu/workflows/1421?version=1, https://workflowhub.eu/workflows/1424?version=1, https://workflowhub.eu/workflows/1434?version=1, https://workflowhub.eu/workflows/1438?version=1, https://workflowhub.eu/workflows/1446?version=1, https://workflowhub.eu/workflows/1449?version=1, https://workflowhub.eu/workflows/1452?version=1, https://workflowhub.eu/workflows/1463?version=1, https://workflowhub.eu/workflows/613?version=2 |
proteomics/DIA_Analysis_OSW, proteomics/DIA_lib_OSW, proteomics/database-handling, proteomics/ntails, proteomics/protein-id-oms, proteomics/protein-id-sg-ps, proteomics/protein-quant-sil |
|
packmol |
packmol |
PACKMOL is a package for creating starting structures for Molecular Dynamics simulations |
2018-10-04 |
http://m3g.iqm.unicamp.br/packmol/home.shtml |
18.169.1 |
packmol |
|
To update |
Molecular Dynamics, Computational chemistry |
|
|
|
|
chemteam |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
30 |
36 |
208 |
300 |
12 |
12 |
434 |
434 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
734 |
642 |
48 |
42 |
|
|
|
pampa |
pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm |
Tools to compute and analyse biodiversity metrics |
2020-06-06 |
|
0.0.2 |
|
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/ColineRoyaux/PAMPA-Galaxy |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA |
|
|
|
|
0 |
5 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
4 |
50 |
53 |
1997 |
2045 |
0 |
0 |
0 |
0 |
26 |
26 |
1141 |
1141 |
1 |
1 |
1 |
1 |
3187 |
3139 |
80 |
77 |
https://usegalaxy.eu/published/workflow?id=428be4c7d1fd828f, https://usegalaxy.eu/published/workflow?id=7c45c90fffe40aca, https://usegalaxy.eu/published/workflow?id=d33ab07e4cf44f8c, https://workflowhub.eu/workflows/1696?version=1 |
ecology/PAMPA-toolsuite-tutorial |
|
pathifier |
pathifier |
pathifier |
2019-09-03 |
https:// |
1.40.0 |
bioconductor-pathifier |
1.44.0 |
To update |
Transcriptomics, Statistics |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier |
https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
13 |
13 |
265 |
265 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
265 |
265 |
13 |
13 |
|
|
|
pep_pointer |
pep_pointer |
PepPointer categorizes peptides by their genomic coordinates. |
2017-12-19 |
|
0.1.3+galaxy1 |
python |
|
To update |
Genomic Interval Operations, Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
73 |
78 |
603 |
666 |
16 |
16 |
27 |
27 |
12 |
12 |
215 |
215 |
0 |
0 |
0 |
0 |
908 |
845 |
106 |
101 |
https://usegalaxy.eu/published/workflow?id=08bbf87ab2a2230e, https://usegalaxy.eu/published/workflow?id=09194b5a549f7979, https://usegalaxy.eu/published/workflow?id=3a178ff6884a5d6d, https://usegalaxy.eu/published/workflow?id=4bd0827030df02a3, https://usegalaxy.eu/published/workflow?id=d375fb9af8d46793, https://usegalaxy.eu/published/workflow?id=f946efa49bd41a43, https://usegalaxy.org.au/published/workflow?id=c049ae8f729b2d7e, https://usegalaxy.org.au/published/workflow?id=cf5ab8fe4e2c0859, https://usegalaxy.org/published/workflow?id=336d74481d2f721a, https://workflowhub.eu/workflows/1457?version=1, https://workflowhub.eu/workflows/1467?version=1, https://workflowhub.eu/workflows/1790?version=1 |
proteomics/neoantigen-variant-annotation, proteomics/proteogenomics-novel-peptide-analysis |
|
pepquery |
pepquery |
A peptide-centric MS search engine for novel peptide identification and validation. |
2020-01-22 |
https://pepquery.org |
1.6.2 |
pepquery |
2.0.2 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
75 |
77 |
7231 |
7437 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7437 |
7231 |
77 |
75 |
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|
|
pepquery2 |
pepquery2, pepquery2_index, pepquery2_show_sets |
PepQuery2 peptide-centric MS search for peptide identification and validation |
2022-10-02 |
https://pepquery.org |
2.0.2 |
pepquery |
2.0.2 |
Up-to-date |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 |
|
|
|
|
0 |
1 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
0 |
34 |
34 |
5598 |
5598 |
5 |
5 |
67 |
67 |
8 |
8 |
251 |
251 |
0 |
0 |
0 |
0 |
5916 |
5916 |
47 |
47 |
https://usegalaxy.eu/published/workflow?id=5374daf356516a40, https://usegalaxy.eu/published/workflow?id=6d3332794ceca465, https://usegalaxy.eu/published/workflow?id=71816adecac46e74, https://usegalaxy.eu/published/workflow?id=73dc2384535bf6af, https://usegalaxy.eu/published/workflow?id=8e997deae5a382c4, https://usegalaxy.eu/published/workflow?id=9b4e6c5f2c1babce, https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d, https://usegalaxy.org.au/published/workflow?id=762791e094457bf2, https://usegalaxy.org.au/published/workflow?id=832a30759469d3fe, https://usegalaxy.org.au/published/workflow?id=9281258aefd17c0c, https://usegalaxy.org/published/workflow?id=42331381df05b956, https://usegalaxy.org/published/workflow?id=8ecc114eb9097855, https://usegalaxy.org/published/workflow?id=d0847ce8261eb922, https://workflowhub.eu/workflows/1218?version=1, https://workflowhub.eu/workflows/1406?version=1, https://workflowhub.eu/workflows/1416?version=1, https://workflowhub.eu/workflows/1425?version=1, https://workflowhub.eu/workflows/1464?version=1, https://workflowhub.eu/workflows/1789?version=1, https://workflowhub.eu/workflows/1791?version=1 |
microbiome/clinical-mp-3-verification, proteomics/clinical-mp-3-verification, proteomics/neoantigen-hla-binding-novel-peptides, proteomics/neoantigen-peptide-verification |
|
peptide_genomic_coordinate |
peptide_genomic_coordinate |
Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files |
2019-03-29 |
|
1.0.0 |
python |
|
To update |
Proteomics |
|
|
|
|
galaxyp |
|
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
72 |
76 |
520 |
566 |
11 |
11 |
17 |
17 |
8 |
8 |
199 |
199 |
0 |
0 |
0 |
0 |
782 |
736 |
95 |
91 |
https://usegalaxy.eu/published/workflow?id=08bbf87ab2a2230e, https://usegalaxy.eu/published/workflow?id=09194b5a549f7979, https://usegalaxy.eu/published/workflow?id=3a178ff6884a5d6d, https://usegalaxy.org.au/published/workflow?id=c049ae8f729b2d7e, https://workflowhub.eu/workflows/1467?version=1 |
proteomics/proteogenomics-novel-peptide-analysis |
|
peptideshaker |
fasta_cli, ident_params, peptide_shaker, search_gui |
PeptideShaker and SearchGUI |
2015-01-31 |
http://compomics.github.io |
|
searchgui |
4.3.15 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker |
|
|
|
|
0 |
4 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
4 |
2 |
541 |
635 |
10278 |
19384 |
236 |
236 |
1790 |
1790 |
54 |
54 |
3790 |
3855 |
2 |
3 |
15 |
21 |
25050 |
15873 |
928 |
833 |
https://usegalaxy.eu/published/workflow?id=03e52c8c71710cae, https://usegalaxy.eu/published/workflow?id=0aee7ffa5f6384bd, https://usegalaxy.eu/published/workflow?id=0e0be913c3e27022, https://usegalaxy.eu/published/workflow?id=1706bfa819bbfa89, https://usegalaxy.eu/published/workflow?id=1809fcaec264eac9, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=249c7569b61fb349, https://usegalaxy.eu/published/workflow?id=2a7e63d1cc583002, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41d096891bada138, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=41e9882300fa2386, https://usegalaxy.eu/published/workflow?id=4c81726bde25c36a, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=607ca3a9d45bd080, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6766bed39f614b7c, https://usegalaxy.eu/published/workflow?id=68967c922de149ae, https://usegalaxy.eu/published/workflow?id=6aca8a72626c521b, https://usegalaxy.eu/published/workflow?id=6b7b86756060659b, https://usegalaxy.eu/published/workflow?id=6bd8311554412c38, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6e5f0d05c91876c2, https://usegalaxy.eu/published/workflow?id=7463b26aab6a965d, https://usegalaxy.eu/published/workflow?id=78e1769f1dcb797b, https://usegalaxy.eu/published/workflow?id=7dd7908f4c8d722a, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=8af41219411062ad, https://usegalaxy.eu/published/workflow?id=8fc1ea9e94bc723d, https://usegalaxy.eu/published/workflow?id=912b81c444e35045, https://usegalaxy.eu/published/workflow?id=9a8b5e99ca9500e3, https://usegalaxy.eu/published/workflow?id=9c0132dd81297afe, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=a4d6b9dc6b396933, https://usegalaxy.eu/published/workflow?id=a657b412b37b971b, https://usegalaxy.eu/published/workflow?id=b73fa5f8c0403454, https://usegalaxy.eu/published/workflow?id=b89cf3cb6a25c999, https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=c4119ea7ffd29094, https://usegalaxy.eu/published/workflow?id=c6b6ba35e5b6500a, https://usegalaxy.eu/published/workflow?id=c750484145c9903b, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=d1d5a6bd6571d47f, https://usegalaxy.eu/published/workflow?id=d2a9d4eb5b3c72a2, https://usegalaxy.eu/published/workflow?id=d5756e3ebfa285ef, https://usegalaxy.eu/published/workflow?id=d9e7a940b2d410bc, https://usegalaxy.eu/published/workflow?id=df926c5ab8d27192, https://usegalaxy.eu/published/workflow?id=eb54512829d8509c, https://usegalaxy.eu/published/workflow?id=edea08c943ff9c5e, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.eu/published/workflow?id=f34c76e2d8045725, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d, https://usegalaxy.org.au/published/workflow?id=1b9bfe7ce484fdc2, https://usegalaxy.org.au/published/workflow?id=33922db405a97cbb, https://usegalaxy.org.au/published/workflow?id=ba217a34d7e1b5ee, https://usegalaxy.org.au/published/workflow?id=c2f449e69d06ccf5, https://usegalaxy.org.au/published/workflow?id=f9f685d6150e48c5, https://usegalaxy.org/published/workflow?id=e97da2da9e0290a7, https://workflowhub.eu/workflows/1225?version=1, https://workflowhub.eu/workflows/1394?version=1, https://workflowhub.eu/workflows/1396?version=1, https://workflowhub.eu/workflows/1399?version=1, https://workflowhub.eu/workflows/1429?version=1, https://workflowhub.eu/workflows/1435?version=1, https://workflowhub.eu/workflows/1443?version=1, https://workflowhub.eu/workflows/1450?version=1 |
microbiome/clinical-mp-2-discovery, proteomics/clinical-mp-2-discovery, proteomics/metaproteomics, proteomics/metaquantome-data-creation, proteomics/protein-id-sg-ps, proteomics/proteogenomics-dbsearch |
|
pepxml_to_xls |
|
Convert PepXML to Tabular |
2015-01-24 |
|
|
|
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
percolator |
batched_set_list_creator, percolator, percolator_input_converters, pout2mzid |
Percolator |
2016-04-12 |
|
3.5 |
percolator |
3.7.1 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator |
|
|
|
|
0 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
6 |
7 |
58 |
378 |
0 |
0 |
0 |
0 |
4 |
4 |
1434 |
1454 |
0 |
0 |
0 |
0 |
1832 |
1492 |
11 |
10 |
|
|
|
phabox |
phabox_cherry, phabox_contamination, phabox_end_to_end, phabox_phagcn, phabox_phamer, phabox_phatyp, phabox_phavip, phabox_tree, phabox_votu |
Identify and analyze phage contigs in metagenomic data |
2024-11-12 |
https://github.com/KennthShang/PhaBOX |
2.1.11 |
phabox |
2.1.12 |
To update |
Metagenomics |
Sequence assembly, Taxonomic classification, Visualisation |
Sequence assembly, Taxonomic classification, Visualisation |
Metagenomics, Microbial ecology, Sequence assembly, Taxonomy |
Metagenomics, Microbial ecology, Sequence assembly, Taxonomy |
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phabox |
phabox |
PhaBOX |
Web server for identifying and characterizing phage contigs in metagenomic data. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
phi_toolkit_report |
phi_toolkit_report |
Phage host interaction toolkit report generator |
2025-06-04 |
https://git.ufz.de/borimcor/phage-host-analysis |
0.2.0 |
bioconductor-biostrings |
2.74.0 |
To update |
Metagenomics |
|
|
|
|
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phi-toolkit |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
pindel |
pindel |
Pindel detects genome-wide structural variation. |
2021-09-29 |
http://artbio.fr |
0.2.5b9 |
pindel |
0.2.5b9 |
Up-to-date |
Variant Analysis |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel |
https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
plot_tools_astro_tool |
plot_tools_astro_tool |
Plot Tools |
2024-11-22 |
|
0.0.1+galaxy0 |
pandas |
|
To update |
Astronomy |
|
|
|
|
astroteam |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/plot-tools |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
1 |
1 |
https://workflowhub.eu/workflows/1369?version=1 |
|
|
pmd_fdr |
pmd_fdr |
Calculate Precursor Mass Discrepancy (PMD) for MS/MS |
2019-10-01 |
https://github.com/slhubler/PMD-FDR-for-Galaxy-P |
1.4.0 |
r-base |
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
positions2snv_alignment |
positions2snv_alignment |
Generate alignment of SNVs from SNVPhyl variant table. |
2016-11-04 |
https://snvphyl.readthedocs.io/en/latest/ |
1.8.2 |
snvphyl-tools |
1.8.2 |
Up-to-date |
Variant Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/snvphyl-galaxy |
https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
positions2snv_invariant_alignment |
positions2snv_invariant_alignment |
Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. |
2016-11-07 |
https://snvphyl.readthedocs.io/en/latest/ |
1.8.2 |
snvphyl-tools |
1.8.2 |
Up-to-date |
Variant Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/snvphyl-galaxy |
https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
probecoverage |
probecoverage |
computes and plots read coverage of genomic regions by sequencing datasets |
2017-09-22 |
http://artbio.fr |
0.22.0 |
pysam |
0.23.3 |
To update |
Sequence Analysis, Genomic Interval Operations, Graphics, Statistics |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage |
https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
proteinpilot |
convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml |
|
2015-01-24 |
|
0.1 |
|
|
To update |
|
|
|
|
|
galaxyp |
|
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
proteomics_moff |
proteomics_moff |
moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. |
2017-12-11 |
https://github.com/compomics/moFF |
2.0.3 |
moff |
2.0.3 |
Up-to-date |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
14 |
35 |
280 |
787 |
0 |
0 |
0 |
0 |
4 |
4 |
172 |
181 |
0 |
0 |
0 |
0 |
968 |
452 |
39 |
18 |
|
|
|
proteomiqon_joinquantpepionswithproteins |
proteomiqon_joinquantpepionswithproteins |
The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. |
2021-09-16 |
https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html |
0.0.1 |
proteomiqon-joinquantpepionswithproteins |
0.0.2 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
5 |
5 |
372 |
372 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
372 |
372 |
5 |
5 |
|
|
|
proteomiqon_labeledproteinquantification |
proteomiqon_labeledproteinquantification |
The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions. |
2021-09-16 |
https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html |
0.0.1 |
proteomiqon-labeledproteinquantification |
0.0.3 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
10 |
10 |
19 |
19 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
19 |
19 |
10 |
10 |
|
|
|
proteomiqon_labelfreeproteinquantification |
proteomiqon_labelfreeproteinquantification |
The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. |
2021-10-13 |
https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html |
0.0.1 |
proteomiqon-labelfreeproteinquantification |
0.0.3 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
7 |
7 |
11 |
11 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
11 |
11 |
7 |
7 |
|
|
|
proteomiqon_mzmltomzlite |
proteomiqon_mzmltomzlite |
The tool MzMLToMzLite allows to convert mzML files to mzLite files. |
2021-06-30 |
https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html |
0.0.8 |
proteomiqon-mzmltomzlite |
0.0.8 |
Up-to-date |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
10 |
10 |
723 |
723 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
723 |
723 |
10 |
10 |
|
|
|
proteomiqon_peptidedb |
proteomiqon_peptidedb |
The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format. |
2021-07-04 |
https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html |
0.0.7 |
proteomiqon-peptidedb |
0.0.7 |
Up-to-date |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
12 |
12 |
96 |
96 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
96 |
96 |
12 |
12 |
|
|
|
proteomiqon_peptidespectrummatching |
proteomiqon_peptidespectrummatching |
Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem. |
2021-07-15 |
https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html |
0.0.7 |
proteomiqon-peptidespectrummatching |
0.0.7 |
Up-to-date |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
5 |
5 |
686 |
686 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
686 |
686 |
5 |
5 |
|
|
|
proteomiqon_proteininference |
proteomiqon_proteininference |
MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from. |
2021-07-09 |
https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html |
0.0.7 |
proteomiqon-proteininference |
0.0.7 |
Up-to-date |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
6 |
6 |
89 |
89 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
89 |
89 |
6 |
6 |
|
|
|
proteomiqon_psmbasedquantification |
proteomiqon_psmbasedquantification |
The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. |
2021-07-09 |
https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html |
0.0.8 |
proteomiqon-psmbasedquantification |
0.0.9 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
4 |
4 |
604 |
604 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
604 |
604 |
4 |
4 |
|
|
|
proteomiqon_psmstatistics |
proteomiqon_psmstatistics |
The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. |
2021-07-09 |
https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html |
0.0.8 |
proteomiqon-psmstatistics |
0.0.8 |
Up-to-date |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
6 |
6 |
694 |
694 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
694 |
694 |
6 |
6 |
|
|
|
proteore_venn_diagram |
proteore_venn_diagram |
ProteoRE JVenn Diagram |
2021-05-17 |
|
2021.06.08 |
python |
|
To update |
Proteomics |
|
|
|
|
galaxyp |
|
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
15 |
15 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
15 |
15 |
1 |
1 |
|
|
|
protxml_to_xls |
protxml_to_xls |
|
2015-01-24 |
|
0.1.0 |
trans_proteomic_pipeline |
|
To update |
|
|
|
|
|
galaxyp |
|
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
psm_eval |
psm_eval |
|
2015-01-24 |
|
0.1.0 |
binaries_for_psm_eval |
|
To update |
|
|
|
|
|
galaxyp |
|
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
psm_to_sam |
PSMtoSAM |
PSM to SAM |
2017-10-06 |
https://bioconductor.org/packages/release/bioc/html/proBAMr.html |
1.3.2.1 |
r-base |
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam |
|
|
|
|
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
psm_validation |
psmvalidator |
Validate PSM from Ion Fragmentation |
2020-10-13 |
https://github.com/galaxyproteomics/psm_fragments.git |
1.0.3 |
|
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
4 |
4 |
20 |
20 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
20 |
20 |
4 |
4 |
|
|
|
psy_maps |
psy_maps |
Visualization of regular geographical data on a map with psyplot |
2019-03-15 |
https://github.com/Chilipp/psy-maps |
1.3.1 |
python |
|
To update |
Visualization, Climate Analysis |
|
|
|
|
climate |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
60 |
70 |
303 |
563 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
563 |
303 |
70 |
60 |
https://usegalaxy.eu/published/workflow?id=21363a774a7575f0, https://usegalaxy.eu/published/workflow?id=392a5d91ac221104, https://usegalaxy.eu/published/workflow?id=6df53b44018b2235, https://workflowhub.eu/workflows/1441?version=1 |
climate/climate-101 |
|
ptxqc |
maxquant_ptxqc |
Quality control reports for MaxQuant results |
2025-04-16 |
https://github.com/cbielow/PTXQC |
1.1.2 |
r-ptxqc |
|
To update |
Proteomics |
Validation |
Validation |
Proteomics |
Proteomics |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ptxqc |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ptxqc |
ptxqc |
PTXQC |
PTXQC is a quality control pipeline for proteomics results generated by MaxQuant. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
pyprophet |
pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample |
Semi-supervised learning and scoring of OpenSWATH results. |
2015-02-06 |
https://github.com/PyProphet/pyprophet |
2.1.4 |
pyprophet |
3.0.1 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet |
|
|
|
|
0 |
5 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
6 |
6 |
35 |
37 |
1794 |
2725 |
0 |
0 |
0 |
0 |
5 |
5 |
1052 |
1052 |
0 |
0 |
0 |
0 |
3777 |
2846 |
42 |
40 |
https://workflowhub.eu/workflows/1463?version=1 |
proteomics/DIA_Analysis_OSW |
|
pyteomics |
mztab2tsv |
Tools using the pyteomics library |
2021-01-15 |
https://pyteomics.readthedocs.io/en/latest/ |
4.4.1 |
pyteomics |
4.7.5 |
To update |
Proteomics, Metabolomics |
Protein identification |
Protein identification |
Proteomics, Proteomics experiment |
Proteomics, Proteomics experiment |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics |
pyteomics |
Pyteomics |
Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more. |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
5 |
5 |
93 |
93 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
93 |
93 |
5 |
5 |
|
|
|
quantp |
quantp |
Correlation between protein and transcript abundance |
2018-09-13 |
|
1.1.2 |
r-data.table |
1.11.6 |
To update |
Proteomics |
|
|
|
|
galaxyp |
|
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
13 |
23 |
71 |
244 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
244 |
71 |
23 |
13 |
|
|
|
quantwiz_iq |
quantwiz_iq |
Isobaric Quantitation using QuantWiz-IQ |
2020-01-21 |
https://sourceforge.net/projects/quantwiz/ |
2.0 |
quantwiz-iq |
2.0 |
Up-to-date |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
2 |
4 |
26 |
57 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
57 |
26 |
4 |
2 |
|
|
|
query |
query |
Execute an SQL statement on a set of tables |
2020-12-09 |
|
0.2 |
click |
|
To update |
Text Manipulation |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/query |
https://github.com/RECETOX/galaxytools/tree/master/tools/query |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
qupath_roi_splitter |
qupath_roi_splitter |
Split ROI coordinates of QuPath TMA annotation by cell type |
2023-04-12 |
https://github.com/npinter/ROIsplitter |
0.3.2 |
geojson |
|
To update |
Imaging |
|
|
|
|
galaxyp |
hhttps://github.com/npinter/ROIsplitter |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
11 |
11 |
232 |
232 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
232 |
232 |
11 |
11 |
|
|
|
ramclustr |
ramclustr, ramclustr_define_experiment |
|
2020-11-05 |
https://rdrr.io/cran/RAMClustR/ |
1.3.1 |
r-ramclustr |
1.3.1 |
Up-to-date |
Metabolomics |
Imputation, Standardisation and normalisation, Clustering, Correlation |
Imputation, Standardisation and normalisation, Clustering, Correlation |
Metabolomics |
Metabolomics |
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr |
https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr |
ramclustr |
RAMClustR |
A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. |
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
36 |
36 |
103 |
103 |
15 |
15 |
37 |
37 |
3 |
3 |
707 |
707 |
42 |
42 |
304 |
304 |
1151 |
1151 |
96 |
96 |
https://usegalaxy.eu/published/workflow?id=3086366b744e8da9, https://usegalaxy.fr/published/workflow?id=1407c1703f360f07, https://workflowhub.eu/workflows/1582?version=1 |
metabolomics/gc_ms_with_xcms |
|
rawtools |
rawtools |
Raw Tools |
2019-02-28 |
https://github.com/kevinkovalchik/RawTools |
|
rawtools |
2.0.4 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
35 |
44 |
72 |
204 |
0 |
0 |
0 |
0 |
15 |
16 |
522 |
550 |
0 |
0 |
0 |
0 |
754 |
594 |
60 |
50 |
|
|
|
rcx_boxplot |
rcx_boxplot |
recetox-boxplot is a tool for plotting boxplots from a tabular/csv/parquet data file. |
2025-01-31 |
https://github.com/RECETOX/galaxytools |
3.5.1 |
r-ggplot2 |
2.2.1 |
To update |
Visualization |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools |
https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_boxplot |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
rcx_tk |
rcx-tk |
Tools to process metadata or alkane files. |
2024-08-01 |
https://github.com/RECETOX/rcx-tk |
0.1.0 |
rcx-tk |
0.1.0 |
Up-to-date |
Metabolomics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/ |
https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
reactome_pathwaymatcher |
reactome_pathwaymatcher |
Reactome Pathway Matcher |
2018-06-08 |
https://github.com/LuisFranciscoHS/PathwayMatcher |
|
pathwaymatcher |
1.9.1 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
70 |
95 |
127 |
280 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
280 |
127 |
95 |
70 |
|
|
|
recetox-aplcms |
recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise |
Peak detection tool for HRMS profile data. |
2021-06-17 |
https://github.com/RECETOX/recetox-aplcms |
0.13.4 |
r-recetox-aplcms |
0.14.1 |
To update |
Metabolomics |
Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment |
Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment |
Metabolomics |
Metabolomics |
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms |
https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms |
recetox-aplcms |
recetox-aplcms |
recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. |
|
0 |
8 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
0 |
7 |
7 |
1540 |
1540 |
0 |
0 |
0 |
0 |
1 |
1 |
410 |
410 |
3 |
3 |
928 |
928 |
2878 |
2878 |
11 |
11 |
https://usegalaxy.eu/published/workflow?id=3086366b744e8da9 |
|
|
recetox-msfinder |
recetox_msfinder |
|
2022-11-28 |
https://github.com/RECETOX/recetox-msfinder |
v3.5.2 |
|
|
To update |
Metabolomics |
Annotation |
Annotation |
Metabolomics |
Metabolomics |
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder |
https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder |
recetox-msfinder |
recetox-msfinder |
This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
9 |
9 |
77 |
77 |
0 |
0 |
0 |
0 |
1 |
1 |
132 |
132 |
7 |
7 |
19 |
19 |
228 |
228 |
17 |
17 |
https://workflowhub.eu/workflows/888?version=2 |
|
|
recetox-xmsannotator |
recetox_xmsannotator_advanced |
|
2021-07-13 |
https://github.com/RECETOX/recetox-xMSannotator |
0.10.0 |
r-recetox-xmsannotator |
0.10.0 |
Up-to-date |
Metabolomics |
Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation |
Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation |
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator |
https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator |
recetox-xmsannotator |
recetox-xMSannotator |
Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
2 |
2 |
9 |
9 |
0 |
0 |
0 |
0 |
3 |
3 |
184 |
184 |
0 |
0 |
0 |
0 |
193 |
193 |
5 |
5 |
|
|
|
regex_find_replace |
regex1, regexColumn1 |
Use python regular expressions to find and replace text |
2017-01-13 |
|
1.0.3 |
python |
|
To update |
Text Manipulation |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace |
|
|
|
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
1008 |
1062 |
112043 |
114777 |
806 |
806 |
23975 |
23983 |
201 |
302 |
7586 |
9717 |
35 |
36 |
743 |
744 |
149221 |
144347 |
2206 |
2050 |
https://usegalaxy.eu/published/workflow?id=0909859a02040efc, https://usegalaxy.eu/published/workflow?id=09c7069ae409c362, https://usegalaxy.eu/published/workflow?id=0c6dd9e75d9a2130, https://usegalaxy.eu/published/workflow?id=152223c8aed27357, https://usegalaxy.eu/published/workflow?id=1590085d315aa80e, https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=1b72af1870c540d6, https://usegalaxy.eu/published/workflow?id=1d4e81b51eae43c4, https://usegalaxy.eu/published/workflow?id=22c4a7a4d41a3f06, https://usegalaxy.eu/published/workflow?id=2a73d658446747de, https://usegalaxy.eu/published/workflow?id=2ae4a83327615155, https://usegalaxy.eu/published/workflow?id=344cd3a3c2ce5302, https://usegalaxy.eu/published/workflow?id=376119528377a3ae, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a25999d71a2343a, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, 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climate/pangeo, data-science/data-manipulation-olympics, digital-humanities/open-refine-tutorial, ecology/ENA_Biodiv_submission, ecology/Ecoregionalization_tutorial, ecology/PAMPA-toolsuite-tutorial, ecology/biodiversity-data-exploration, ecology/ecoregiolifetraits, ecology/marine_omics_bgc, ecology/openrefine_gbif, ecology/phylogeny-data-prep, ecology/regionalGAM, genome-annotation/gene-centric, introduction/data-manipulation-olympics, microbiome/pathogen-detection-from-nanopore-foodborne-data, proteomics/metaquantome-data-creation, proteomics/neoantigen-fusion-database-generation, proteomics/neoantigen-non-reference-database-generation, proteomics/neoantigen-variant-annotation, proteomics/proteogenomics-dbcreation, sequence-analysis/Manage_AB1_Sanger, single-cell/EBI-retrieval, single-cell/bulk-music-2-preparescref, single-cell/bulk-music-3-preparebulk, single-cell/scrna-case_monocle3-trajectories, single-cell/scrna-data-ingest, variant-analysis/trio-analysis |
|
regionalgam |
regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend |
|
2019-06-18 |
https://github.com/RetoSchmucki/regionalGAM |
1.5 |
r-mgcv |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam |
|
|
|
|
0 |
0 |
7 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
7 |
7 |
18 |
39 |
129 |
547 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
547 |
129 |
39 |
18 |
https://usegalaxy.eu/published/workflow?id=8e92a65d3307d87e, https://workflowhub.eu/workflows/1707?version=1 |
ecology/regionalGAM |
|
rem_complex |
rem_complex |
Removes molecular coordination complexes. |
2023-11-21 |
https://github.com/RECETOX/galaxytools |
1.0.0 |
pandas |
|
To update |
Metabolomics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex |
https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
32 |
32 |
0 |
0 |
0 |
0 |
1 |
1 |
180 |
180 |
0 |
0 |
0 |
0 |
212 |
212 |
5 |
5 |
https://workflowhub.eu/workflows/888?version=2 |
|
|
rename_annotated_feature |
rename_annotated_feature |
Update column names in an abundance table using a annotation table with spectral matching results |
2024-05-13 |
https://github.com/RECETOX/galaxytools/ |
1.0.0 |
pandas |
|
To update |
Metabolomics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature |
https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
6 |
6 |
0 |
0 |
0 |
0 |
1 |
1 |
90 |
90 |
0 |
0 |
0 |
0 |
96 |
96 |
5 |
5 |
https://usegalaxy.eu/published/workflow?id=3086366b744e8da9 |
|
|
repenrich |
edger-repenrich, repenrich |
Repeat element profiling |
2017-05-22 |
https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich |
2.31.1 |
|
|
To update |
Transcriptomics |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich |
https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich |
|
|
|
|
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
39 |
42 |
1902 |
2173 |
0 |
0 |
0 |
0 |
2173 |
1902 |
42 |
39 |
|
|
|
repenrich2 |
edger-repenrich2, repenrich2 |
Repeat element profiling using bowtie2 aligner |
2024-04-20 |
https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 |
2.31.1 |
|
|
To update |
Transcriptomics |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 |
https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
retip |
retip_apply, retip_descriptors, retip_filter_rt, retip_train |
|
2020-09-07 |
https://github.com/PaoloBnn/Retip |
0.5.4 |
|
|
To update |
Metabolomics |
Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition |
Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition |
Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry |
Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry |
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/retip |
https://github.com/RECETOX/galaxytools/tree/master/tools/retip |
retip |
Retip |
Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
retrieve_bold |
retrieve_bold |
Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers |
2024-06-21 |
https://anaconda.org/conda-forge/r-bold |
1.3.0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/wpearman1996/MARES_database_pipeline/tree/master |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
15 |
15 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
15 |
15 |
8 |
8 |
|
|
|
retrieve_ensembl_bed |
retrieve_ensembl_bed |
Retrieve cDNA features from Ensembl REST API in BED format |
2018-01-14 |
http://rest.ensembl.org/ |
0.1.0 |
|
|
To update |
Data Source |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
revertr2orientationinbam |
revertR2orientationInBam |
Revert the mapped orientation of R2 mates in a bam. |
2019-04-17 |
|
0.0.2 |
samtools |
1.22.1 |
To update |
SAM |
|
|
|
|
lldelisle |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
12 |
12 |
60 |
60 |
37 |
37 |
637 |
637 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
697 |
697 |
49 |
49 |
https://usegalaxy.eu/published/workflow?id=6ebd09100fc98878, https://usegalaxy.eu/published/workflow?id=c98a14fcf5998159, https://usegalaxy.eu/published/workflow?id=d3494c6124f820b2, https://usegalaxy.eu/published/workflow?id=ef1d11b79a2e1727, https://usegalaxy.eu/published/workflow?id=fa53b172def3fe75, https://usegalaxy.org.au/published/workflow?id=5cd9b9338e75f254, https://usegalaxy.org/published/workflow?id=1f28e673ea725541, https://usegalaxy.org/published/workflow?id=53fdff74729a6780, https://usegalaxy.org/published/workflow?id=778a8867b0a6ea4f, https://usegalaxy.org/published/workflow?id=868acaf49d0743ec, https://usegalaxy.org/published/workflow?id=93e69c7e7a857ca3, https://usegalaxy.org/published/workflow?id=f3c8093c5b8a7233, https://workflowhub.eu/workflows/401?version=13 |
|
|
riassigner |
riassigner, riassigner_from_comment |
|
2021-08-19 |
https://github.com/RECETOX/RIAssigner |
0.4.1 |
riassigner |
0.5.0 |
To update |
Metabolomics |
Standardisation and normalisation |
Standardisation and normalisation |
Metabolomics, Compound libraries and screening, Data submission, annotation and curation |
Metabolomics, Compound libraries and screening, Data submission, annotation and curation |
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner |
https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner |
riassigner |
RIAssigner |
RIAssigner is a python tool for retention index (RI) computation for GC-MS data. |
|
0 |
2 |
2 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
29 |
29 |
75 |
75 |
5 |
5 |
16 |
16 |
1 |
1 |
178 |
178 |
27 |
27 |
161 |
161 |
430 |
430 |
62 |
62 |
https://usegalaxy.eu/published/workflow?id=3086366b744e8da9, https://usegalaxy.fr/published/workflow?id=1407c1703f360f07, https://workflowhub.eu/workflows/1582?version=1 |
metabolomics/gc_ms_with_xcms |
|
rmassbank |
rmassbank |
RMassBank is an R package for processing tandem MS files and building of MassBank records. |
2021-02-25 |
https://github.com/MassBank/RMassBank |
3.0.0 |
python |
|
To update |
Metabolomics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank |
https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
94 |
94 |
2 |
2 |
2 |
2 |
96 |
96 |
3 |
3 |
|
|
|
rsem |
extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie |
transcript quantification from RNA-Seq data |
2017-12-18 |
https://github.com/deweylab/RSEM |
|
rsem |
1.3.3 |
To update |
Transcriptomics, RNA |
|
|
|
|
artbio |
https://github.com/artbio/tools-artbio/tree/master/tools/rsem |
https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
166 |
210 |
345 |
485 |
0 |
0 |
0 |
0 |
4 |
39 |
11 |
146 |
0 |
0 |
0 |
0 |
631 |
356 |
249 |
170 |
|
|
|
salmon_kallisto_mtx_to_10x |
_salmon_kallisto_mtx_to_10x |
Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data |
2019-11-07 |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary |
0.0.1+galaxy6 |
scipy |
|
To update |
Sequence Analysis |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
221 |
232 |
777 |
858 |
90 |
91 |
361 |
363 |
5 |
5 |
5 |
5 |
2 |
2 |
6 |
6 |
1232 |
1149 |
330 |
318 |
https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=83ae28e23099a3f6, https://usegalaxy.eu/published/workflow?id=9a9bbd8046da7b19, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d, https://workflowhub.eu/workflows/1533?version=1, https://workflowhub.eu/workflows/1537?version=1 |
single-cell/scrna-case_alevin |
|
sambamba |
sambamba_sample_or_filter |
filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM |
2020-05-19 |
http://artbio.fr |
0.7.1+galaxy1 |
sambamba |
1.0.1 |
To update |
SAM |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba |
https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba |
|
|
|
|
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
25 |
25 |
1087 |
1087 |
0 |
0 |
0 |
0 |
1087 |
1087 |
25 |
25 |
|
|
|
saqc |
saqc, saqc_executor |
System for automated Quality Control |
2025-01-13 |
https://git.ufz.de/rdm-software/saqc |
2.6.0 |
saqc |
|
To update |
Statistics |
|
|
|
|
ufz |
https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/saqc |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
sashimi_plot |
sashimi_plot |
Generates a sashimi plot from bam files. |
2019-08-21 |
http://artbio.fr |
0.1.1 |
python |
|
To update |
RNA, Transcriptomics, Graphics, Visualization |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot |
https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
scaffold |
scaffold, scaffold_export |
|
2015-01-24 |
|
0.1.0 |
scaffold |
|
To update |
|
|
|
|
|
galaxyp |
|
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
scanpy_scripts |
anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data |
scanpy-scripts, command-line wrapper scripts around Scanpy. |
2018-11-05 |
https://scanpy.readthedocs.io |
1.9.3 |
scanpy-scripts |
1.9.301 |
To update |
Transcriptomics, Sequence Analysis, RNA |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy |
|
|
|
|
0 |
27 |
27 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
14 |
13 |
456 |
501 |
45988 |
53754 |
223 |
223 |
12069 |
12159 |
48 |
48 |
3493 |
3493 |
0 |
0 |
0 |
0 |
69406 |
61550 |
772 |
727 |
https://usegalaxy.eu/published/workflow?id=030e978022e19375, https://usegalaxy.eu/published/workflow?id=0909859a02040efc, https://usegalaxy.eu/published/workflow?id=0d7c643d7720ee31, https://usegalaxy.eu/published/workflow?id=0e6e181234b48121, https://usegalaxy.eu/published/workflow?id=171d6fca2c3339e2, https://usegalaxy.eu/published/workflow?id=1d4e81b51eae43c4, https://usegalaxy.eu/published/workflow?id=37e51e215684bdcc, https://usegalaxy.eu/published/workflow?id=50f8693fac7e134b, https://usegalaxy.eu/published/workflow?id=5b8e4ae3447934d9, https://usegalaxy.eu/published/workflow?id=715ca378c1d68de3, https://usegalaxy.eu/published/workflow?id=71f7725b261c6c83, https://usegalaxy.eu/published/workflow?id=73aa794916b91bb2, https://usegalaxy.eu/published/workflow?id=73b41b975da284d5, https://usegalaxy.eu/published/workflow?id=767f8c990316b66a, https://usegalaxy.eu/published/workflow?id=78dc6fca5b58ec05, https://usegalaxy.eu/published/workflow?id=8f677efac7100097, https://usegalaxy.eu/published/workflow?id=9a0275211e74698a, https://usegalaxy.eu/published/workflow?id=9d15b328d8408715, https://usegalaxy.eu/published/workflow?id=ae79275d3568ad31, https://usegalaxy.eu/published/workflow?id=aeb0f5b74e51f5c2, https://usegalaxy.eu/published/workflow?id=b3cf397fd4d1bea8, https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af, https://usegalaxy.eu/published/workflow?id=d7c0c972c471d514, https://usegalaxy.eu/published/workflow?id=decd6ad0b41289ef, https://usegalaxy.eu/published/workflow?id=e2391c40d24d403f, https://usegalaxy.eu/published/workflow?id=e4e969e9943cdaa5, https://usegalaxy.eu/published/workflow?id=e97bdba3834ac465, https://usegalaxy.eu/published/workflow?id=ebfd7cabc0dc97f8, https://usegalaxy.eu/published/workflow?id=f05754467a439134, https://usegalaxy.eu/published/workflow?id=f27abf3c623d3062, https://usegalaxy.eu/published/workflow?id=ffbbb905164d4c11, https://usegalaxy.org/published/workflow?id=802f5ff14a924e42, https://usegalaxy.org/published/workflow?id=dd43ae9a5b303086, https://workflowhub.eu/workflows/1077?version=1, https://workflowhub.eu/workflows/1356?version=1, https://workflowhub.eu/workflows/1362?version=1, https://workflowhub.eu/workflows/1490?version=1, https://workflowhub.eu/workflows/1496?version=1, https://workflowhub.eu/workflows/1510?version=1, https://workflowhub.eu/workflows/1529?version=1, https://workflowhub.eu/workflows/1535?version=1, https://workflowhub.eu/workflows/1539?version=1, https://workflowhub.eu/workflows/1548?version=1, https://workflowhub.eu/workflows/1550?version=1, https://workflowhub.eu/workflows/1551?version=1, https://workflowhub.eu/workflows/1565?version=1, https://workflowhub.eu/workflows/1745?version=2, https://workflowhub.eu/workflows/467?version=4, https://workflowhub.eu/workflows/468?version=3, https://workflowhub.eu/workflows/512?version=2, https://workflowhub.eu/workflows/513?version=3, https://workflowhub.eu/workflows/646?version=2 |
imaging/multiplex-tissue-imaging-TMA, single-cell/EBI-retrieval, single-cell/bulk-music-2-preparescref, single-cell/scanpy_parameter_iterator, single-cell/scatac-standard-processing-snapatac2, single-cell/scrna-case_alevin-combine-datasets, single-cell/scrna-case_basic-pipeline, single-cell/scrna-case_cell-cycle, single-cell/scrna-case_trajectories, single-cell/scrna-data-ingest, single-cell/scrna-ncbi-anndata |
|
sceasy |
sceasy_convert |
Convert scRNA data object between popular formats |
2019-10-14 |
|
0.0.5 |
r-sceasy |
0.0.7 |
To update |
Transcriptomics |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
301 |
310 |
1543 |
1615 |
103 |
104 |
521 |
522 |
5 |
5 |
349 |
349 |
1 |
1 |
2 |
2 |
2488 |
2415 |
420 |
410 |
https://usegalaxy.eu/published/workflow?id=0e6e181234b48121, https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=9a9bbd8046da7b19, https://usegalaxy.eu/published/workflow?id=a0f1959a9f4533f7, https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d, https://workflowhub.eu/workflows/1533?version=1, https://workflowhub.eu/workflows/1537?version=1 |
single-cell/EBI-retrieval, single-cell/scrna-case_alevin, single-cell/scrna-data-ingest |
|
scripting tools |
singularity_scriptrunner |
suite_scripting |
2023-07-29 |
https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ |
0.3 |
|
|
To update |
Text Manipulation |
|
|
|
|
mbernt |
https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
sdmpredictors |
sdmpredictors_list_layers |
Terrestrial and marine predictors for species distribution modelling. |
2024-03-29 |
https://cran.r-project.org/web/packages/sdmpredictors/index.html |
0.2.15 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
4 |
4 |
|
|
|
sequence_format_converter |
sequence_format_converter |
various fasta to tabular conversions |
2017-09-04 |
http://artbio.fr |
2.2.0 |
python |
|
To update |
Convert Formats, Fasta Manipulation |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter |
https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
sgwb_astro_tool |
sgwb_astro_tool |
SGWB |
2024-04-17 |
|
0.0.1+galaxy0 |
ipython |
|
To update |
Astronomy |
|
|
|
|
astroteam |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
4 |
4 |
https://workflowhub.eu/workflows/815?version=2, https://workflowhub.eu/workflows/831?version=1 |
|
|
shift_longitudes |
shyft_longitudes |
Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees |
2019-03-15 |
https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ |
0.1.0 |
python |
|
To update |
Climate Analysis |
|
|
|
|
climate |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
4 |
5 |
27 |
80 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
80 |
27 |
5 |
4 |
|
|
|
sixgill |
sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge |
Six-frame Genome-Inferred Libraries for LC-MS/MS |
2016-10-11 |
|
0.2.4 |
sixgill |
0.2.4 |
Up-to-date |
Proteomics, MetaProteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill |
|
|
|
|
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
37 |
41 |
167 |
320 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
320 |
167 |
41 |
37 |
https://usegalaxy.eu/published/workflow?id=799b924edd3c401b |
|
|
small_rna_clusters |
small_rna_clusters |
clusters small rna reads in alignment BAM files |
2019-10-06 |
http://artbio.fr |
1.3.0 |
pysam |
0.23.3 |
To update |
RNA, SAM, Graphics, Next Gen Mappers |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters |
https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
small_rna_maps |
small_rna_maps |
Generates small read maps from alignment BAM files |
2017-07-23 |
http://artbio.fr |
3.1.1 |
numpy |
|
To update |
RNA, SAM, Graphics, Next Gen Mappers |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps |
https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
small_rna_signatures |
overlapping_reads, signature |
Computes the tendency of small RNAs to overlap with each other. |
2017-08-28 |
http://artbio.fr |
3.4.2 |
pysam |
0.23.3 |
To update |
RNA |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures |
https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
smithsonian_volcanoes |
smithsonian_volcanoes |
Retrieve data from Volcanoes of the World (VOTW) Database |
2019-04-15 |
https://volcano.si.edu/gvp_votw.cfm |
0.1.0 |
python |
|
To update |
Retrieve Data |
|
|
|
|
climate |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes |
https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
snv_matrix |
snvmatrix |
Generate matrix of SNV distances |
2016-01-21 |
https://snvphyl.readthedocs.io/en/latest/ |
1.8.2 |
snvphyl-tools |
1.8.2 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/snvphyl-galaxy |
https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
snvtocnv |
sequenzaindex, snvtocnv |
infer copy number variations from a vcf file with SNVs using R sequenza |
2021-03-07 |
http://artbio.fr |
3.0.0+galaxy1 |
sequenza-utils |
3.0.0 |
To update |
Variant Analysis |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv |
https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
source_extractor_astro_tool |
source_extractor_astro_tool |
Tool to extract luminous sources from astronomical sky images |
2025-07-18 |
|
0.0.1+galaxy0 |
astropy |
|
To update |
Astronomy |
|
|
|
|
astroteam |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools |
https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/source-extractor |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
7 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
7 |
2 |
2 |
|
|
|
spec2vec |
spec2vec_similarity, spec2vec_training |
Mass spectra similarity scoring using a trained Spec2Vec model. |
2022-11-29 |
https://github.com/iomega/spec2vec |
0.8.0 |
spec2vec |
0.8.0 |
Up-to-date |
Metabolomics |
Spectrum calculation, Spectral library search, Database search, Natural product identification |
Spectrum calculation, Spectral library search, Database search, Natural product identification |
Proteomics experiment, Metabolomics, Natural language processing, Proteomics |
Proteomics experiment, Metabolomics, Natural language processing, Proteomics |
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec |
https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec |
spec2vec |
Spec2Vec |
Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. |
|
0 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
1 |
1 |
176 |
176 |
0 |
0 |
0 |
0 |
177 |
177 |
2 |
2 |
|
|
|
spectrast2spectrast_irt |
gp_spectrast2spectrast_irt |
Filter from spectraST files to swath input files |
2015-04-13 |
|
0.1.0 |
msproteomicstools |
0.11.0 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
spectrast2tsv |
gp_spectrast2tsv |
Filter from spectraST files to swath input files |
2015-02-06 |
|
0.1.0 |
msproteomicstools |
0.11.0 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
spocc_occ |
spocc_occ |
Get species occurences data |
2019-05-23 |
https://cran.r-project.org/web/packages/spocc/index.html |
1.2.2 |
|
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
123 |
146 |
706 |
976 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
28 |
28 |
1004 |
734 |
158 |
135 |
https://usegalaxy.eu/published/workflow?id=3b0803542deff026, https://usegalaxy.eu/published/workflow?id=b0b6c8756070650b, https://workflowhub.eu/workflows/1670?version=1, https://workflowhub.eu/workflows/1687?version=1, https://workflowhub.eu/workflows/404?version=1 |
climate/earth_system, ecology/gbif_cleaning, ecology/species-distribution-modeling |
|
sr_bowtie |
bowtieForSmallRNA |
bowtie wrapper tool to align small RNA sequencing reads |
2017-09-02 |
http://artbio.fr |
2.3.1 |
bowtie |
1.3.1 |
To update |
RNA, Next Gen Mappers |
|
|
Microbiology, Biology |
Microbiology |
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie |
https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie |
sr_bowtie |
sr_bowtie |
Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25... _Bowtie: http://bowtie-bio.sourceforge.net/index.shtmlA generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.However, this Bowtie wrapper tool only takes FASTQ files as inputs.The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis. |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
98 |
98 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
98 |
98 |
2 |
2 |
|
|
|
sr_bowtie_dataset_annotation |
sr_bowtie_dataset_annotation |
Maps iteratively small RNA sequencing datasets to reference sequences. |
2017-09-11 |
http://artbio.fr |
2.8 |
bowtie |
1.3.1 |
To update |
RNA |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation |
https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
srs_tools |
srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata |
Compute biodiversity indicators for remote sensing data from Sentinel 2 |
2022-11-16 |
|
0.0.1 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/Marie59/Sentinel_2A/srs_tools |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools |
|
|
|
|
0 |
0 |
7 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
7 |
0 |
8 |
8 |
274 |
274 |
5 |
5 |
48 |
48 |
0 |
0 |
0 |
0 |
3 |
3 |
22 |
22 |
344 |
344 |
16 |
16 |
https://usegalaxy.eu/published/workflow?id=1d2cd0af01a30a46, https://usegalaxy.eu/published/workflow?id=da88448ab15d167d, https://workflowhub.eu/workflows/1669?version=2, https://workflowhub.eu/workflows/657?version=1 |
ecology/remote-sensing |
|
stoceps |
stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic |
Tools to analyse STOC data. |
2019-09-26 |
|
0.0.2 |
|
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc |
|
|
|
|
0 |
0 |
5 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
24 |
26 |
180 |
354 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
354 |
180 |
26 |
24 |
https://usegalaxy.eu/published/workflow?id=01274dfdbdfcaa88 |
|
|
suite_cell_types_analysis |
ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals |
Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis |
2020-04-07 |
|
1.1.1 |
cell-types-analysis |
0.1.11 |
To update |
Transcriptomics, RNA, Statistics |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis |
|
|
|
|
0 |
0 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
10 |
10 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
4 |
4 |
https://usegalaxy.eu/published/workflow?id=4091c0e2b471fc92, https://usegalaxy.eu/published/workflow?id=6a2c373b3b5d97df, https://usegalaxy.eu/published/workflow?id=a496111beb6e23d0, https://usegalaxy.eu/published/workflow?id=d9e9424dd755729d |
|
|
suite_celltypist |
celltypist_predict |
celltypist - Automated cell type annotation |
2025-02-14 |
https://celltypist.readthedocs.io/en/latest/ |
1.6.3+galaxy1 |
celltypist |
1.7.1 |
To update |
Transcriptomics |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/celltypist |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
suite_decoupler |
score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk |
decoupler - Ensemble of methods to infer biological activities |
2023-09-24 |
https://decoupler-py.readthedocs.io/en/latest/ |
1.4.0+galaxy3 |
decoupler |
1.5.0 |
To update |
Transcriptomics |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
157 |
157 |
5 |
5 |
37 |
37 |
1 |
1 |
3 |
3 |
2 |
2 |
6 |
6 |
203 |
203 |
20 |
20 |
https://usegalaxy.eu/published/workflow?id=04df470a38b10e94, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=c7b9fb6872444809, https://usegalaxy.eu/published/workflow?id=d1b3b62e7f91e217, https://usegalaxy.eu/published/workflow?id=e04be1ab5a16eb9f, https://usegalaxy.org.au/published/workflow?id=5fe66b29dcfb22ab, https://usegalaxy.org/published/workflow?id=13a3954b8894e1b1, https://workflowhub.eu/workflows/1207?version=2, https://workflowhub.eu/workflows/1556?version=1 |
single-cell/pseudobulk-analysis |
|
suite_dropletutils |
dropletutils_empty_drops, dropletutils_read_10x |
De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 |
2019-01-22 |
|
1.0.4 |
dropletutils-scripts |
0.0.5 |
To update |
Transcriptomics, RNA, Statistics, Sequence Analysis |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils |
|
|
|
|
0 |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
290 |
306 |
2109 |
2283 |
126 |
127 |
717 |
720 |
3 |
3 |
5 |
5 |
1 |
1 |
4 |
4 |
3012 |
2835 |
437 |
420 |
https://usegalaxy.eu/published/workflow?id=1e2d27fae8a41ac1, https://usegalaxy.eu/published/workflow?id=4091c0e2b471fc92, https://usegalaxy.eu/published/workflow?id=49a6ddcba35bf085, https://usegalaxy.eu/published/workflow?id=6a2c373b3b5d97df, https://usegalaxy.eu/published/workflow?id=95fe49cafa1dff7e, https://usegalaxy.eu/published/workflow?id=9a9bbd8046da7b19, https://usegalaxy.eu/published/workflow?id=a496111beb6e23d0, https://usegalaxy.eu/published/workflow?id=c6adc3b665828a6f, https://usegalaxy.eu/published/workflow?id=dc9bfa4f633c49b4, https://usegalaxy.eu/published/workflow?id=df455b86fff16116, https://usegalaxy.eu/published/workflow?id=e06934a35fc18f2c, https://usegalaxy.eu/published/workflow?id=f474eb2f45f1d684, https://usegalaxy.eu/published/workflow?id=f944ad0c35d1a472, https://usegalaxy.org/published/workflow?id=1fe6b25825d9b736, https://usegalaxy.org/published/workflow?id=a2a924b871b1c96d, https://workflowhub.eu/workflows/1523?version=1, https://workflowhub.eu/workflows/1533?version=1, https://workflowhub.eu/workflows/1537?version=1 |
single-cell/scrna-case_alevin, single-cell/scrna-data-ingest |
|
suite_ebi_expression_atlas |
retrieve_scxa |
Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home |
2019-07-02 |
|
v0.0.2+galaxy2 |
wget |
|
To update |
Transcriptomics, Sequence Analysis |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
264 |
301 |
1075 |
1259 |
155 |
155 |
448 |
448 |
13 |
13 |
145 |
145 |
4 |
4 |
13 |
13 |
1865 |
1681 |
473 |
436 |
https://usegalaxy.eu/published/workflow?id=030e978022e19375, https://usegalaxy.eu/published/workflow?id=0909859a02040efc, https://usegalaxy.eu/published/workflow?id=0e6e181234b48121, https://usegalaxy.eu/published/workflow?id=1d4e81b51eae43c4, https://usegalaxy.eu/published/workflow?id=290373b2f5fb8c6c, https://usegalaxy.eu/published/workflow?id=5d31bafd82547d5d, https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af, https://usegalaxy.eu/published/workflow?id=dd73bdcbac8649a3, https://usegalaxy.eu/published/workflow?id=e2391c40d24d403f, https://usegalaxy.eu/published/workflow?id=ebfd7cabc0dc97f8, https://usegalaxy.eu/published/workflow?id=f05754467a439134, https://workflowhub.eu/workflows/1356?version=1, https://workflowhub.eu/workflows/1535?version=1, https://workflowhub.eu/workflows/1548?version=1, https://workflowhub.eu/workflows/1552?version=1, https://workflowhub.eu/workflows/1570?version=1 |
single-cell/EBI-retrieval, single-cell/bulk-music-2-preparescref, single-cell/scrna-case_FilterPlotandExplore_SeuratTools, single-cell/scrna-case_basic-pipeline |
|
suite_garnett |
garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file |
De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 |
2020-04-03 |
|
0.2.8 |
garnett-cli |
0.0.5 |
To update |
Transcriptomics, RNA, Statistics, Sequence Analysis |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett |
|
|
|
|
0 |
0 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
4 |
25 |
27 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
27 |
25 |
4 |
3 |
https://usegalaxy.eu/published/workflow?id=8762437178c9a3cf, https://usegalaxy.eu/published/workflow?id=d9e9424dd755729d |
|
|
suite_human_cell_atlas_tools |
hca_matrix_downloader |
Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects |
2019-07-02 |
|
v0.0.4+galaxy0 |
hca-matrix-downloader |
0.0.4 |
To update |
Transcriptomics, Sequence Analysis |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
87 |
114 |
431 |
566 |
1 |
2 |
2 |
3 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
569 |
433 |
116 |
88 |
https://usegalaxy.eu/published/workflow?id=71f7725b261c6c83 |
single-cell/EBI-retrieval |
|
suite_monocle3 |
monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers |
De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. |
2019-09-09 |
|
0.1.4 |
monocle3-cli |
0.0.9 |
To update |
Transcriptomics, RNA, Statistics, Sequence Analysis |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 |
|
|
|
|
0 |
0 |
9 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
76 |
81 |
3733 |
3956 |
60 |
61 |
1939 |
1971 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5927 |
5672 |
142 |
136 |
https://usegalaxy.eu/published/workflow?id=35c092316cdc27d1, https://usegalaxy.eu/published/workflow?id=8762437178c9a3cf, https://usegalaxy.eu/published/workflow?id=a3a7c1853ae7047b, https://usegalaxy.eu/published/workflow?id=a7fcfab658a2cc33, https://usegalaxy.eu/published/workflow?id=d9e9424dd755729d, https://usegalaxy.eu/published/workflow?id=f689faf267fbe504, https://workflowhub.eu/workflows/1516?version=1, https://workflowhub.eu/workflows/1524?version=1, https://workflowhub.eu/workflows/1531?version=1 |
single-cell/scrna-case_monocle3-trajectories, single-cell/scrna-data-ingest |
|
suite_ogs |
ogs_addlayer, ogs_extractboundary, ogs_extractsurface, ogs_generatestructuredmesh, ogs_identifysubdomains, ogs_simulation |
A suite of tools for OpenGeoSys (ogs) |
2025-03-06 |
https://gitlab.opengeosys.org/ogs/ogs |
6.5.3 |
|
|
To update |
Geo Science |
|
|
|
|
ufz |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogs/ |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogs |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
suite_ogs_tools |
msh2vtu, shp2msh |
A suite of tools for OpenGeoSys (ogs) |
2025-03-03 |
https://gitlab.opengeosys.org/ogs/tools/ogstools |
0.4.0 |
ogstools |
|
To update |
Geo Science |
|
|
|
|
ufz |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogstools |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogstools |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
suite_pyscenic |
pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn |
PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ |
2024-08-20 |
|
0.12.1 |
|
|
To update |
Transcriptomics, RNA, Sequence Analysis |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
suite_sc3 |
sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare |
De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. |
2018-11-05 |
|
1.8.0 |
sc3-scripts |
0.0.6 |
To update |
Transcriptomics, RNA, Statistics, Sequence Analysis |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 |
|
|
|
|
0 |
0 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
6 |
9 |
13 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
13 |
9 |
6 |
4 |
|
|
|
suite_scater |
scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results |
De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. |
2018-10-11 |
|
1.10.0 |
scater-scripts |
0.0.5 |
To update |
Transcriptomics, RNA, Statistics, Sequence Analysis |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater |
|
|
|
|
0 |
2 |
6 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
2 |
67 |
80 |
254 |
398 |
5 |
5 |
18 |
18 |
7 |
8 |
387 |
429 |
0 |
0 |
0 |
0 |
845 |
659 |
93 |
79 |
https://usegalaxy.eu/published/workflow?id=f055b8fa294d4be8, https://usegalaxy.org.au/published/workflow?id=3c9140288202aa76, https://workflowhub.eu/workflows/1511?version=1 |
single-cell/scrna-scater-qc |
|
suite_scmap |
scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features |
De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. |
2019-08-30 |
|
1.6.4 |
scmap-cli |
0.1.0 |
To update |
Transcriptomics, RNA, Statistics, Sequence Analysis |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap |
|
|
|
|
0 |
0 |
7 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
11 |
11 |
105 |
114 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
114 |
105 |
11 |
11 |
https://usegalaxy.eu/published/workflow?id=6a2c373b3b5d97df, https://usegalaxy.eu/published/workflow?id=95fe49cafa1dff7e, https://usegalaxy.eu/published/workflow?id=a496111beb6e23d0, https://usegalaxy.eu/published/workflow?id=bcec217b62ccc7af, https://usegalaxy.eu/published/workflow?id=dc9bfa4f633c49b4 |
|
|
suite_scpred |
scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model |
De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 |
2020-04-07 |
|
1.0.2 |
scpred-cli |
0.1.0 |
To update |
Transcriptomics, RNA, Statistics, Sequence Analysis |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred |
|
|
|
|
0 |
0 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
25 |
25 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
25 |
25 |
2 |
2 |
https://usegalaxy.eu/published/workflow?id=4091c0e2b471fc92, https://usegalaxy.eu/published/workflow?id=f474eb2f45f1d684 |
|
|
suite_seurat |
seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features |
De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 |
2018-07-09 |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ |
4.0.0 |
seurat-scripts |
4.4.0 |
To update |
Transcriptomics, RNA, Statistics, Sequence Analysis |
|
|
|
|
ebi-gxa |
|
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat |
|
|
|
|
0 |
14 |
14 |
11 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
19 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
124 |
154 |
5535 |
5985 |
155 |
155 |
3504 |
3504 |
9 |
9 |
563 |
563 |
4 |
4 |
106 |
106 |
10158 |
9708 |
322 |
292 |
https://usegalaxy.eu/published/workflow?id=0909859a02040efc, https://usegalaxy.eu/published/workflow?id=10c5d0560b977a6f, https://usegalaxy.eu/published/workflow?id=26deb6f2521742ea, https://usegalaxy.eu/published/workflow?id=290373b2f5fb8c6c, https://usegalaxy.eu/published/workflow?id=5d31bafd82547d5d, https://usegalaxy.eu/published/workflow?id=704e6c9bc51db49f, https://usegalaxy.eu/published/workflow?id=a0f1959a9f4533f7, https://usegalaxy.eu/published/workflow?id=c52e8b5ab3e8e958, https://usegalaxy.eu/published/workflow?id=d773cbc76253afbf, https://usegalaxy.org/published/workflow?id=59554bfcad77e307, https://workflowhub.eu/workflows/1527?version=1, https://workflowhub.eu/workflows/1535?version=1, https://workflowhub.eu/workflows/1555?version=1, https://workflowhub.eu/workflows/1560?version=1, https://workflowhub.eu/workflows/1570?version=1 |
single-cell/EBI-retrieval, single-cell/scrna-case_FilterPlotandExplore_SeuratTools, single-cell/scrna-data-ingest, single-cell/scrna-seurat-pbmc3k |
|
suite_snvphyl_1_2_3 |
|
SNVPhyl suite defining all dependencies for SNVPhyl |
2015-08-05 |
|
|
|
|
To update |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/snvphyl-galaxy |
https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
tables |
table_pandas_arithmetics, table_pandas_rename_column, table_pandas_rename_columns_regex, table_pandas_transform, table_scipy_interpolate |
Tools to manipulate and analyze data tables. |
2024-11-14 |
https://github.com/RECETOX/galaxytools |
|
scipy |
|
To update |
Metabolomics, Statistics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/tables |
https://github.com/RECETOX/galaxytools/tree/master/tools/tables |
|
|
|
|
0 |
0 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
78 |
78 |
718 |
718 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
718 |
718 |
78 |
78 |
|
|
|
tarfast5 |
tarfast5 |
produces a tar.gz archive of fast5 sequence files |
2021-05-05 |
http://artbio.fr |
0.6.1 |
pigz |
|
To update |
Nanopore |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 |
https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
terrabyte_ogc_api_processes |
terrabyte_ogc_api_processes |
This tool is a wrapper for OGC API Processes (OTB) coming from terrabyte (https://docs.terrabyte.lrz.de/). |
2024-11-11 |
https://github.com/AquaINFRA/galaxy |
0.1.0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/AquaINFRA/tools-ecology/tree/terrabyte_ogc_api_process |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/terrabyte_ogc_api_processes |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
12 |
12 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
12 |
12 |
2 |
2 |
|
|
|
thermo_raw_file_converter |
thermo_raw_file_converter |
Thermo RAW file converter |
2018-09-14 |
https://github.com/compomics/ThermoRawFileParser |
1.3.4 |
thermorawfileparser |
1.4.5 |
To update |
Proteomics |
Conversion, Filtering, Peak detection |
Conversion, Filtering, Peak detection |
Proteomics, Proteomics experiment, Metabolomics |
Proteomics, Proteomics experiment, Metabolomics |
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser |
ThermoRawFileParser |
ThermoRawFileParser |
Open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML |
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
99 |
146 |
2568 |
3222 |
0 |
0 |
0 |
0 |
21 |
21 |
1294 |
1326 |
0 |
0 |
0 |
0 |
4548 |
3862 |
167 |
120 |
https://usegalaxy.eu/published/workflow?id=3086366b744e8da9 |
|
|
topologyeditors |
gromacs_modify_topology, gromacs_extract_topology |
Set of python scripts and associated tool files that can be used to modify topology files. |
2021-12-23 |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors |
0 |
python |
|
To update |
Molecular Dynamics, Computational chemistry |
|
|
|
|
chemteam |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors |
|
|
|
|
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
0 |
7 |
7 |
74 |
74 |
5 |
5 |
25 |
25 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
99 |
99 |
12 |
12 |
https://usegalaxy.eu/published/workflow?id=2a1b21d39ebb6e49, https://usegalaxy.eu/published/workflow?id=3729015f676693c8, https://usegalaxy.eu/published/workflow?id=bf99d06567288766, https://usegalaxy.eu/published/workflow?id=d4d8e907e26c8587, https://workflowhub.eu/workflows/761?version=1, https://workflowhub.eu/workflows/762?version=1, https://workflowhub.eu/workflows/763?version=1, https://workflowhub.eu/workflows/764?version=1 |
|
|
translate_bed |
translate_bed |
Translate BED transcript CDS or cDNA in 3 frames |
2018-01-14 |
http://rest.ensembl.org/ |
0.1.0 |
|
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
185 |
200 |
697 |
914 |
123 |
123 |
505 |
505 |
27 |
27 |
1081 |
1081 |
0 |
0 |
0 |
0 |
2500 |
2283 |
350 |
335 |
https://usegalaxy.eu/published/workflow?id=17916f0229e3c868, https://usegalaxy.eu/published/workflow?id=39afbf843b5513bf, https://usegalaxy.eu/published/workflow?id=3a8150c81b90a3a7, https://usegalaxy.eu/published/workflow?id=6e6cf59bfeb938bf, https://usegalaxy.eu/published/workflow?id=a2f36d4dd48d8ec2, https://usegalaxy.eu/published/workflow?id=a7638e7f908fd90d, https://usegalaxy.org.au/published/workflow?id=0ebaaecf61dfc921, https://usegalaxy.org.au/published/workflow?id=157e7614ae18849b, https://usegalaxy.org.au/published/workflow?id=7cd4fcc8e06ce4fd, https://usegalaxy.org/published/workflow?id=6a3e47124e32e260, https://usegalaxy.org/published/workflow?id=e336bca259abd474, https://workflowhub.eu/workflows/1407?version=1, https://workflowhub.eu/workflows/1437?version=1, https://workflowhub.eu/workflows/1788?version=1 |
proteomics/neoantigen-non-reference-database-generation, proteomics/proteogenomics-dbcreation |
|
translate_bed_sequences |
translate_bed_sequences |
Perform 3 frame translation of BED file augmented with a sequence column |
2016-01-13 |
|
0.2.0 |
biopython |
1.70 |
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
14 |
23 |
37 |
72 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
72 |
37 |
23 |
14 |
|
|
|
ucsc_cell_browser |
ucsc_cell_browser |
Python pipeline and Javascript scatter plot library for single-cell datasets |
2018-09-11 |
https://cells.ucsc.edu/ |
1.0.0+galaxy1 |
ucsc-cell-browser |
1.2.15 |
To update |
Transcriptomics |
|
|
|
|
ebi-gxa |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml |
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
148 |
189 |
731 |
1002 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1002 |
731 |
189 |
148 |
https://usegalaxy.eu/published/workflow?id=5d31bafd82547d5d, https://usegalaxy.eu/published/workflow?id=71f7725b261c6c83, https://usegalaxy.eu/published/workflow?id=ebfd7cabc0dc97f8, https://usegalaxy.eu/published/workflow?id=f27abf3c623d3062 |
|
|
unipept |
unipept |
Unipept retrieves metaproteomics information |
2015-04-03 |
https://github.com/galaxyproteomics/tools-galaxyp |
6.2.4+galaxy0 |
python |
|
To update |
Proteomics |
Prediction and recognition, Visualisation |
Prediction and recognition, Visualisation |
Proteomics, Proteogenomics, Biodiversity, Workflows |
Proteomics, Proteogenomics, Biodiversity, Workflows |
galaxyp |
https://unipept.ugent.be/apidocs |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept |
unipept |
Unipept |
Metaproteomics data analysis with a focus on interactive data visualizations. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
282 |
314 |
4723 |
6047 |
102 |
102 |
384 |
384 |
33 |
33 |
1383 |
1383 |
1 |
1 |
1 |
1 |
7815 |
6491 |
450 |
418 |
https://usegalaxy.eu/published/workflow?id=00e246ea459b0991, https://usegalaxy.eu/published/workflow?id=02700454f57eb556, https://usegalaxy.eu/published/workflow?id=0e0be913c3e27022, https://usegalaxy.eu/published/workflow?id=1706bfa819bbfa89, https://usegalaxy.eu/published/workflow?id=17a1433d0b681d4a, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=28af61ead68e0976, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=50d85103f2275d38, https://usegalaxy.eu/published/workflow?id=58db3e1996a8f093, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6766bed39f614b7c, https://usegalaxy.eu/published/workflow?id=68967c922de149ae, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=6da171871d4f3fd5, https://usegalaxy.eu/published/workflow?id=755ede37d94dc456, https://usegalaxy.eu/published/workflow?id=78e1769f1dcb797b, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=8a85663218676b59, https://usegalaxy.eu/published/workflow?id=8f3cafa3bc59ff82, https://usegalaxy.eu/published/workflow?id=8fc1ea9e94bc723d, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=a4d6b9dc6b396933, https://usegalaxy.eu/published/workflow?id=a657b412b37b971b, https://usegalaxy.eu/published/workflow?id=ba3a5d59b3879764, https://usegalaxy.eu/published/workflow?id=bfe26679d670bb5e, https://usegalaxy.eu/published/workflow?id=c6b6ba35e5b6500a, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231, https://usegalaxy.eu/published/workflow?id=d0e062aee910086a, https://usegalaxy.eu/published/workflow?id=d148459a4d4b91f1, https://usegalaxy.eu/published/workflow?id=d9e7a940b2d410bc, https://usegalaxy.eu/published/workflow?id=df926c5ab8d27192, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.eu/published/workflow?id=fc42cc9467c6ee8d, https://usegalaxy.org.au/published/workflow?id=050a66ff6d4c2b53, https://usegalaxy.org.au/published/workflow?id=f9f685d6150e48c5, https://usegalaxy.org/published/workflow?id=3f797bfb67130883, https://workflowhub.eu/workflows/1219?version=1, https://workflowhub.eu/workflows/1433?version=1, https://workflowhub.eu/workflows/1443?version=1, https://workflowhub.eu/workflows/1450?version=1, https://workflowhub.eu/workflows/1482?version=1 |
microbiome/clinical-mp-5-data-interpretation, proteomics/clinical-mp-5-data-interpretation, proteomics/metaproteomics, proteomics/metaquantome-data-creation |
|
uniprotxml_downloader |
uniprotxml_downloader |
Download UniProt proteome in XML or fasta format |
2016-03-08 |
https://www.uniprot.org/help/programmatic_access |
2.5.0 |
requests |
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
239 |
313 |
1805 |
2133 |
73 |
73 |
143 |
143 |
41 |
41 |
1139 |
1139 |
0 |
0 |
0 |
0 |
3415 |
3087 |
427 |
353 |
https://usegalaxy.eu/published/workflow?id=0ab3e47ebd3b520e, https://usegalaxy.eu/published/workflow?id=229a955d29bd4064, https://usegalaxy.eu/published/workflow?id=24eaa682897379c8, https://usegalaxy.eu/published/workflow?id=3e01a2c6d954ae6e, https://usegalaxy.eu/published/workflow?id=41df8c7821b5f2fc, https://usegalaxy.eu/published/workflow?id=5374daf356516a40, https://usegalaxy.eu/published/workflow?id=5be158931abca947, https://usegalaxy.eu/published/workflow?id=5e4774036aa20b80, https://usegalaxy.eu/published/workflow?id=612dc5bdf388585f, https://usegalaxy.eu/published/workflow?id=6306656ec10bd18f, https://usegalaxy.eu/published/workflow?id=6cb85fe1ad0c9f3b, https://usegalaxy.eu/published/workflow?id=71816adecac46e74, https://usegalaxy.eu/published/workflow?id=73dc2384535bf6af, https://usegalaxy.eu/published/workflow?id=82b6871682f1659a, https://usegalaxy.eu/published/workflow?id=9a60ecf98d4f8134, https://usegalaxy.eu/published/workflow?id=9ef76d764d9961b2, https://usegalaxy.eu/published/workflow?id=c6aecbdbeb27585f, https://usegalaxy.eu/published/workflow?id=cb9a26ea53ce7a27, https://usegalaxy.eu/published/workflow?id=d87fc6685e47d27d, https://usegalaxy.eu/published/workflow?id=eeb6cff210cac091, https://usegalaxy.eu/published/workflow?id=f0bec337f9998289, https://usegalaxy.org.au/published/workflow?id=9281258aefd17c0c, https://usegalaxy.org/published/workflow?id=42331381df05b956, https://workflowhub.eu/workflows/1218?version=1, https://workflowhub.eu/workflows/1425?version=1, https://workflowhub.eu/workflows/1464?version=1, https://workflowhub.eu/workflows/37?version=1, https://workflowhub.eu/workflows/38?version=1, https://workflowhub.eu/workflows/39?version=1, https://workflowhub.eu/workflows/40?version=1 |
microbiome/clinical-mp-1-database-generation, microbiome/clinical-mp-3-verification, proteomics/clinical-mp-1-database-generation, proteomics/clinical-mp-3-verification |
|
upload_roi_and_measures_to_omero |
uploadROIandMeasuresToOMERO |
Upload the ROI coordinates and the measurements to the omero server |
2022-01-18 |
|
0.0.5 |
omero-py |
5.11.1 |
To update |
Imaging |
|
|
|
|
lldelisle |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero |
https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
validate_fasta_database |
validate_fasta_database |
runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. |
2017-09-14 |
|
0.1.5 |
validate-fasta-database |
1.0 |
To update |
Fasta Manipulation, Proteomics |
|
|
|
|
galaxyp |
|
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database |
|
|
|
|
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
68 |
68 |
414 |
414 |
39 |
39 |
148 |
148 |
9 |
9 |
164 |
164 |
0 |
0 |
0 |
0 |
726 |
726 |
116 |
116 |
https://usegalaxy.eu/published/workflow?id=8ef3379dded2490a, https://usegalaxy.eu/published/workflow?id=bee2a7669a7dea5b, https://usegalaxy.org.au/published/workflow?id=9365a7de314c9f85, https://usegalaxy.org/published/workflow?id=e3a30c0583183c1e, https://workflowhub.eu/workflows/1410?version=1, https://workflowhub.eu/workflows/1793?version=1 |
proteomics/neoantigen-fragpipe-discovery |
|
varscan_vaf |
varscan_vaf |
Compute variant allele frequency in vcf files generated by varscan. |
2022-11-28 |
http://artbio.fr |
0.1 |
python |
|
To update |
Variant Analysis |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf |
https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
vcf2snvalignment |
vcf2snvalignment |
Generates multiple alignment of variant calls |
2016-01-20 |
https://snvphyl.readthedocs.io/en/latest/ |
1.8.2 |
snvphyl-tools |
1.8.2 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/snvphyl-galaxy |
https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
verify_map |
verify_map |
Checks the mapping quality of all BAM(s) |
2015-05-15 |
https://snvphyl.readthedocs.io/en/latest/ |
1.8.2 |
snvphyl-tools |
1.8.2 |
Up-to-date |
Sequence Analysis |
|
|
|
|
nml |
https://github.com/phac-nml/snvphyl-galaxy |
https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
vibrant |
vibrant |
Virus Identification By iteRative ANnoTation |
2024-09-11 |
https://github.com/AnantharamanLab/VIBRANT |
1.2.1 |
vibrant |
1.2.1 |
Up-to-date |
Metagenomics |
Sequence trimming, Scaffolding, Genome annotation |
Sequence trimming, Scaffolding, Genome annotation |
Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism |
Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism |
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant |
VIBRANT |
VIBRANT |
Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions |
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
65 |
65 |
1586 |
1586 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1586 |
1586 |
65 |
65 |
https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95 |
|
|
vigiechiro |
vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid |
Tools created by the vigiechiro team to analyses and identify chiro sounds files. |
2019-03-13 |
https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro |
0.1.1 |
|
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro |
|
|
|
|
0 |
0 |
4 |
4 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
4 |
4 |
258 |
284 |
14141 |
17115 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
17115 |
14141 |
284 |
258 |
https://usegalaxy.eu/published/workflow?id=596b073ab7249aa2, https://usegalaxy.eu/published/workflow?id=c0888e0a0fb53ed3 |
|
|
virsorter |
virsorter |
VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes. |
2024-06-20 |
https://github.com/jiarong/VirSorter2/ |
2.2.4 |
virsorter |
2.2.4 |
Up-to-date |
Metagenomics |
Taxonomic classification |
Taxonomic classification |
Metagenomics |
Metagenomics |
ufz |
https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter |
virsorter |
virsorter |
Identify DNA and RNA virus sequences. |
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
144 |
144 |
2379 |
2379 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2379 |
2379 |
144 |
144 |
https://usegalaxy.eu/published/workflow?id=87231a6a7938cb95 |
|
|
vmd |
|
vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations |
2019-10-24 |
https://www.ks.uiuc.edu/Research/vmd/ |
|
|
|
To update |
Computational chemistry |
|
|
|
|
chemteam |
https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd |
https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
waveica |
waveica |
Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. |
2021-02-10 |
https://github.com/RECETOX/WaveICA |
0.2.0 |
r-recetox-waveica |
0.2.1 |
To update |
Metabolomics |
Standardisation and normalisation |
Standardisation and normalisation |
Metabolomics |
Metabolomics |
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/waveica |
https://github.com/RECETOX/galaxytools/tree/master/tools/waveica |
waveica |
WaveICA |
Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform. |
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
9 |
9 |
58 |
58 |
6 |
6 |
8 |
8 |
2 |
2 |
538 |
538 |
4 |
4 |
13 |
13 |
617 |
617 |
21 |
21 |
https://usegalaxy.eu/published/workflow?id=3086366b744e8da9 |
metabolomics/gc_ms_with_xcms |
|
wisecondorx |
wisecondorx_npz_converter, wisecondorx_predict, wisecondorx_reference_builder |
WisecondorX |
2024-12-15 |
https://github.com/CenterForMedicalGeneticsGhent/WisecondorX/tree/master |
1.2.9 |
wisecondorx |
1.2.9 |
Up-to-date |
Variant Analysis |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/wisecondorx |
https://github.com/ARTbio/tools-artbio/tree/main/tools/wisecondorx |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
wtv |
wtv |
A cli/python library for ion selection in mass spectrometry. |
2025-06-02 |
https://github.com/RECETOX/wtv |
0.1.0 |
wtv |
0.1.0 |
Up-to-date |
Metabolomics |
Feature selection |
Feature selection |
Metabolomics |
Metabolomics |
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/wtv |
https://github.com/RECETOX/galaxytools/tree/master/tools/wtv |
wtv |
wtv |
A CLI/python library that selects characteristic qualitative ions based on https://github.com/yuanhonglun/WTV_2.0 |
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
xarray |
timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select |
xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. |
2020-05-06 |
http://xarray.pydata.org |
2022.3.0 |
xarray |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray |
|
|
|
|
0 |
2 |
6 |
5 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
6 |
2 |
132 |
133 |
6057 |
6116 |
12 |
12 |
113 |
113 |
2 |
2 |
436 |
436 |
4 |
4 |
18 |
18 |
6683 |
6624 |
151 |
150 |
https://usegalaxy.eu/published/workflow?id=0c6dd9e75d9a2130, https://usegalaxy.eu/published/workflow?id=4f0f3b911b4e4921, https://usegalaxy.eu/published/workflow?id=6afc245029ce5008, https://usegalaxy.eu/published/workflow?id=6df53b44018b2235, https://usegalaxy.eu/published/workflow?id=7b50e72deb46c6e8, https://usegalaxy.eu/published/workflow?id=a0eff33b83ac1d1e, https://usegalaxy.eu/published/workflow?id=a80f9b926ba43892, https://usegalaxy.eu/published/workflow?id=b4bfcbf8acee9cc3, https://usegalaxy.eu/published/workflow?id=d94460f342b70eb3, https://usegalaxy.eu/published/workflow?id=f774cf05ddff3612, https://usegalaxy.eu/published/workflow?id=fc33ea1679e5f1b7, https://workflowhub.eu/workflows/1427?version=1, https://workflowhub.eu/workflows/1432?version=1, https://workflowhub.eu/workflows/1436?version=1, https://workflowhub.eu/workflows/1652?version=1 |
climate/argo_pangeo, climate/fates, climate/pangeo, ecology/x-array-map-plot |
|
xarray_import_data |
xarray_import_data |
A data import tool for opening OPeNDAP datasets and storing as netCDF files. |
2025-08-14 |
http://xarray.pydata.org |
0.1.0 |
xarray |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/xarray_import_data |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/xarray_import_data |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
2 |
2 |
8 |
8 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
8 |
8 |
2 |
2 |
https://usegalaxy.eu/published/workflow?id=a0eff33b83ac1d1e |
|
|
xlsx2tsv |
xlsx2tsv |
Convert an xlsx file to a tabular |
2024-12-16 |
https://github.com/Helmholtz-UFZ/galaxy-tools |
0.1.0+galaxy0 |
pandas |
|
To update |
Text Manipulation |
|
|
|
|
ufz |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/xls2tsv |
https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/xls2tsv |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
60 |
60 |
490 |
490 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
490 |
490 |
60 |
60 |
|
|
|
xmlstarlet |
xmlstarlet |
Tool to convert a xml file from one metadata standard to another |
2021-10-18 |
|
1.6.1 |
xmlstarlet |
|
To update |
Convert Formats |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet |
|
|
|
|
0 |
0 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
18 |
18 |
102 |
102 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
3 |
3 |
105 |
105 |
21 |
21 |
https://usegalaxy.eu/published/workflow?id=8a81615501be20fd, https://usegalaxy.eu/published/workflow?id=f98560da584d5abf |
|
|
xpore |
xpore_dataprep, xpore_diffmod |
Identification and quantification of differential RNA modifications from direct RNA sequencing |
2021-05-26 |
https://github.com/GoekeLab/xpore |
2.1+galaxy0 |
xpore |
2.1 |
To update |
Nanopore |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore |
https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
xtb_molecular_optimization |
xtb_molecular_optimization |
Performs semiempirical molecular optimization. |
2023-08-24 |
https://github.com/grimme-lab/xtb |
6.6.1 |
xtb |
|
To update |
Metabolomics |
|
|
|
|
recetox |
https://github.com/RECETOX/galaxytools/tree/master/tools/xtb |
https://github.com/RECETOX/galaxytools/tree/master/tools/xtb |
|
|
|
|
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
10 |
10 |
2773 |
2773 |
0 |
0 |
0 |
0 |
2 |
2 |
177 |
177 |
0 |
0 |
0 |
0 |
2950 |
2950 |
12 |
12 |
https://usegalaxy.eu/published/workflow?id=4e9a2e12467bc02e, https://usegalaxy.eu/published/workflow?id=5465916d9b51f411, https://workflowhub.eu/workflows/1597?version=1, https://workflowhub.eu/workflows/897?version=3 |
metabolomics/qcxms-predictions |
|
yac_clipper |
yac |
Clips 3' adapters for small RNA sequencing reads. |
2015-06-17 |
http://artbio.fr |
2.5.1 |
python |
|
To update |
RNA, Fastq Manipulation |
|
|
|
|
artbio |
https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper |
https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper |
|
|
|
|
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
|
|
|
zeiss_lmd_converter |
ZeissLMDconverter |
Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems |
2024-06-29 |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter |
2.0.4 |
shapely |
|
To update |
Proteomics |
|
|
|
|
galaxyp |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter |
https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
3 |
3 |
54 |
54 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
54 |
54 |
3 |
3 |
|
|
|
zoo_project_ogc_api_processes |
zoo_project_ogc_api_processes |
This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information. |
2024-05-03 |
https://github.com/AquaINFRA/galaxy |
0.1.0 |
r-base |
|
To update |
Ecology |
|
|
|
|
ecology |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper |
https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes |
|
|
|
|
0 |
0 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
5 |
5 |
28 |
28 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
0 |
28 |
28 |
5 |
5 |
https://usegalaxy.eu/published/workflow?id=e95bfab07fdec632 |
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