|
Galaxy Server administration |
Galaxy on the Cloud |
https://training.galaxyproject.org//topics/admin/tutorials/cloudbursting/slides.html |
|
|
2019-01-31 |
2024-12-19 |
7 |
False |
True |
False |
False |
|
|
|
0 |
|
2844954 |
7529722 |
2.450000 |
0 |
|
Galaxy Server administration |
Reference Data with Data Managers |
https://training.galaxyproject.org//topics/admin/tutorials/reference-genomes/tutorial.html |
|
Read mapping, Sequence alignment, Generation, Genome indexing |
2019-01-28 |
2023-04-21 |
7 |
True |
True |
False |
False |
bwa, bwa_mem_index_builder_data_manager, data_manager_fetch_genome_all_fasta_dbkey |
|
|
0 |
|
2845508 |
7530446 |
6.900000 |
0 |
|
Galaxy Server administration |
Advanced customisation of a Galaxy instance |
https://training.galaxyproject.org//topics/admin/tutorials/advanced-galaxy-customisation/slides.html |
|
|
2017-06-27 |
2023-04-17 |
18 |
False |
True |
False |
False |
|
|
|
0 |
|
2844954 |
7529722 |
2.450000 |
0 |
|
Galaxy Server administration |
Connecting Galaxy to a compute cluster |
https://training.galaxyproject.org//topics/admin/tutorials/connect-to-compute-cluster/tutorial.html |
|
|
2018-01-07 |
2025-04-08 |
59 |
True |
True |
True |
False |
|
|
|
0 |
|
2848976 |
7536676 |
5.716667 |
0 |
|
Galaxy Server administration |
Setting up Celery Workers for Galaxy |
https://training.galaxyproject.org//topics/admin/tutorials/celery/tutorial.html |
|
|
2022-07-16 |
2025-04-08 |
12 |
True |
True |
False |
False |
|
|
|
0 |
|
1990818 |
4709175 |
3.883333 |
0 |
|
Galaxy Server administration |
Empathy |
https://training.galaxyproject.org//topics/admin/tutorials/empathy/slides.html |
|
|
2019-01-31 |
2021-04-06 |
4 |
False |
True |
False |
False |
|
|
|
0 |
|
2844954 |
7529722 |
2.450000 |
0 |
|
Galaxy Server administration |
Galaxy Monitoring with gxadmin |
https://training.galaxyproject.org//topics/admin/tutorials/gxadmin/tutorial.html |
|
|
2019-01-28 |
2024-08-08 |
27 |
True |
True |
True |
False |
|
|
|
0 |
|
2845823 |
7531085 |
5.166667 |
0 |
|
Galaxy Server administration |
User, Role, Group, Quota, and Authentication managment |
https://training.galaxyproject.org//topics/admin/tutorials/users-groups-quotas/slides.html |
|
|
2018-01-07 |
2024-08-08 |
19 |
False |
True |
True |
False |
|
|
|
0 |
|
2844954 |
7529722 |
2.450000 |
0 |
|
Galaxy Server administration |
External Authentication |
https://training.galaxyproject.org//topics/admin/tutorials/external-auth/tutorial.html |
|
|
2019-01-28 |
2022-10-18 |
14 |
True |
True |
False |
False |
|
|
|
0 |
|
2845650 |
7530820 |
3.250000 |
0 |
|
Galaxy Server administration |
Running Jobs on Remote Resources with Pulsar |
https://training.galaxyproject.org//topics/admin/tutorials/pulsar/tutorial.html |
|
|
2019-01-28 |
2025-04-08 |
49 |
True |
True |
True |
False |
|
|
|
0 |
|
2847466 |
7533865 |
5.283333 |
0 |
|
Galaxy Server administration |
Gearing towards production |
https://training.galaxyproject.org//topics/admin/tutorials/production/slides.html |
|
|
2019-01-28 |
2025-04-08 |
10 |
False |
True |
True |
False |
|
|
|
0 |
|
2844954 |
7529723 |
2.450000 |
0 |
|
Galaxy Server administration |
uWSGI |
https://training.galaxyproject.org//topics/admin/tutorials/uwsgi/slides.html |
|
|
2019-01-28 |
2022-03-01 |
9 |
False |
True |
False |
False |
|
|
|
0 |
|
2844954 |
7529723 |
2.450000 |
0 |
|
Galaxy Server administration |
Distributed Object Storage |
https://training.galaxyproject.org//topics/admin/tutorials/object-store/tutorial.html |
|
|
2019-01-28 |
2025-03-24 |
28 |
True |
True |
True |
False |
|
|
|
0 |
|
2846296 |
7531829 |
4.000000 |
0 |
|
Galaxy Server administration |
Galactic Database |
https://training.galaxyproject.org//topics/admin/tutorials/database/slides.html |
|
|
2019-01-28 |
2022-06-16 |
5 |
False |
True |
True |
False |
|
|
|
0 |
|
2844954 |
7529723 |
2.450000 |
0 |
|
Galaxy Server administration |
Server Maintenance: Cleanup, Backup, and Restoration |
https://training.galaxyproject.org//topics/admin/tutorials/backup-cleanup/tutorial.html |
Database management, Informatics, Data management |
|
2019-01-31 |
2024-08-09 |
5 |
True |
True |
True |
False |
|
|
|
0 |
|
2845513 |
7530470 |
11.633333 |
0 |
|
Galaxy Server administration |
Galaxy Troubleshooting |
https://training.galaxyproject.org//topics/admin/tutorials/troubleshooting/slides.html |
|
|
2019-01-28 |
2024-06-25 |
15 |
False |
True |
False |
False |
|
|
|
0 |
|
2844954 |
7529723 |
2.450000 |
0 |
|
Galaxy Server administration |
Galaxy from an administrator's point of view |
https://training.galaxyproject.org//topics/admin/tutorials/introduction/slides.html |
|
|
2017-06-12 |
2024-06-25 |
6 |
False |
True |
False |
False |
|
|
|
0 |
|
2844954 |
7529723 |
2.450000 |
0 |
|
Galaxy Server administration |
Ansible |
https://training.galaxyproject.org//topics/admin/tutorials/ansible/tutorial.html |
|
|
2018-07-11 |
2024-08-08 |
48 |
True |
True |
True |
False |
|
|
|
0 |
|
2851328 |
7541143 |
4.116667 |
0 |
|
Galaxy Server administration |
Docker and Galaxy |
https://training.galaxyproject.org//topics/admin/tutorials/galaxy-docker/slides.html |
|
|
2016-09-29 |
2022-10-18 |
16 |
False |
True |
False |
False |
|
|
|
0 |
|
2844954 |
7529723 |
2.450000 |
0 |
|
Galaxy Server administration |
Reference Data with CVMFS |
https://training.galaxyproject.org//topics/admin/tutorials/cvmfs/tutorial.html |
|
|
2019-01-27 |
2025-04-03 |
50 |
True |
True |
True |
False |
|
|
|
0 |
|
2847053 |
7532836 |
5.600000 |
0 |
|
Galaxy Server administration |
Controlling Galaxy with systemd or Supervisor |
https://training.galaxyproject.org//topics/admin/tutorials/systemd-supervisor/slides.html |
|
|
2019-01-28 |
2023-04-16 |
5 |
False |
True |
True |
False |
|
|
|
0 |
|
2844954 |
7529723 |
2.450000 |
0 |
|
Galaxy Server administration |
Data Libraries |
https://training.galaxyproject.org//topics/admin/tutorials/data-library/tutorial.html |
|
|
2021-01-14 |
2024-06-14 |
32 |
True |
True |
True |
False |
|
|
|
0 |
|
2828550 |
7466343 |
4.500000 |
0 |
|
Galaxy Server administration |
Galaxy Tool Management with Ephemeris |
https://training.galaxyproject.org//topics/admin/tutorials/tool-management/tutorial.html |
|
|
2019-01-27 |
2025-04-03 |
39 |
True |
True |
True |
False |
|
|
|
0 |
|
2846727 |
7532262 |
5.916667 |
0 |
|
Galaxy Server administration |
Galaxy Monitoring |
https://training.galaxyproject.org//topics/admin/tutorials/general-monitoring/slides.html |
|
|
2019-04-26 |
2022-03-01 |
5 |
False |
True |
False |
False |
|
|
|
0 |
|
2844954 |
7529723 |
2.450000 |
0 |
|
Galaxy Server administration |
Server: Other |
https://training.galaxyproject.org//topics/admin/tutorials/stuff/slides.html |
|
|
2018-01-07 |
2023-02-17 |
6 |
False |
True |
False |
False |
|
|
|
0 |
|
2844954 |
7529723 |
2.450000 |
0 |
|
Galaxy Server administration |
Galaxy Installation with Ansible |
https://training.galaxyproject.org//topics/admin/tutorials/ansible-galaxy/tutorial.html |
Database management, Informatics, Data management |
|
2019-01-28 |
2025-04-08 |
102 |
True |
True |
True |
False |
|
|
|
0 |
|
2870349 |
7577049 |
4.183333 |
0 |
|
Galaxy Server administration |
Galaxy Monitoring with Telegraf and Grafana |
https://training.galaxyproject.org//topics/admin/tutorials/monitoring/tutorial.html |
|
|
2019-01-31 |
2024-12-18 |
47 |
True |
True |
True |
False |
|
|
|
0 |
|
2847807 |
7535025 |
3.316667 |
0 |
|
Galaxy Server administration |
Galaxy Administrator Time Burden and Technology Usage |
https://training.galaxyproject.org//topics/admin/tutorials/poll-ssa/slides.html |
|
|
2024-07-10 |
2024-07-10 |
1 |
False |
True |
False |
False |
|
|
|
0 |
|
833446 |
1933808 |
2.250000 |
0 |
|
Galaxy Server administration |
Galaxy Interactive Tools |
https://training.galaxyproject.org//topics/admin/tutorials/interactive-tools/tutorial.html |
|
|
2020-02-27 |
2025-04-08 |
27 |
True |
True |
True |
False |
|
|
|
0 |
|
2847210 |
7533129 |
5.166667 |
0 |
|
Galaxy Server administration |
Upgrading Galaxy |
https://training.galaxyproject.org//topics/admin/tutorials/upgrading/tutorial.html |
|
|
2021-06-08 |
2024-11-25 |
10 |
True |
False |
True |
False |
|
|
|
0 |
|
682 |
1061 |
3.000000 |
0 |
|
Galaxy Server administration |
How I learned to stop worrying and love the systemd |
https://training.galaxyproject.org//topics/admin/tutorials/stop-worrying-love-systemd/tutorial.html |
|
|
2022-07-06 |
2023-09-28 |
3 |
True |
False |
False |
False |
|
|
|
0 |
|
669 |
771 |
0.633333 |
0 |
|
Galaxy Server administration |
Galaxy Database schema |
https://training.galaxyproject.org//topics/admin/tutorials/database-schema/tutorial.html |
|
|
2016-07-20 |
2025-04-08 |
23 |
True |
False |
False |
False |
|
|
|
0 |
|
3013 |
4938 |
1.066667 |
0 |
|
Galaxy Server administration |
Customizing the look of Galaxy (Manual) |
https://training.galaxyproject.org//topics/admin/tutorials/customization-manual/tutorial.html |
|
|
2023-04-16 |
2025-04-08 |
2 |
True |
False |
False |
False |
|
|
|
0 |
|
191 |
230 |
2.216667 |
0 |
|
Galaxy Server administration |
Reference Data with CVMFS without Ansible |
https://training.galaxyproject.org//topics/admin/tutorials/cvmfs-manual/tutorial.html |
|
|
2020-06-17 |
2023-11-23 |
9 |
True |
False |
False |
False |
|
|
|
0 |
|
389 |
525 |
2.466667 |
0 |
|
Galaxy Server administration |
Automation with Jenkins |
https://training.galaxyproject.org//topics/admin/tutorials/jenkins/tutorial.html |
|
|
2019-08-06 |
2022-10-18 |
10 |
True |
False |
False |
False |
|
|
|
0 |
|
8218 |
16273 |
0.650000 |
0 |
|
Galaxy Server administration |
Performant Uploads with TUS |
https://training.galaxyproject.org//topics/admin/tutorials/tus/tutorial.html |
|
|
2022-03-01 |
2024-06-14 |
17 |
True |
False |
True |
False |
|
|
|
0 |
|
851 |
1247 |
5.333333 |
0 |
|
Galaxy Server administration |
Deploying a Beacon v1 in Galaxy |
https://training.galaxyproject.org//topics/admin/tutorials/beacon/tutorial.html |
|
|
2023-04-16 |
2024-12-18 |
5 |
True |
False |
False |
False |
|
|
|
0 |
|
141 |
159 |
2.133333 |
0 |
|
Galaxy Server administration |
Galaxy Monitoring with Reports |
https://training.galaxyproject.org//topics/admin/tutorials/reports/tutorial.html |
|
|
2019-01-31 |
2025-04-08 |
43 |
True |
False |
False |
False |
|
|
|
0 |
|
493 |
659 |
2.783333 |
0 |
|
Galaxy Server administration |
Enable upload via FTP |
https://training.galaxyproject.org//topics/admin/tutorials/ftp/tutorial.html |
|
|
2021-06-18 |
2024-02-20 |
23 |
True |
False |
False |
False |
|
|
|
0 |
|
1231 |
1692 |
1.650000 |
0 |
|
Galaxy Server administration |
Customizing the look of Galaxy |
https://training.galaxyproject.org//topics/admin/tutorials/customization/tutorial.html |
|
|
2023-04-16 |
2025-04-08 |
5 |
True |
False |
False |
False |
|
|
|
0 |
|
571 |
699 |
4.666667 |
0 |
|
Galaxy Server administration |
Training Infrastructure as a Service (TIaaS) |
https://training.galaxyproject.org//topics/admin/tutorials/tiaas/tutorial.html |
|
|
2020-02-12 |
2024-12-18 |
38 |
True |
False |
True |
False |
|
|
|
0 |
|
536 |
717 |
3.383333 |
0 |
|
Galaxy Server administration |
Use Apptainer containers for running Galaxy jobs |
https://training.galaxyproject.org//topics/admin/tutorials/apptainer/tutorial.html |
|
|
2021-01-08 |
2025-04-08 |
13 |
True |
False |
True |
False |
|
|
|
0 |
|
1050 |
1340 |
2.600000 |
0 |
|
Galaxy Server administration |
Configuring the Onedata connectors (remotes, Object Store, BYOS, BYOD) |
https://training.galaxyproject.org//topics/admin/tutorials/onedata-configuration/tutorial.html |
|
|
2025-03-24 |
2025-04-08 |
2 |
True |
False |
False |
False |
|
|
|
0 |
|
40 |
45 |
4.900000 |
0 |
|
Galaxy Server administration |
Mapping Jobs to Destinations using TPV |
https://training.galaxyproject.org//topics/admin/tutorials/job-destinations/tutorial.html |
|
|
2021-01-17 |
2024-06-14 |
36 |
True |
False |
True |
False |
|
|
|
0 |
|
1653 |
2598 |
3.266667 |
0 |
|
Galaxy Server administration |
Adding file-sources to Galaxy |
https://training.galaxyproject.org//topics/admin/tutorials/file_sources/tutorial.html |
|
|
2025-01-20 |
2025-01-20 |
1 |
True |
False |
False |
False |
|
|
|
0 |
|
49 |
67 |
3.316667 |
0 |
|
Galaxy Server administration |
Create a subdomain for your community on UseGalaxy.eu |
https://training.galaxyproject.org//topics/admin/tutorials/subdomain/tutorial.html |
|
|
2024-11-27 |
2024-12-13 |
2 |
True |
False |
False |
False |
|
|
|
0 |
|
30 |
35 |
4.683333 |
0 |
|
Galaxy Server administration |
Monitoring Galaxy and Pulsar with Sentry |
https://training.galaxyproject.org//topics/admin/tutorials/sentry/tutorial.html |
|
|
2023-04-19 |
2024-03-18 |
6 |
True |
False |
False |
False |
|
|
|
0 |
|
211 |
256 |
1.083333 |
0 |
|
Galaxy Server administration |
Alternative Celery Deployment for Galaxy |
https://training.galaxyproject.org//topics/admin/tutorials/celeryless/tutorial.html |
|
|
2024-11-07 |
2024-11-07 |
1 |
True |
False |
False |
False |
|
|
|
0 |
|
56 |
62 |
3.666667 |
0 |
|
Galaxy Server administration |
Galaxy Installation on Kubernetes |
https://training.galaxyproject.org//topics/admin/tutorials/k8s-deploying-galaxy/tutorial.html |
|
|
2019-07-02 |
2024-06-30 |
7 |
True |
False |
False |
False |
|
|
|
0 |
|
1598 |
2648 |
2.283333 |
0 |
|
Galaxy Server administration |
Managing Galaxy on Kubernetes |
https://training.galaxyproject.org//topics/admin/tutorials/k8s-managing-galaxy/tutorial.html |
|
|
2019-07-02 |
2024-12-19 |
7 |
True |
False |
False |
False |
|
|
|
0 |
|
656 |
966 |
2.166667 |
0 |
|
Galaxy Server administration |
Galaxy usage on SURF Research Cloud |
https://training.galaxyproject.org//topics/admin/tutorials/surf-research-cloud-galaxy/tutorial.html |
Informatics, Data management |
|
2024-12-18 |
2025-08-05 |
4 |
True |
False |
False |
False |
|
|
|
0 |
|
63 |
82 |
2.116667 |
0 |
|
Galaxy Server administration |
Pulsar usage on SURF Research Cloud |
https://training.galaxyproject.org//topics/admin/tutorials/surf-research-cloud-pulsar/tutorial.html |
Informatics, Data management |
|
2024-12-18 |
2024-12-19 |
3 |
True |
False |
False |
False |
|
|
|
0 |
|
54 |
62 |
0.500000 |
0 |
|
Galaxy Server administration |
Deploying Tailscale/Headscale for private mesh networking |
https://training.galaxyproject.org//topics/admin/tutorials/wireguard-headscale/tutorial.html |
Data security, Software engineering |
|
2022-09-21 |
2024-12-19 |
4 |
True |
False |
False |
False |
|
|
|
0 |
|
2342 |
3025 |
0.433333 |
0 |
|
Galaxy Server administration |
Deploying Wireguard for private mesh networking |
https://training.galaxyproject.org//topics/admin/tutorials/wireguard/tutorial.html |
|
|
2022-09-21 |
2024-12-19 |
4 |
True |
False |
False |
False |
|
|
|
0 |
|
1097 |
1251 |
0.333333 |
0 |
|
Galaxy Server administration |
Deploying a compute cluster in OpenStack via Terraform |
https://training.galaxyproject.org//topics/admin/tutorials/terraform/tutorial.html |
|
|
2018-10-27 |
2024-12-19 |
15 |
True |
True |
False |
False |
|
|
|
0 |
|
2860781 |
7559499 |
3.366667 |
0 |
|
Image analysis using Deep Learning |
Contribute to the BioImage.IO models |
https://training.galaxyproject.org//topics/ai4life/tutorials/contribute-materials/slides.html |
|
|
2023-05-18 |
2023-05-24 |
3 |
False |
True |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
1483114 |
3421577 |
2.300000 |
0 |
|
Image analysis using Deep Learning |
BioImage Model Zoo: Advanced models in one-click |
https://training.galaxyproject.org//topics/ai4life/tutorials/getting-started/slides.html |
|
|
2023-04-18 |
2023-05-24 |
4 |
False |
True |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
1544330 |
3557349 |
2.300000 |
0 |
|
Image analysis using Deep Learning |
Welcome to the BioImage Model Zoo |
https://training.galaxyproject.org//topics/ai4life/tutorials/welcome-bioimageio/slides.html |
|
|
2023-05-11 |
2023-05-18 |
3 |
False |
True |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
1497391 |
3453953 |
2.300000 |
0 |
|
Assembly |
An Introduction to Genome Assembly |
https://training.galaxyproject.org//topics/assembly/tutorials/general-introduction/tutorial.html |
|
Statistical calculation, Formatting, Sequence composition calculation, Validation, Visualisation, De-novo assembly, Sequencing quality control, Sequence assembly validation |
2017-05-23 |
2024-09-12 |
29 |
True |
True |
True |
True |
fastq_paired_end_interlacer, velvetg, multiqc, fastqc, velveth, quast |
Galaxy@AuBi, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr |
0 |
|
2880158 |
7587603 |
5.300000 |
0 |
|
Assembly |
Decontamination of a genome assembly |
https://training.galaxyproject.org//topics/assembly/tutorials/assembly-decontamination/tutorial.html |
Genomics, Sequence assembly, Biodiversity |
Data handling, Taxonomic classification |
2024-09-04 |
2025-06-04 |
5 |
True |
False |
True |
True |
ncbi_blastn_wrapper, tp_sed_tool, parse_mito_blast, Filter1, ncbi_dustmasker_wrapper, kraken2, Cut1, gfastats, tp_cat |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
1536 |
1921 |
2.533333 |
0 |
|
Assembly |
Unicycler Assembly |
https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html |
Sequence assembly, Genomics, Microbiology |
Statistical calculation, Genome assembly, Coding region prediction, Sequencing quality control, Genome annotation, Gene prediction, Aggregation, Sequence composition calculation, Validation, Visualisation, Sequence assembly validation |
2017-10-11 |
2025-05-15 |
24 |
True |
True |
False |
True |
unicycler, multiqc, fastqc, prokka, quast |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
2857850 |
7551800 |
4.516667 |
0 |
|
Assembly |
Chloroplast genome assembly |
https://training.galaxyproject.org//topics/assembly/tutorials/chloroplast-assembly/tutorial.html |
|
Generation, Analysis, Sequence assembly visualisation, Coding region prediction, Box-Whisker plot plotting, Read alignment, Genome indexing, Genome assembly, Mapping assembly, Genome visualisation, Cross-assembly, Genome annotation, Gene prediction, Sequence alignment, Scatter plot plotting, Read mapping, De-novo assembly, Sequence assembly |
2020-12-04 |
2025-05-15 |
21 |
True |
False |
True |
True |
bandage_image, bwa_mem, jbrowse, upload1, prokka, fasta-stats, nanoplot, pilon, bandage_info, flye |
UseGalaxy.eu |
GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) |
0 |
|
7834 |
12151 |
2.800000 |
0 |
|
Assembly |
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads |
https://training.galaxyproject.org//topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html |
|
Read mapping, Genome assembly, Sequence assembly visualisation, Sequence contamination filtering, Box-Whisker plot plotting, Data handling, Sequencing quality control, Scatter plot plotting, Aggregation, Validation, Pairwise sequence alignment, Sequence file editing |
2020-04-21 |
2025-05-15 |
14 |
True |
True |
True |
True |
unicycler, multiqc, seqtk_sample, fasterq_dump, collapse_dataset, fasta_filter_by_length, samtools_view, nanoplot, minimap2, bandage_info, fastp, samtools_fastx, bandage_image, bowtie2, samtools_stats, __ZIP_COLLECTION__ |
UseGalaxy.eu, UseGalaxy.org.au |
Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) |
0 |
|
2850785 |
7539499 |
5.733333 |
0 |
|
Assembly |
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data |
https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html |
Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology |
Statistical calculation, Genome assembly, Sequence assembly visualisation, Sequencing quality control, Sequence composition calculation, Read mapping, Visualisation, Sequence contamination filtering, Sequence assembly validation |
2021-03-24 |
2025-03-20 |
16 |
True |
False |
True |
True |
shovill, upload1, fastqc, falco, bandage_info, fastp, bandage_image, quast |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
|
0 |
|
9861 |
15245 |
3.633333 |
0 |
|
Assembly |
Making sense of a newly assembled genome |
https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html |
Sequence assembly, Genomics, Microbiology |
Sequence alignment, Mapping, Sequence visualisation, Read mapping, Genome visualisation |
2018-06-14 |
2024-06-24 |
29 |
True |
False |
False |
True |
random_lines1, tp_sed_tool, tp_replace_in_line, circos_interval_to_tiles, collapse_dataset, bedtools_sortbed, tp_cat, circos, join1, tp_replace_in_column, bedtools_complementbed, circos_aln_to_links, tp_sort_header_tool, fasta_filter_by_length, lastz_wrapper_2, Grep1, mergeCols1, tp_grep_tool, datamash_ops, bedtools_intersectbed, jbrowse, upload1, addValue, Filter1, cat1, Cut1, fasta_compute_length |
|
|
0 |
|
6714 |
12964 |
2.933333 |
0 |
|
Assembly |
Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data |
https://training.galaxyproject.org//topics/assembly/tutorials/vgp_workflow_training/tutorial.html |
Sequence assembly, Chromosome conformation capture |
Visualisation, Sequence assembly validation |
2022-04-06 |
2025-09-09 |
26 |
True |
False |
True |
False |
quast |
Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.no |
0 |
|
3427 |
4757 |
2.716667 |
0 |
|
Assembly |
Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step |
https://training.galaxyproject.org//topics/assembly/tutorials/vgp_genome_assembly/tutorial.html |
Genomics, Sequence assembly, Biodiversity |
Genome assembly, k-mer counting, Read binning, Sequence trimming, Primer removal, Mapping, Data handling, De-novo assembly, Phasing, Sequence alignment, Read pre-processing, Scaffolding, Visualisation, Pairwise sequence alignment, Sequence assembly validation |
2021-06-04 |
2025-06-04 |
57 |
True |
False |
True |
True |
purge_dups, pretext_snapshot, collapse_dataset, Add_a_column1, yahs, tp_find_and_replace, tp_cut_tool, busco, minimap2, genomescope, quast, pretext_map, bwa_mem2, merqury, tp_grep_tool, bellerophon, bionano_scaffold, cutadapt, bedtools_bamtobed, cat1, collection_column_join, Convert characters1, salsa, gfa_to_fa, sort1, gfastats, meryl, hifiasm |
|
UseGalaxy.cz |
0 |
|
15552 |
23573 |
2.000000 |
0 |
|
Assembly |
ERGA post-assembly QC |
https://training.galaxyproject.org//topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html |
Genomics, Sequence assembly, Biodiversity |
Genome assembly, Sequence assembly visualisation, k-mer counting, Sequence alignment analysis, Sequence trimming, Data parsing, Data handling, De-novo assembly, Phasing, Data deposition, Sequence alignment, Genotyping, Scaffolding, Visualisation, Pairwise sequence alignment, Sequence assembly validation |
2023-06-23 |
2025-06-04 |
8 |
True |
False |
True |
True |
pretext_snapshot, collapse_dataset, tp_find_and_replace, samtools_stats, bg_diamond, busco, minimap2, interactive_tool_blobtoolkit, genomescope, smudgeplot, pretext_map, bwa_mem2, merqury, __EXTRACT_DATASET__, blobtoolkit, bellerophon, CONVERTER_gz_to_uncompressed, bandage_image, gfastats, meryl |
UseGalaxy.eu |
UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
1868 |
2396 |
1.966667 |
0 |
|
Assembly |
Assembly of metagenomic sequencing data |
https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html |
Metagenomics, Sequence assembly |
Genome assembly, Sequence assembly visualisation, Data handling, Variant calling, Local alignment, Formatting, Read mapping, Visualisation, Sequence file editing, Read pre-processing, Statistical calculation, Sequence alignment analysis, Sequence trimming, Primer removal, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering, Sequence assembly validation |
2025-10-19 |
2025-10-19 |
0 |
True |
False |
True |
True |
coverm_contig, filter_tabular, random_lines1, cutadapt, fastqc, megahit_contig2fastg, ngsutils_bam_filter, megahit, bg_uniq, bandage_info, collection_column_join, seqtk_subseq, bandage_image, metaspades, bowtie2, quast, bamtools, tp_cat |
|
UseGalaxy.cz, UseGalaxy.eu |
0 |
|
1 |
2 |
0.000000 |
0 |
|
Assembly |
Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) |
https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html |
Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial resistance |
Statistical calculation, Sequence assembly validation, Genome assembly, Sequence assembly visualisation, Box-Whisker plot plotting, Sequencing error detection, Filtering, Sequencing quality control, Cross-assembly, Sequence alignment, Scatter plot plotting, Sequence composition calculation, Read mapping, Visualisation, De-novo assembly, Sequence contamination filtering, Mapping assembly |
2021-03-24 |
2024-11-29 |
15 |
True |
False |
False |
True |
CONVERTER_bz2_to_uncompressed, bandage_image, bwa_mem2, upload1, fastqc, porechop, nanoplot, fastp, filtlong, polypolish, flye, quast |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr |
0 |
|
10187 |
15281 |
3.416667 |
0 |
|
Assembly |
De Bruijn Graph Assembly |
https://training.galaxyproject.org//topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html |
|
Optimisation and refinement, Genome assembly, Sequence assembly |
2017-05-24 |
2024-02-01 |
25 |
True |
True |
False |
True |
velvetoptimiser, spades, fasta-stats |
Galaxy@AuBi, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
2851324 |
7539810 |
5.050000 |
0 |
|
Assembly |
Genome Assembly Quality Control |
https://training.galaxyproject.org//topics/assembly/tutorials/assembly-quality-control/tutorial.html |
Biodiversity, Sequence assembly, Data quality management |
Genome assembly, Phasing, k-mer counting, Scaffolding, Visualisation, De-novo assembly, Sequence assembly validation |
2022-08-26 |
2025-06-04 |
6 |
True |
True |
False |
True |
merqury, busco, chromeister, quast, meryl |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
1943408 |
4575657 |
4.516667 |
0 |
|
Assembly |
Large genome assembly and polishing |
https://training.galaxyproject.org//topics/assembly/tutorials/largegenome/tutorial.html |
Genomics, Sequence assembly, Biodiversity |
Genome assembly, Sequence assembly visualisation, Box-Whisker plot plotting, Variant calling, Scatter plot plotting, Validation, Visualisation, De-novo assembly, Mapping assembly, Statistical calculation, Sequence assembly, Sequencing quality control, Cross-assembly, Sequence composition calculation, Base-calling, Pairwise sequence alignment, Sequence contamination filtering, Sequence assembly validation |
2023-03-06 |
2025-06-04 |
14 |
True |
False |
True |
True |
bandage_image, barchart_gnuplot, medaka_consensus_pipeline, racon, busco, multiqc, fastqc, fasta-stats, nanoplot, minimap2, fastp, genomescope, flye, quast, meryl |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
7105 |
9251 |
2.033333 |
0 |
|
Assembly |
Assembly of the mitochondrial genome from PacBio HiFi reads |
https://training.galaxyproject.org//topics/assembly/tutorials/mitochondrion-assembly/tutorial.html |
Genomics, Sequence assembly, Biodiversity, Mitochondria |
|
2024-09-03 |
2025-06-04 |
4 |
True |
False |
True |
True |
mitohifi, compress_file |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
809 |
992 |
2.050000 |
0 |
|
Assembly |
Genome assembly using PacBio data |
https://training.galaxyproject.org//topics/assembly/tutorials/hifi-assembly/tutorial.html |
Genomics, Sequence assembly, Biodiversity |
Genome assembly, Mapping assembly, Cross-assembly, Visualisation, De-novo assembly, Sequence assembly validation |
2021-11-29 |
2025-06-04 |
2 |
True |
False |
False |
True |
busco, fasta-stats, flye, gfa_to_fa, quast, hifiasm |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
GalaxyTrakr, UseGalaxy.cz |
0 |
|
702 |
831 |
1.483333 |
0 |
|
Assembly |
Genome assembly and assembly QC - Introduction short version |
https://training.galaxyproject.org//topics/assembly/tutorials/assembly_and_qc_short/slides.html |
|
|
2025-04-22 |
2025-04-23 |
2 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
385632 |
820746 |
1.816667 |
0 |
|
Assembly |
An introduction to get started in genome assembly and annotation |
https://training.galaxyproject.org//topics/assembly/tutorials/get-started-genome-assembly/slides.html |
|
|
2021-11-30 |
2023-10-23 |
7 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2363443 |
5904672 |
2.400000 |
0 |
|
Assembly |
Deeper look into Genome Assembly algorithms |
https://training.galaxyproject.org//topics/assembly/tutorials/algorithms-introduction/slides.html |
|
|
2021-01-12 |
2021-01-12 |
1 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2824191 |
7461190 |
2.450000 |
0 |
|
Climate |
Ocean's variables study |
https://training.galaxyproject.org//topics/climate/tutorials/ocean-variables/tutorial.html |
|
|
2023-11-29 |
2025-05-10 |
5 |
True |
False |
False |
True |
interactive_tool_odv, divand_full_analysis, interactive_tool_divand |
UseGalaxy.eu |
|
0 |
|
210 |
253 |
1.933333 |
0 |
|
Climate |
Nitrate DMQC for autonomous platforms such as Argo floats |
https://training.galaxyproject.org//topics/climate/tutorials/ocean_qcv_analysis/tutorial.html |
|
|
2025-08-08 |
2025-09-16 |
3 |
True |
False |
False |
True |
interactive_tool_odv, tool_biogeochemical_calibration, harmonize_insitu_to_netcdf, tool_odv_history, tool_odv |
UseGalaxy.eu |
|
0 |
|
31 |
42 |
2.650000 |
0 |
|
Climate |
Getting your hands-on climate data |
https://training.galaxyproject.org//topics/climate/tutorials/climate-101/tutorial.html |
|
Visualisation |
2020-04-30 |
2025-05-10 |
14 |
True |
False |
False |
True |
tp_awk_tool, climate_stripes, ggplot2_point, psy_maps, Grep1, interactive_tool_panoply, cds_essential_variability, datamash_ops |
UseGalaxy.eu |
|
0 |
|
1040 |
1446 |
1.283333 |
0 |
|
Climate |
Pangeo Notebook in Galaxy - Introduction to Xarray |
https://training.galaxyproject.org//topics/climate/tutorials/pangeo-notebook/tutorial.html |
|
|
2022-02-18 |
2025-05-10 |
11 |
True |
True |
True |
True |
interactive_tool_pangeo_notebook |
UseGalaxy.eu |
|
0 |
|
2238295 |
5505288 |
4.400000 |
0 |
|
Climate |
Functionally Assembled Terrestrial Ecosystem Simulator (FATES) |
https://training.galaxyproject.org//topics/climate/tutorials/fates/tutorial.html |
|
Visualisation |
2020-10-25 |
2025-05-10 |
18 |
True |
True |
True |
True |
xarray_select, xarray_metadata_info, interactive_tool_panoply, ggplot2_point, tp_find_and_replace, ctsm_fates, __EXTRACT_DATASET__ |
UseGalaxy.eu, UseGalaxy.org (Main) |
|
0 |
|
2846418 |
7532045 |
4.283333 |
0 |
|
Climate |
Analyse Argo data |
https://training.galaxyproject.org//topics/climate/tutorials/argo_pangeo/tutorial.html |
|
|
2024-03-24 |
2025-05-10 |
2 |
True |
False |
False |
True |
interactive_tool_odv, timeseries_extraction, xarray_metadata_info, argo_getdata, xarray_coords_info |
UseGalaxy.eu |
|
0 |
|
294 |
355 |
1.200000 |
0 |
|
Climate |
Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools |
https://training.galaxyproject.org//topics/climate/tutorials/pangeo/tutorial.html |
|
Visualisation |
2022-02-18 |
2025-05-10 |
6 |
True |
True |
True |
True |
__MERGE_COLLECTION__, xarray_netcdf2netcdf, xarray_select, xarray_metadata_info, climate_stripes, ggplot2_point, regexColumn1, xarray_mapplot, xarray_coords_info, graphicsmagick_image_montage, __EXTRACT_DATASET__ |
UseGalaxy.eu, UseGalaxy.org (Main) |
UseGalaxy.cz |
0 |
|
2238085 |
5504794 |
5.266667 |
0 |
|
Climate |
Sentinel 5P data visualisation |
https://training.galaxyproject.org//topics/climate/tutorials/sentinel5_data/tutorial.html |
|
|
2024-01-26 |
2025-05-10 |
2 |
True |
False |
False |
True |
interactive_tool_copernicus, interactive_tool_panoply, interactive_tool_copernicus_notebook |
|
|
0 |
|
288 |
334 |
0.533333 |
0 |
|
Climate |
Introduction to climate data |
https://training.galaxyproject.org//topics/climate/tutorials/introduction/slides.html |
|
|
2020-10-11 |
2025-05-10 |
2 |
False |
True |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2844954 |
7529728 |
2.450000 |
0 |
|
Climate |
Collaboration with JupyterGIS |
https://training.galaxyproject.org//topics/climate/tutorials/jupytergis_collaboration/tutorial.html |
|
|
2025-04-03 |
2025-05-10 |
4 |
True |
False |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
169 |
211 |
0.866667 |
0 |
|
Climate |
Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab |
https://training.galaxyproject.org//topics/climate/tutorials/fates-jupyterlab/tutorial.html |
|
|
2020-10-25 |
2025-05-10 |
16 |
True |
False |
False |
False |
interactive_tool_jupyter_notebook |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
545 |
952 |
1.800000 |
0 |
|
Climate |
Ocean Data View (ODV) |
https://training.galaxyproject.org//topics/climate/tutorials/ocean-data-view/tutorial.html |
|
|
2023-11-27 |
2025-05-10 |
2 |
True |
False |
False |
False |
interactive_tool_odv |
UseGalaxy.eu, UseGalaxy.fr |
|
0 |
|
392 |
474 |
1.166667 |
0 |
|
Climate |
Visualize Climate data with Panoply netCDF viewer |
https://training.galaxyproject.org//topics/climate/tutorials/panoply/tutorial.html |
|
|
2020-03-05 |
2025-05-10 |
18 |
True |
False |
False |
False |
interactive_tool_panoply |
UseGalaxy.eu, UseGalaxy.org (Main) |
|
0 |
|
6271 |
10232 |
0.800000 |
0 |
|
Climate |
Getting your hands-on earth data |
https://training.galaxyproject.org//topics/climate/tutorials/earth_system/tutorial.html |
|
|
2024-10-04 |
2025-05-10 |
2 |
True |
False |
False |
False |
argo_getdata, spocc_occ, obis_data, c3s |
UseGalaxy.eu |
|
0 |
|
94 |
128 |
2.700000 |
0 |
|
Galaxy Community Building |
Creation of resources listing all the tools and their metadata relevant to your community |
https://training.galaxyproject.org//topics/community/tutorials/community-tool-table/tutorial.html |
|
|
2024-03-13 |
2025-10-04 |
4 |
True |
False |
False |
False |
|
|
|
0 |
|
71 |
94 |
3.316667 |
0 |
|
Galaxy Community Building |
Creation of the labs in the different Galaxy instances for your community |
https://training.galaxyproject.org//topics/community/tutorials/community-lab/tutorial.html |
|
|
2025-10-04 |
2025-10-04 |
1 |
True |
False |
False |
False |
|
|
|
0 |
|
5 |
5 |
0.000000 |
0 |
|
Galaxy Community Building |
What's a Special Interest Group? |
https://training.galaxyproject.org//topics/community/tutorials/sig_define/tutorial.html |
|
|
2024-07-08 |
2024-12-20 |
3 |
True |
False |
False |
False |
|
|
|
0 |
|
75 |
106 |
3.933333 |
0 |
|
Galaxy Community Building |
Creation of resources listing Galaxy workflow for your community |
https://training.galaxyproject.org//topics/community/tutorials/community-workflow-table/tutorial.html |
|
|
2025-09-17 |
2025-09-17 |
1 |
True |
False |
False |
False |
|
|
|
0 |
|
5 |
6 |
0.000000 |
0 |
|
Galaxy Community Building |
Creation of a Galaxy tutorial table for your community |
https://training.galaxyproject.org//topics/community/tutorials/community-tutorial-table/tutorial.html |
|
|
2025-09-17 |
2025-09-17 |
1 |
True |
False |
False |
False |
|
|
|
0 |
|
6 |
7 |
0.000000 |
0 |
|
Galaxy Community Building |
Make your tools available on your subdomain |
https://training.galaxyproject.org//topics/community/tutorials/tools_subdomains/tutorial.html |
|
|
2024-12-03 |
2024-12-20 |
2 |
True |
False |
False |
False |
|
|
|
0 |
|
40 |
55 |
10.416667 |
0 |
|
Galaxy Community Building |
Creating community content |
https://training.galaxyproject.org//topics/community/tutorials/community_content/tutorial.html |
|
|
2024-12-20 |
2024-12-20 |
4 |
True |
False |
False |
False |
|
|
|
0 |
|
44 |
57 |
0.116667 |
0 |
|
Galaxy Community Building |
Creating a Special Interest Group |
https://training.galaxyproject.org//topics/community/tutorials/sig_create/tutorial.html |
|
|
2024-07-08 |
2024-12-20 |
2 |
True |
False |
False |
False |
|
|
|
0 |
|
99 |
109 |
2.366667 |
0 |
|
Computational chemistry |
Data management in Medicinal Chemistry |
https://training.galaxyproject.org//topics/computational-chemistry/tutorials/med-chem-data/tutorial.html |
|
|
2024-01-08 |
2024-09-13 |
4 |
True |
False |
True |
True |
ctb_silicos_qed, ctb_im_rxn_maker, openbabel_compound_convert, chembl, md_converter, get_pdb, openbabel_svg_depiction |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.no |
0 |
|
431 |
518 |
1.750000 |
0 |
|
Computational chemistry |
Protein-ligand docking |
https://training.galaxyproject.org//topics/computational-chemistry/tutorials/cheminformatics/tutorial.html |
|
|
2019-10-19 |
2023-11-09 |
16 |
True |
False |
False |
True |
sdf_to_tab, openbabel_compound_convert, collapse_dataset, ctb_chemfp_butina_clustering, tp_find_and_replace, openbabel_svg_depiction, tp_cat, ctb_np-likeness-calculator, ctb_chemfp_mol2fps, ctb_change_title, ctb_compound_convert, prepare_receptor, ctb_remIons, ctb_online_data_fetch, ctb_remDuplicates, ctb_chemfp_nxn_clustering, docking, fpocket, ctb_filter, tp_grep_tool, prepare_box, chembl, get_pdb, ctb_obgrep |
|
UseGalaxy.org (Main) |
0 |
|
19080 |
32741 |
1.550000 |
0 |
|
Computational chemistry |
Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring |
https://training.galaxyproject.org//topics/computational-chemistry/tutorials/covid19-docking/tutorial.html |
|
|
2020-03-27 |
2023-11-09 |
10 |
True |
False |
False |
True |
sucos_max_score, xchem_pose_scoring, ctb_frankenstein_ligand, openbabel_compound_convert, rxdock_rbdock, collapse_dataset, xchem_transfs_scoring, rdock_rbcavity, split_file_to_collection, rdock_rbdock, rxdock_rbcavity, enumerate_charges |
|
|
0 |
|
3160 |
5211 |
3.050000 |
0 |
|
Computational chemistry |
Analysis of molecular dynamics simulations |
https://training.galaxyproject.org//topics/computational-chemistry/tutorials/analysis-md-simulations/tutorial.html |
|
|
2019-06-03 |
2023-11-09 |
13 |
True |
False |
False |
True |
bio3d_rmsd, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_ramachandran_plot, mdanalysis_rdf, bio3d_pca, bio3d_rmsf, mdanalysis_cosine_analysis |
UseGalaxy.eu, UseGalaxy.org (Main) |
Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
32255 |
57257 |
1.233333 |
0 |
|
Computational chemistry |
Protein target prediction of a bioactive ligand with Align-it and ePharmaLib |
https://training.galaxyproject.org//topics/computational-chemistry/tutorials/zauberkugel/tutorial.html |
|
|
2022-02-15 |
2024-06-14 |
10 |
True |
False |
False |
True |
ctb_alignit, openbabel_addh, rdconf, split_file_to_collection, sort1, tp_cat |
UseGalaxy.cz |
|
0 |
|
1212 |
1764 |
2.450000 |
0 |
|
Computational chemistry |
Running molecular dynamics simulations using GROMACS |
https://training.galaxyproject.org//topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.html |
|
|
2019-06-03 |
2023-11-09 |
15 |
True |
False |
False |
True |
gmx_em, gmx_editconf, gmx_solvate, gmx_sim, gmx_setup, get_pdb, tp_grep_tool |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no |
0 |
|
26370 |
47375 |
1.416667 |
0 |
|
Computational chemistry |
Running molecular dynamics simulations using NAMD |
https://training.galaxyproject.org//topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.html |
|
|
2019-06-03 |
2023-11-09 |
9 |
True |
False |
False |
True |
setup, namd_nvt, namd_npt, minimizer |
|
|
0 |
|
4185 |
7031 |
1.216667 |
0 |
|
Computational chemistry |
High Throughput Molecular Dynamics and Analysis |
https://training.galaxyproject.org//topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html |
|
|
2020-05-20 |
2025-04-08 |
19 |
True |
False |
True |
True |
bio3d_rmsd, ambertools_acpype, gmx_em, openbabel_compound_convert, gmx_merge_topology_files, vmd_hbonds, gmx_editconf, bio3d_pca_visualize, gmx_energy, gmx_solvate, bio3d_pca, gmx_sim, md_converter, gmx_setup, get_pdb, bio3d_rmsf, mdanalysis_cosine_analysis, tp_grep_tool |
UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no |
0 |
|
10647 |
18768 |
2.433333 |
0 |
|
Computational chemistry |
Setting up molecular systems |
https://training.galaxyproject.org//topics/computational-chemistry/tutorials/setting-up-molecular-systems/tutorial.html |
|
|
2019-06-03 |
2023-11-09 |
14 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
1775 |
2395 |
1.666667 |
0 |
|
Contributing to the Galaxy Training Material |
Contributing to the Galaxy Training Network with GitHub |
https://training.galaxyproject.org//topics/contributing/tutorials/github-contribution/tutorial.html |
|
|
2017-06-12 |
2025-03-14 |
2 |
True |
True |
False |
False |
|
|
|
0 |
|
2845040 |
7529828 |
3.616667 |
0 |
|
Contributing to the Galaxy Training Material |
Overview of the Galaxy Training Material |
https://training.galaxyproject.org//topics/contributing/tutorials/introduction/slides.html |
|
|
2017-06-25 |
2025-03-14 |
2 |
False |
True |
False |
False |
|
|
|
0 |
|
2844954 |
7529729 |
2.450000 |
0 |
|
Contributing to the Galaxy Training Material |
Adding auto-generated video to your slides |
https://training.galaxyproject.org//topics/contributing/tutorials/slides-with-video/tutorial.html |
|
|
2020-10-20 |
2023-11-09 |
12 |
True |
False |
False |
False |
|
|
|
0 |
|
264 |
346 |
3.866667 |
0 |
|
Contributing to the Galaxy Training Material |
GTN Metadata |
https://training.galaxyproject.org//topics/contributing/tutorials/schemas/tutorial.html |
|
|
2022-06-02 |
2024-10-15 |
8 |
True |
False |
False |
False |
|
|
|
0 |
|
262 |
349 |
2.866667 |
0 |
|
Contributing to the Galaxy Training Material |
Teaching Python |
https://training.galaxyproject.org//topics/contributing/tutorials/python/tutorial.html |
|
|
2022-10-19 |
2023-11-23 |
4 |
True |
False |
False |
False |
|
|
|
0 |
|
244 |
537 |
1.166667 |
0 |
|
Contributing to the Galaxy Training Material |
Generating PDF artefacts of the website |
https://training.galaxyproject.org//topics/contributing/tutorials/generating-pdf/tutorial.html |
|
|
2018-06-04 |
2023-11-09 |
12 |
True |
False |
False |
False |
|
|
|
0 |
|
75 |
92 |
2.733333 |
0 |
|
Contributing to the Galaxy Training Material |
FAIR-by-Design methodology |
https://training.galaxyproject.org//topics/contributing/tutorials/fair-by-design/tutorial.html |
|
|
2024-10-17 |
2024-10-17 |
1 |
True |
False |
False |
False |
|
|
|
0 |
|
33 |
38 |
0.716667 |
0 |
|
Contributing to the Galaxy Training Material |
Contributing with GitHub via its interface |
https://training.galaxyproject.org//topics/contributing/tutorials/github-interface-contribution/tutorial.html |
|
|
2018-06-12 |
2023-11-09 |
17 |
True |
False |
False |
False |
|
|
|
0 |
|
678 |
1029 |
2.366667 |
0 |
|
Contributing to the Galaxy Training Material |
Including a new topic |
https://training.galaxyproject.org//topics/contributing/tutorials/create-new-topic/tutorial.html |
|
|
2018-06-04 |
2025-03-14 |
32 |
True |
False |
False |
False |
|
|
|
0 |
|
1219 |
1677 |
0.566667 |
0 |
|
Contributing to the Galaxy Training Material |
Creating Interactive Galaxy Tours |
https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-tours/tutorial.html |
|
|
2017-06-25 |
2025-04-08 |
13 |
True |
False |
False |
False |
|
|
|
0 |
|
289 |
447 |
2.500000 |
0 |
|
Contributing to the Galaxy Training Material |
Design and plan session, course, materials |
https://training.galaxyproject.org//topics/contributing/tutorials/design/tutorial.html |
|
|
2022-09-23 |
2025-03-11 |
12 |
True |
False |
False |
False |
|
|
|
0 |
|
571 |
761 |
2.883333 |
0 |
|
Contributing to the Galaxy Training Material |
Adding Quizzes to your Tutorial |
https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-quiz/tutorial.html |
|
|
2022-05-19 |
2022-10-18 |
3 |
True |
False |
False |
False |
|
|
|
0 |
|
101 |
115 |
0.316667 |
0 |
|
Contributing to the Galaxy Training Material |
Preview the GTN website as you edit your training material |
https://training.galaxyproject.org//topics/contributing/tutorials/rendering_gtn/tutorial.html |
|
|
2025-03-14 |
2025-07-02 |
3 |
True |
False |
True |
False |
|
|
|
0 |
|
318 |
443 |
5.150000 |
0 |
|
Contributing to the Galaxy Training Material |
Updating diffs in admin training |
https://training.galaxyproject.org//topics/contributing/tutorials/admin-knitting/tutorial.html |
|
|
2021-06-07 |
2023-11-23 |
9 |
True |
False |
False |
False |
|
|
|
0 |
|
56 |
98 |
0.816667 |
0 |
|
Contributing to the Galaxy Training Material |
Principles of learning and how they apply to training and teaching |
https://training.galaxyproject.org//topics/contributing/tutorials/learning-principles/tutorial.html |
|
|
2022-09-23 |
2025-03-11 |
17 |
True |
False |
False |
False |
|
|
|
0 |
|
5367 |
6398 |
0.783333 |
0 |
|
Contributing to the Galaxy Training Material |
Tools, Data, and Workflows for tutorials |
https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-technical/tutorial.html |
|
|
2017-06-25 |
2025-04-08 |
26 |
True |
False |
False |
False |
|
|
|
0 |
|
550 |
741 |
1.650000 |
0 |
|
Contributing to the Galaxy Training Material |
Creating a new tutorial |
https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial/tutorial.html |
|
Data handling, Sequence trimming, Primer removal, Read mapping, Sequence file editing, Read pre-processing |
2018-06-20 |
2025-03-14 |
32 |
True |
False |
True |
True |
tp_cut_tool, random_lines1, tp_sed_tool, cutadapt, tp_sorted_uniq, bam_to_sam, Filter1, Cut1, seqtk_subseq, bowtie2, fastq_to_tabular, tp_cat, c3s |
|
|
0 |
|
1768 |
2623 |
5.016667 |
0 |
|
Contributing to the Galaxy Training Material |
Single Cell Publication - Data Plotting |
https://training.galaxyproject.org//topics/contributing/tutorials/meta-analysis-plot/tutorial.html |
|
|
2024-11-07 |
2024-11-07 |
1 |
True |
False |
False |
False |
|
|
|
0 |
|
38 |
38 |
0.116667 |
0 |
|
Contributing to the Galaxy Training Material |
Single Cell Publication - Data Analysis |
https://training.galaxyproject.org//topics/contributing/tutorials/meta-analysis-data/tutorial.html |
|
|
2024-11-07 |
2024-11-07 |
1 |
True |
False |
False |
False |
|
|
|
0 |
|
39 |
41 |
0.833333 |
0 |
|
Contributing to the Galaxy Training Material |
FAIR Galaxy Training Material |
https://training.galaxyproject.org//topics/contributing/tutorials/fair-gtn/tutorial.html |
|
|
2025-10-19 |
2025-10-19 |
0 |
True |
False |
False |
False |
|
|
|
0 |
|
1 |
1 |
0.000000 |
0 |
|
Contributing to the Galaxy Training Material |
Creating content in Markdown |
https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-content/tutorial.html |
|
Validation, Sequencing quality control |
2017-06-25 |
2025-04-08 |
85 |
True |
False |
False |
False |
upload1, multiqc |
|
|
0 |
|
3685 |
9683 |
2.100000 |
0 |
|
Contributing to the Galaxy Training Material |
Creating Slides |
https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-slides/slides.html |
|
|
2018-06-13 |
2024-11-08 |
17 |
False |
True |
True |
False |
|
|
|
0 |
|
2844954 |
7529730 |
2.450000 |
0 |
|
Contributing to the Galaxy Training Material |
Updating tool versions in a tutorial |
https://training.galaxyproject.org//topics/contributing/tutorials/updating_tutorial/tutorial.html |
|
|
2024-11-29 |
2024-11-29 |
1 |
True |
False |
False |
False |
|
|
|
0 |
|
90 |
109 |
4.766667 |
0 |
|
Sequence analysis |
Removal of human reads from SARS-CoV-2 sequencing data |
https://training.galaxyproject.org//topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html |
|
Generation, Sequence alignment, Data handling, Genome indexing, Read mapping, Sequence file editing |
2021-08-04 |
2023-11-09 |
5 |
True |
False |
False |
True |
bwa_mem, trimmomatic, tp_replace_in_line, seqtk_subseq, samtools_fastx, Grep1, __UNZIP_COLLECTION__, __ZIP_COLLECTION__ |
UseGalaxy.fr, UseGalaxy.org (Main) |
Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
4025 |
5635 |
2.300000 |
0 |
|
Using Galaxy and Managing your Data |
Submitting sequence data to ENA |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-data-to-ena/tutorial.html |
|
|
2021-08-10 |
2024-12-11 |
10 |
True |
True |
False |
True |
ena_consensus_submit, ena_upload |
|
|
0 |
|
2524059 |
6439180 |
3.833333 |
0 |
|
Using Galaxy and Managing your Data |
Automating Galaxy workflows using the command line |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-automation/tutorial.html |
|
Tree-based sequence alignment, Variant classification |
2021-06-08 |
2025-04-08 |
9 |
True |
False |
True |
True |
pangolin, compose_text_param, bcftools_consensus, snpSift_filter, collapse_dataset |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr |
0 |
|
2834 |
3440 |
2.083333 |
0 |
|
Variant Analysis |
Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html |
|
Tree-based sequence alignment, Methylation analysis, Variant classification, Variant calling |
2021-06-30 |
2025-03-28 |
18 |
True |
False |
True |
False |
pangolin, fasta_regex_finder, nextclade, upload1, Filter1, datamash_ops |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) |
|
0 |
|
7292 |
13084 |
3.433333 |
0 |
|
Variant Analysis |
From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2/tutorial.html |
|
Generation, Data handling, Genome indexing, Validation, Sequencing quality control, Formatting, Sequence alignment, SNP detection, Read mapping, Sequence contamination filtering |
2020-06-24 |
2024-06-14 |
16 |
True |
False |
True |
True |
tp_cut_tool, picard_MarkDuplicates, bwa_mem, multiqc, lofreq_call, lofreq_indelqual, snpeff_sars_cov_2, fasterq_dump, Filter1, snpSift_extractFields, fastp, lofreq_viterbi, Grep1, samtools_stats |
UseGalaxy.eu, UseGalaxy.org (Main) |
MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
13610 |
20501 |
2.883333 |
0 |
|
Using Galaxy and Managing your Data |
SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.html |
|
SNP detection, Data handling |
2021-05-31 |
2024-06-14 |
12 |
True |
True |
True |
False |
fastq_dump, snpeff_sars_cov_2, query_tabular, fasterq_dump, jq, tp_cat, fastq_to_fasta_python |
UseGalaxy.be, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no |
0 |
|
2625549 |
6775155 |
4.166667 |
0 |
|
Sequence analysis |
SARS-CoV-2 Viral Sample Alignment and Variant Visualization |
https://training.galaxyproject.org//topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.html |
|
Statistical calculation, Generation, Genome visualisation, Sequence alignment, Genome indexing, Sequence composition calculation, Read mapping, Sequencing quality control |
2023-07-10 |
2024-02-29 |
2 |
True |
False |
False |
False |
bwa_mem, fastqc, jbrowse |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz |
0 |
|
1219 |
1580 |
4.200000 |
0 |
|
Foundations of Data Science |
Data Manipulation Olympics |
https://training.galaxyproject.org//topics/data-science/tutorials/data-manipulation-olympics/tutorial.html |
|
|
2025-10-19 |
2025-10-19 |
0 |
True |
False |
False |
True |
Grouping1, {{version_join}}, tp_sorted_uniq, {{version_count}}, {{version_select_first}}, {{version_cut_advanced}}, {{version_cat}}, Add_a_column1, {{version_sort}}, Count1, {{version_remove_beginning}}, {{version_split}}, tp_cat, {{version_unique}}, join1, {{version_wc}}, {{version_replace_text_line}}, Remove beginning1, tp_sort_header_tool, regexColumn1, {{version_remove_columns_by_header}}, wc_gnu, {{version_paste}}, datamash_ops, tp_split_on_column, upload1, {{version_datamash}}, {{version_replace_text_column}}, Filter1, tabular_to_csv, Show beginning1, Cut1, cat1, {{version_cut_columns}}, {{version_filter}}, {{version_compute}} |
|
|
0 |
|
0 |
0 |
0.000000 |
0 |
|
Foundations of Data Science |
Learning about one gene across biological resources and formats |
https://training.galaxyproject.org//topics/data-science/tutorials/online-resources-gene/tutorial.html |
|
|
2023-09-07 |
2023-11-09 |
3 |
True |
True |
True |
False |
ncbi_blastp_wrapper |
Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, PepSimili, UseGalaxy.no |
0 |
|
1280868 |
2979056 |
5.266667 |
0 |
|
Foundations of Data Science |
A (very) brief history of genomics |
https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture1/tutorial.html |
|
|
2024-01-09 |
2024-02-20 |
2 |
True |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
1125216 |
2628698 |
3.400000 |
0 |
|
Foundations of Data Science |
SQL Educational Game - Murder Mystery |
https://training.galaxyproject.org//topics/data-science/tutorials/sql-game/tutorial.html |
|
|
2021-10-11 |
2023-11-23 |
6 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
668 |
723 |
0.383333 |
0 |
|
Foundations of Data Science |
Introduction to SQL |
https://training.galaxyproject.org//topics/data-science/tutorials/sql-basic/tutorial.html |
|
|
2021-10-11 |
2024-12-13 |
8 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
558 |
685 |
1.383333 |
0 |
|
Foundations of Data Science |
Version Control with Git |
https://training.galaxyproject.org//topics/data-science/tutorials/bash-git/tutorial.html |
|
|
2022-07-06 |
2023-10-23 |
6 |
True |
False |
False |
False |
interactive_tool_rstudio |
UseGalaxy.eu, UseGalaxy.org.au |
|
0 |
|
280 |
511 |
0.633333 |
0 |
|
Foundations of Data Science |
CLI Educational Game - Bashcrawl |
https://training.galaxyproject.org//topics/data-science/tutorials/cli-bashcrawl/tutorial.html |
|
|
2021-09-30 |
2024-10-15 |
7 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2011 |
2290 |
0.566667 |
0 |
|
Foundations of Data Science |
SQL with Python |
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https://training.galaxyproject.org//topics/data-science/tutorials/python-math/tutorial.html |
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Foundations of Data Science |
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Foundations of Data Science |
Basics of using Git from the Command Line |
https://training.galaxyproject.org//topics/data-science/tutorials/git-cli/tutorial.html |
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Foundations of Data Science |
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https://training.galaxyproject.org//topics/data-science/tutorials/python-warmup-stat-ml/tutorial.html |
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Advanced CLI in Galaxy |
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Foundations of Data Science |
One protein along the UniProt page |
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Foundations of Data Science |
Variant Calling Workflow |
https://training.galaxyproject.org//topics/data-science/tutorials/bash-variant-calling/tutorial.html |
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Foundations of Data Science |
SQL with R |
https://training.galaxyproject.org//topics/data-science/tutorials/sql-r/tutorial.html |
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2023-11-16 |
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Foundations of Data Science |
Introduction to sequencing with Python (part one) |
https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture2/tutorial.html |
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Foundations of Data Science |
Advanced R in Galaxy |
https://training.galaxyproject.org//topics/data-science/tutorials/r-advanced/tutorial.html |
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Foundations of Data Science |
Python - Functions |
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2023-02-13 |
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Foundations of Data Science |
Advanced Python |
https://training.galaxyproject.org//topics/data-science/tutorials/python-advanced-np-pd/tutorial.html |
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Foundations of Data Science |
Data visualisation Olympics - Visualization in R |
https://training.galaxyproject.org//topics/data-science/tutorials/data-manipulation-olympics-viz-r/tutorial.html |
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Foundations of Data Science |
Data Manipulation Olympics - SQL |
https://training.galaxyproject.org//topics/data-science/tutorials/data-manipulation-olympics-sql/tutorial.html |
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2023-06-16 |
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Foundations of Data Science |
dplyr & tidyverse for data processing |
https://training.galaxyproject.org//topics/data-science/tutorials/r-dplyr/tutorial.html |
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2021-10-20 |
2024-10-15 |
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Foundations of Data Science |
Plotting in Python |
https://training.galaxyproject.org//topics/data-science/tutorials/python-plotting/tutorial.html |
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2021-11-08 |
2024-10-15 |
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Foundations of Data Science |
Introduction to sequencing with Python (part two) |
https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture3/tutorial.html |
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2024-01-23 |
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Foundations of Data Science |
Python - Basic Types & Type Conversion |
https://training.galaxyproject.org//topics/data-science/tutorials/python-types/tutorial.html |
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2022-04-25 |
2023-02-13 |
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Foundations of Data Science |
Python - Lists & Strings & Dictionaries |
https://training.galaxyproject.org//topics/data-science/tutorials/python-iterables/tutorial.html |
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2022-04-25 |
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Foundations of Data Science |
Introduction to sequencing with Python (part three) |
https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture4/tutorial.html |
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Foundations of Data Science |
Data Manipulation Olympics - JQ |
https://training.galaxyproject.org//topics/data-science/tutorials/data-manipulation-olympics-jq/tutorial.html |
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2023-06-16 |
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Foundations of Data Science |
Introduction to sequencing with Python (part four) |
https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture5/tutorial.html |
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Foundations of Data Science |
Python - Flow Control |
https://training.galaxyproject.org//topics/data-science/tutorials/python-flow/tutorial.html |
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2023-02-13 |
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Foundations of Data Science |
Python - Loops |
https://training.galaxyproject.org//topics/data-science/tutorials/python-loops/tutorial.html |
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2023-02-13 |
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Foundations of Data Science |
Data manipulation with Pandas |
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Foundations of Data Science |
Versioning your code and data with git |
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Foundations of Data Science |
Python - Files & CSV |
https://training.galaxyproject.org//topics/data-science/tutorials/python-files/tutorial.html |
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Foundations of Data Science |
Python - Try & Except |
https://training.galaxyproject.org//topics/data-science/tutorials/python-exceptions/tutorial.html |
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2022-04-25 |
2023-02-13 |
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Foundations of Data Science |
Python - Introductory Graduation |
https://training.galaxyproject.org//topics/data-science/tutorials/python-basics-recap/tutorial.html |
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2022-04-25 |
2023-02-13 |
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Foundations of Data Science |
Conda Environments For Software Development |
https://training.galaxyproject.org//topics/data-science/tutorials/python-conda/tutorial.html |
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2023-05-18 |
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Foundations of Data Science |
Python - Testing |
https://training.galaxyproject.org//topics/data-science/tutorials/python-testing/tutorial.html |
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2023-02-13 |
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Foundations of Data Science |
Python - Type annotations |
https://training.galaxyproject.org//topics/data-science/tutorials/python-typing/tutorial.html |
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2023-02-13 |
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Foundations of Data Science |
Python - Argparse |
https://training.galaxyproject.org//topics/data-science/tutorials/python-argparse/tutorial.html |
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2022-04-25 |
2023-01-24 |
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Foundations of Data Science |
Virtual Environments For Software Development |
https://training.galaxyproject.org//topics/data-science/tutorials/python-venv/tutorial.html |
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2022-10-19 |
2023-05-18 |
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Foundations of Data Science |
Python - Globbing |
https://training.galaxyproject.org//topics/data-science/tutorials/python-glob/tutorial.html |
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2022-04-25 |
2023-02-13 |
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Foundations of Data Science |
Python - Subprocess |
https://training.galaxyproject.org//topics/data-science/tutorials/python-subprocess/tutorial.html |
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2022-04-25 |
2023-02-13 |
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Foundations of Data Science |
Python - Coding Style |
https://training.galaxyproject.org//topics/data-science/tutorials/python-linting/tutorial.html |
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2022-11-03 |
2023-05-18 |
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Foundations of Data Science |
Python - Multiprocessing |
https://training.galaxyproject.org//topics/data-science/tutorials/python-multiprocessing/tutorial.html |
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2022-10-19 |
2023-11-16 |
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https://training.galaxyproject.org//topics/dev/tutorials/conda/slides.html |
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2023-04-14 |
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Galaxy Code Architecture |
https://training.galaxyproject.org//topics/dev/tutorials/architecture/slides.html |
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2024-06-14 |
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Development in Galaxy |
Prerequisites for building software/conda packages |
https://training.galaxyproject.org//topics/dev/tutorials/conda_sys/slides.html |
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2018-02-15 |
2021-05-28 |
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2844954 |
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Development in Galaxy |
JavaScript plugins |
https://training.galaxyproject.org//topics/dev/tutorials/visualization-charts/tutorial.html |
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2017-06-22 |
2025-04-08 |
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Development in Galaxy |
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https://training.galaxyproject.org//topics/dev/tutorials/visualization-generic/tutorial.html |
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2023-11-09 |
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True |
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2845292 |
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Development in Galaxy |
Galaxy Interactive Environments |
https://training.galaxyproject.org//topics/dev/tutorials/interactive-environments/slides.html |
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2017-02-05 |
2023-02-17 |
16 |
False |
True |
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2844954 |
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Development in Galaxy |
ToolFactory: Generating Tools From Simple Scripts |
https://training.galaxyproject.org//topics/dev/tutorials/tool-generators/tutorial.html |
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2021-05-26 |
2024-06-14 |
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Development in Galaxy |
Galaxy Webhooks |
https://training.galaxyproject.org//topics/dev/tutorials/webhooks/tutorial.html |
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2017-04-03 |
2025-04-08 |
16 |
True |
True |
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2845140 |
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Development in Galaxy |
Galaxy Interactive Tours |
https://training.galaxyproject.org//topics/dev/tutorials/interactive-tours/slides.html |
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2017-01-12 |
2021-07-27 |
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True |
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2844954 |
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Development in Galaxy |
Tool Dependencies and Containers |
https://training.galaxyproject.org//topics/dev/tutorials/containers/slides.html |
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2017-06-20 |
2022-10-18 |
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False |
True |
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2844954 |
7529734 |
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Development in Galaxy |
Tool Shed: sharing Galaxy tools |
https://training.galaxyproject.org//topics/dev/tutorials/toolshed/slides.html |
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2017-06-12 |
2022-10-18 |
15 |
False |
True |
False |
False |
|
|
|
0 |
|
2844954 |
7529734 |
2.450000 |
0 |
|
Development in Galaxy |
Scripting Galaxy using the API and BioBlend |
https://training.galaxyproject.org//topics/dev/tutorials/bioblend-api/tutorial.html |
|
|
2017-01-17 |
2023-11-16 |
22 |
True |
True |
True |
False |
|
|
|
0 |
|
2845656 |
7530655 |
4.666667 |
0 |
|
Development in Galaxy |
Tool development and integration into Galaxy |
https://training.galaxyproject.org//topics/dev/tutorials/tool-integration/slides.html |
|
|
2016-09-30 |
2025-04-08 |
30 |
external |
True |
False |
False |
|
|
|
0 |
|
2844957 |
7529738 |
2.450000 |
0 |
|
Development in Galaxy |
Writing Automated Tests for Galaxy |
https://training.galaxyproject.org//topics/dev/tutorials/writing_tests/tutorial.html |
|
|
2022-07-15 |
2024-06-25 |
5 |
True |
False |
False |
False |
|
|
|
0 |
|
255 |
683 |
2.366667 |
0 |
|
Development in Galaxy |
Contributing a New Feature to Galaxy Core |
https://training.galaxyproject.org//topics/dev/tutorials/core-contributing/tutorial.html |
|
|
2021-06-08 |
2025-03-14 |
9 |
True |
False |
False |
False |
|
|
|
0 |
|
706 |
1062 |
2.666667 |
0 |
|
Development in Galaxy |
Creating Galaxy tools from Conda Through Deployment |
https://training.galaxyproject.org//topics/dev/tutorials/tool-from-scratch/tutorial.html |
|
|
2021-06-15 |
2024-10-08 |
15 |
True |
False |
True |
False |
|
|
|
0 |
|
2720 |
4402 |
2.566667 |
0 |
|
Development in Galaxy |
Setting up a dev Onedata instance |
https://training.galaxyproject.org//topics/dev/tutorials/onedata-dev-instance/tutorial.html |
|
|
2025-03-24 |
2025-04-08 |
2 |
True |
False |
False |
False |
|
|
|
0 |
|
18 |
21 |
3.900000 |
0 |
|
Development in Galaxy |
Data source integration |
https://training.galaxyproject.org//topics/dev/tutorials/data-source-integration/tutorial.html |
|
|
2016-09-30 |
2022-10-18 |
15 |
True |
False |
False |
False |
|
|
|
0 |
|
224 |
333 |
3.050000 |
0 |
|
Development in Galaxy |
ToolFactory: Generating Tools From More Complex Scripts |
https://training.galaxyproject.org//topics/dev/tutorials/tool-generators-advanced/tutorial.html |
|
|
2021-05-26 |
2024-09-27 |
12 |
True |
False |
True |
False |
|
|
|
0 |
|
401 |
485 |
1.633333 |
0 |
|
Development in Galaxy |
Adding and updating best practice metadata for Galaxy tools using the bio.tools registry |
https://training.galaxyproject.org//topics/dev/tutorials/tool-annotation/tutorial.html |
|
|
2024-03-06 |
2024-11-06 |
5 |
True |
False |
False |
False |
|
|
|
0 |
|
240 |
287 |
2.700000 |
0 |
|
Development in Galaxy |
Contributing to BioBlend as a developer |
https://training.galaxyproject.org//topics/dev/tutorials/bioblend-dev/tutorial.html |
|
|
2021-05-25 |
2023-11-09 |
8 |
True |
False |
False |
False |
|
|
|
0 |
|
220 |
310 |
3.300000 |
0 |
|
Development in Galaxy |
Debugging Galaxy |
https://training.galaxyproject.org//topics/dev/tutorials/debugging/tutorial.html |
|
|
2021-06-15 |
2024-06-14 |
14 |
True |
False |
False |
False |
|
|
|
0 |
|
582 |
1186 |
2.916667 |
0 |
|
Development in Galaxy |
Galaxy Interactive Tools |
https://training.galaxyproject.org//topics/dev/tutorials/interactive-tools/tutorial.html |
|
|
2022-03-02 |
2024-12-03 |
9 |
True |
False |
False |
False |
|
|
|
0 |
|
1150 |
1536 |
2.816667 |
0 |
|
Digital Humanities |
Text-Mining Differences in Chinese Newspaper Articles |
https://training.galaxyproject.org//topics/digital-humanities/tutorials/text_mining_chinese/tutorial.html |
|
|
2025-02-28 |
2025-09-09 |
5 |
True |
False |
False |
True |
tp_replace_in_line, Filter1, Add_a_column1, Cut1, diff, sort1, wordcloud, datamash_ops |
|
|
0 |
|
138 |
165 |
1.766667 |
0 |
|
Digital Humanities |
Introduction to Digital Humanities in Galaxy |
https://training.galaxyproject.org//topics/digital-humanities/tutorials/introduction_to_dh/tutorial.html |
|
|
2025-09-11 |
2025-09-16 |
3 |
True |
False |
False |
True |
tp_replace_in_line, Remove beginning1, wc_gnu, tp_find_and_replace, diff, wordcloud, tp_grep_tool |
UseGalaxy.eu, UseGalaxy.org.au |
|
0 |
|
44 |
56 |
1.800000 |
0 |
|
Digital Humanities |
OpenRefine Tutorial for researching cultural data |
https://training.galaxyproject.org//topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html |
|
|
2025-09-24 |
2025-09-24 |
1 |
True |
False |
False |
True |
filter_tabular, barchart_gnuplot, compose_text_param, param_value_from_file, tp_head_tool, Remove beginning1, interactive_tool_openrefine, regexColumn1, Cut1, tp_sort_header_tool, wordcloud, datamash_ops, tp_grep_tool |
UseGalaxy.eu |
|
0 |
|
12 |
15 |
0.016667 |
0 |
|
Ecology |
Checking expected species and contamination in bacterial isolate |
https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html |
Whole genome sequencing, Genomics, Microbiology, Microbial ecology |
Statistical calculation, Expression analysis, Cross-assembly, Taxonomic classification |
2024-03-04 |
2024-06-27 |
4 |
True |
False |
False |
True |
recentrifuge, upload1, kraken2, est_abundance |
UseGalaxy.eu, UseGalaxy.fr |
Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main) |
0 |
|
813 |
1091 |
3.350000 |
0 |
|
Ecology |
RAD-Seq to construct genetic maps |
https://training.galaxyproject.org//topics/ecology/tutorials/genetic-map-rad-seq/tutorial.html |
|
Data handling |
2017-02-14 |
2025-06-03 |
13 |
True |
False |
False |
True |
stacks_denovomap, stacks_genotypes |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au |
|
0 |
|
872 |
1229 |
1.333333 |
0 |
|
Ecology |
Regional GAM |
https://training.galaxyproject.org//topics/ecology/tutorials/regionalGAM/tutorial.html |
Ecology |
Visualisation |
2019-07-04 |
2025-06-03 |
18 |
True |
False |
False |
True |
regionalgam_glmmpql, regionalgam_flight_curve, tp_awk_tool, csv2tab_R, ggplot2_point, Remove beginning1, regionalgam_gls, Filter1, regexColumn1, regionalgam_plot_trend, flight-curve, Paste1, regionalgam_ab_index, Count1, regionalgam_autocor_acf, mergeCols1, tab2csv_R |
|
|
0 |
|
335 |
449 |
3.516667 |
0 |
|
Ecology |
Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities |
https://training.galaxyproject.org//topics/ecology/tutorials/MetaShARK_tutorial/tutorial.html |
|
|
2024-03-04 |
2024-09-10 |
7 |
True |
False |
False |
False |
interactive_tool_metashark |
UseGalaxy.eu, UseGalaxy.fr |
|
0 |
|
176 |
217 |
2.066667 |
0 |
|
Ecology |
Data submission using ENA upload Tool |
https://training.galaxyproject.org//topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html |
|
Read mapping, Sequence trimming, Primer removal, Validation, Visualisation, Sequencing quality control, Read pre-processing |
2024-12-13 |
2025-03-20 |
2 |
True |
False |
False |
False |
fastq_groomer, ncbi_blastn_wrapper, multiqc, cutadapt, collection_element_identifiers, regex1, __RELABEL_FROM_FILE__, fastq_filter, falco, ab1_fastq_converter, bg_uniq, Paste1, __FILTER_EMPTY_DATASETS__, fastq_to_fasta_python |
UseGalaxy.eu |
UseGalaxy.cz |
0 |
|
186 |
193 |
0.666667 |
0 |
|
Ecology |
Obis marine indicators |
https://training.galaxyproject.org//topics/ecology/tutorials/obisindicators/tutorial.html |
Biodiversity, Ecology, Data mining |
|
2023-04-11 |
2025-06-03 |
9 |
True |
False |
False |
True |
tp_cut_tool, obisindicators, obis_data |
UseGalaxy.eu |
|
0 |
|
306 |
385 |
2.100000 |
0 |
|
Ecology |
Champs blocs indicators |
https://training.galaxyproject.org//topics/ecology/tutorials/champs-blocs/tutorial.html |
|
|
2023-01-04 |
2025-06-03 |
11 |
True |
False |
False |
True |
cb_div, cb_dissim, cb_qecb, cb_eco, cb_ivr |
|
|
0 |
|
167 |
316 |
2.033333 |
0 |
|
Ecology |
Ecoregionalization workflow tutorial |
https://training.galaxyproject.org//topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html |
|
|
2024-09-16 |
2025-06-03 |
7 |
True |
False |
False |
True |
tp_cut_tool, ecoregion_brt_analysis, ecoregion_taxa_seeker, interactive_tool_jupyter_notebook, ecoregion_clara_cluster, regexColumn1, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, filter_tabular, unzip, ecoregion_eco_map, mergeCols1 |
UseGalaxy.eu |
|
0 |
|
234 |
321 |
3.266667 |
0 |
|
Ecology |
RAD-Seq Reference-based data analysis |
https://training.galaxyproject.org//topics/ecology/tutorials/ref-based-rad-seq/tutorial.html |
|
Statistical calculation, Generation, Data handling, Genome indexing, Validation, Sequencing quality control, Sequence alignment, Sequence composition calculation, Read mapping |
2017-02-14 |
2025-06-03 |
14 |
True |
False |
False |
True |
Summary_Statistics1, bwa, multiqc, stacks_refmap, stacks_populations, fastqc, tp_replace_in_line, addValue, stacks_procrad, bwa_wrapper, Filter1, tp_sort_header_tool, cat1, Cut1, Grep1, Convert characters1, Count1, regex_replace |
|
|
0 |
|
2987 |
4693 |
1.766667 |
0 |
|
Ecology |
Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS |
https://training.galaxyproject.org//topics/ecology/tutorials/Metashrimps_tutorial/tutorial.html |
|
|
2024-01-22 |
2025-06-03 |
6 |
True |
False |
False |
False |
interactive_tool_metashrimps |
UseGalaxy.eu |
|
0 |
|
98 |
105 |
1.983333 |
0 |
|
Ecology |
Biodiversity data exploration |
https://training.galaxyproject.org//topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html |
|
|
2022-03-01 |
2025-06-03 |
15 |
True |
False |
True |
True |
tp_cut_tool, ecology_beta_diversity, ecology_link_between_var, ecology_homogeneity_normality, ecology_stat_presence_abs, ecology_presence_abs_abund, Remove beginning1, tool_anonymization, regexColumn1 |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr |
0 |
|
1582 |
2219 |
2.750000 |
0 |
|
Ecology |
Taxonomic Analysis of eDNA |
https://training.galaxyproject.org//topics/ecology/tutorials/eDNA-taxonomic-analysis/tutorial.html |
|
Sequence contamination filtering, Sequencing quality control |
2025-06-02 |
2025-06-03 |
2 |
True |
False |
False |
True |
ncbi_blastn_wrapper, Count1, cshl_fastq_to_fasta, fastp |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.no |
0 |
|
389 |
494 |
0.800000 |
0 |
|
Ecology |
Sentinel 2 biodiversity |
https://training.galaxyproject.org//topics/ecology/tutorials/remote-sensing/tutorial.html |
|
|
2023-04-13 |
2025-06-03 |
6 |
True |
False |
False |
True |
srs_pca, srs_global_indices, srs_diversity_maps, srs_process_data, srs_preprocess_s2, srs_spectral_indices |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr |
|
0 |
|
589 |
759 |
1.550000 |
0 |
|
Ecology |
Metabarcoding/eDNA through Obitools |
https://training.galaxyproject.org//topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html |
|
Statistical calculation, Sequence analysis, Sequence composition calculation, Sequencing quality control |
2022-02-28 |
2025-06-03 |
12 |
True |
False |
True |
True |
join1, ncbi_blastn_wrapper, obi_annotate, fastqc, unzip, obi_grep, obi_ngsfilter, obi_clean, obi_illumina_pairend, obi_uniq, Filter1, Cut1, wc_gnu, fastq_groomer, obi_stat, obi_tab, seq_filter_by_id |
UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr |
0 |
|
4406 |
6121 |
1.933333 |
0 |
|
Ecology |
Phylodiversity analysis quick tutorial |
https://training.galaxyproject.org//topics/ecology/tutorials/phylodiversity_workflow/tutorial.html |
|
|
2025-06-06 |
2025-06-06 |
1 |
True |
False |
False |
False |
phylogenetic_occupancy_matcher, phylo_index, estimate_endem, crsconverter |
UseGalaxy.eu |
|
0 |
|
66 |
91 |
1.116667 |
0 |
|
Ecology |
Species distribution modeling |
https://training.galaxyproject.org//topics/ecology/tutorials/species-distribution-modeling/tutorial.html |
|
|
2019-07-04 |
2025-06-03 |
18 |
True |
False |
False |
True |
tp_cut_tool, spocc_occ, interactive_tool_wallace, Filter1, tabular_to_csv, tp_find_and_replace |
UseGalaxy.eu, UseGalaxy.fr |
|
0 |
|
3127 |
4746 |
1.150000 |
0 |
|
Ecology |
Compute and analyze biodiversity metrics with PAMPA toolsuite |
https://training.galaxyproject.org//topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html |
|
|
2020-11-19 |
2025-09-03 |
23 |
True |
False |
True |
True |
tp_cut_tool, mergeCols1, pampa_glmcomm, tp_easyjoin_tool, pampa_presabs, regex1, datamash_transpose, regexColumn1, Filter1, pampa_plotglm, pampa_communitymetrics, tp_sort_header_tool, Count1, tp_cat, pampa_glmsp |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au |
0 |
|
1078 |
1425 |
1.850000 |
0 |
|
Ecology |
From NDVI data with OpenEO to time series visualisation with Holoviews |
https://training.galaxyproject.org//topics/ecology/tutorials/ndvi_openeo/tutorial.html |
|
|
2024-01-24 |
2024-06-29 |
3 |
True |
False |
False |
True |
interactive_tool_copernicus_notebook, interactive_tool_holoviz |
UseGalaxy.eu |
|
0 |
|
186 |
224 |
1.183333 |
0 |
|
Ecology |
RAD-Seq de-novo data analysis |
https://training.galaxyproject.org//topics/ecology/tutorials/de-novo-rad-seq/tutorial.html |
|
Statistical calculation, Data handling, Sequence composition calculation, Sequencing quality control |
2017-02-14 |
2025-06-03 |
14 |
True |
False |
False |
True |
stacks_denovomap, fastqc, stacks_populations, stacks_procrad |
UseGalaxy.be, UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
2626 |
4207 |
2.083333 |
0 |
|
Ecology |
Marine Omics identifying biosynthetic gene clusters |
https://training.galaxyproject.org//topics/ecology/tutorials/marine_omics_bgc/tutorial.html |
|
Sequence motif recognition, Genome annotation, Protein feature detection |
2024-08-19 |
2025-06-03 |
3 |
True |
False |
False |
True |
interproscan, regex1, prodigal, SanntiS_marine, sanntis_marine |
|
|
0 |
|
156 |
182 |
2.583333 |
0 |
|
Ecology |
Preparing genomic data for phylogeny reconstruction |
https://training.galaxyproject.org//topics/ecology/tutorials/phylogeny-data-prep/tutorial.html |
|
Genome annotation, Multiple sequence alignment, Sequence clustering, Genetic variation analysis, Sequence analysis, Sequence assembly validation |
2022-10-21 |
2025-06-03 |
5 |
True |
False |
False |
True |
phykit_alignment_based, repeatmasker_wrapper, busco, tp_replace_in_line, regex1, funannotate_predict, proteinortho_grab_proteins, collapse_dataset, Filter1, clipkit, glimmer_gbk_to_orf, clustalw, proteinortho |
|
|
0 |
|
2139 |
2929 |
2.700000 |
0 |
|
Ecology |
Life Traits Ecoregionalization workflow |
https://training.galaxyproject.org//topics/ecology/tutorials/ecoregiolifetraits/tutorial.html |
|
|
2025-06-02 |
2025-06-10 |
3 |
True |
False |
False |
False |
tp_cut_tool, ecoregion_brt_analysis, ecoregion_taxa_seeker, column_remove_by_header, regexColumn1, Filter1, ecoregion_GeoNearestNeighbor, ClaraGuess, unzip, ecoregion_eco_map, WormsMeasurements |
UseGalaxy.eu |
|
0 |
|
24 |
26 |
4.366667 |
0 |
|
Ecology |
Visualization of Climate Data using NetCDF xarray Map Plotting |
https://training.galaxyproject.org//topics/ecology/tutorials/x-array-map-plot/tutorial.html |
|
|
2022-10-26 |
2024-06-27 |
9 |
True |
False |
False |
True |
xarray_metadata_info, cdo_operations, xarray_mapplot, xarray_coords_info, graphicsmagick_image_montage |
UseGalaxy.eu |
UseGalaxy.cz |
0 |
|
2343 |
2714 |
0.466667 |
0 |
|
Ecology |
Cleaning GBIF data for the use in Ecology |
https://training.galaxyproject.org//topics/ecology/tutorials/gbif_cleaning/tutorial.html |
|
|
2022-10-28 |
2025-06-03 |
6 |
True |
False |
False |
True |
Summary_Statistics1, spocc_occ, Filter1, gdal_ogr2ogr, Count1 |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no |
|
0 |
|
618 |
768 |
0.900000 |
0 |
|
Ecology |
Cleaning GBIF data using OpenRefine |
https://training.galaxyproject.org//topics/ecology/tutorials/openrefine_gbif/tutorial.html |
|
|
2025-01-21 |
2025-06-03 |
5 |
True |
False |
False |
False |
interactive_tool_openrefine, regex1 |
UseGalaxy.eu, UseGalaxy.fr |
|
0 |
|
135 |
162 |
0.883333 |
0 |
|
Ecology |
Visualize EBV cube data with Panoply netCDF viewer |
https://training.galaxyproject.org//topics/ecology/tutorials/panoply_ebv/tutorial.html |
|
|
2022-10-28 |
2024-06-27 |
9 |
True |
False |
False |
False |
interactive_tool_panoply |
UseGalaxy.eu, UseGalaxy.org (Main) |
|
0 |
|
222 |
285 |
1.350000 |
0 |
|
Ecology |
Audio data annotation with NEAL (Nature + Energy Audio labeler). |
https://training.galaxyproject.org//topics/ecology/tutorials/NEAL_tutorial/tutorial.html |
|
|
2025-10-14 |
2025-10-15 |
2 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
3 |
6 |
0.000000 |
0 |
|
Ecology |
QGIS Web Feature Services |
https://training.galaxyproject.org//topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.html |
|
|
2023-10-11 |
2025-06-03 |
6 |
True |
False |
False |
False |
interactive_tool_qgis |
UseGalaxy.eu |
|
0 |
|
266 |
307 |
1.633333 |
0 |
|
Statistics and machine learning |
Foundational Aspects of Machine Learning using Python |
https://training.galaxyproject.org//topics/statistics/tutorials/intro-to-ml-with-python/tutorial.html |
|
|
2025-03-11 |
2025-05-19 |
3 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
418 |
506 |
1.100000 |
0 |
|
Statistics and machine learning |
Pretraining a Large Language Model (LLM) from Scratch on DNA Sequences |
https://training.galaxyproject.org//topics/statistics/tutorials/genomic-llm-pretraining/tutorial.html |
|
|
2025-04-17 |
2025-05-22 |
4 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
710 |
837 |
1.750000 |
0 |
|
Teaching and Hosting Galaxy training |
Motivation and Demotivation |
https://training.galaxyproject.org//topics/teaching/tutorials/motivation_demotivation/tutorial.html |
|
|
2022-09-23 |
2025-03-11 |
11 |
True |
False |
False |
False |
|
|
|
0 |
|
1898 |
2252 |
0.666667 |
0 |
|
Teaching and Hosting Galaxy training |
Training techniques to enhance learner participation and engagement |
https://training.galaxyproject.org//topics/teaching/tutorials/learner_participation_engagement/tutorial.html |
|
|
2022-09-23 |
2025-03-11 |
14 |
True |
False |
False |
False |
|
|
|
0 |
|
1582 |
1866 |
0.750000 |
0 |
|
Teaching and Hosting Galaxy training |
Assessment and feedback in training and teachings |
https://training.galaxyproject.org//topics/teaching/tutorials/assessment/tutorial.html |
|
|
2022-09-23 |
2025-03-11 |
11 |
True |
False |
False |
False |
|
|
|
0 |
|
1237 |
1433 |
0.783333 |
0 |
|
Teaching and Hosting Galaxy training |
Train-the-Trainer: putting it all together |
https://training.galaxyproject.org//topics/teaching/tutorials/workshop-final-exercise/tutorial.html |
|
|
2023-06-12 |
2025-03-11 |
3 |
True |
False |
False |
False |
|
|
|
0 |
|
84 |
98 |
0.616667 |
0 |
|
Statistics and machine learning |
Fine-tuning a LLM for DNA Sequence Classification |
https://training.galaxyproject.org//topics/statistics/tutorials/genomic-llm-finetuning/tutorial.html |
|
|
2025-04-17 |
2025-05-22 |
4 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
420 |
489 |
1.366667 |
0 |
|
Statistics and machine learning |
Neural networks using Python |
https://training.galaxyproject.org//topics/statistics/tutorials/neural-networks-with-python/tutorial.html |
|
|
2025-03-11 |
2025-03-11 |
1 |
True |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
465113 |
1012841 |
1.933333 |
0 |
|
Statistics and machine learning |
Predicting Mutation Impact with Zero-shot Learning using a pretrained DNA LLM |
https://training.galaxyproject.org//topics/statistics/tutorials/genomic-llm-zeroshot-prediction/tutorial.html |
|
|
2025-04-17 |
2025-05-22 |
4 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
101 |
105 |
2.600000 |
0 |
|
Statistics and machine learning |
Deep Learning (without Generative Artificial Intelligence) using Python |
https://training.galaxyproject.org//topics/statistics/tutorials/deep-learning-without-gai-with-python/tutorial.html |
|
|
2025-03-11 |
2025-03-11 |
1 |
True |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
465114 |
1012845 |
2.050000 |
0 |
|
Statistics and machine learning |
Generating Artificial Yeast DNA Sequences using a DNA LLM |
https://training.galaxyproject.org//topics/statistics/tutorials/genomic-llm-sequence-generation/tutorial.html |
|
|
2025-04-17 |
2025-05-22 |
4 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
102 |
113 |
0.900000 |
0 |
|
Statistics and machine learning |
Optimizing DNA Sequences for Biological Functions using a DNA LLM |
https://training.galaxyproject.org//topics/statistics/tutorials/genomic-llm-sequence-optimization/tutorial.html |
|
|
2025-04-17 |
2025-05-22 |
2 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
21 |
23 |
0.033333 |
0 |
|
Statistics and machine learning |
Regulations/standards for AI using DOME |
https://training.galaxyproject.org//topics/statistics/tutorials/dome/tutorial.html |
|
|
2025-03-11 |
2025-05-19 |
3 |
True |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
465138 |
1012881 |
3.750000 |
0 |
|
Epigenetics |
Formation of the Super-Structures on the Inactive X |
https://training.galaxyproject.org//topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html |
|
Statistical calculation, Pathway visualisation, Mapping, Sequence trimming, Primer removal, Peak calling, Structure visualisation, Enrichment analysis, Sequencing quality control, Genome visualisation, Sequence composition calculation, Read pre-processing, Read mapping, Gene regulatory network analysis |
2018-09-17 |
2025-04-08 |
14 |
True |
True |
False |
True |
deeptools_bam_compare, deeptools_plot_fingerprint, deeptools_plot_heatmap, bbgtobigwig, fastqc, Filter1, deeptools_compute_matrix, deeptools_plot_correlation, trim_galore, cat1, bedtools_mergebed, macs2_callpeak, deeptools_bam_coverage, bedtools_sortbed, bowtie2, jbrowse2, deeptools_multi_bam_summary, samtools_idxstats |
UseGalaxy.eu, UseGalaxy.org (Main) |
|
0 |
|
2850855 |
7541432 |
6.116667 |
0 |
|
Epigenetics |
DNA Methylation data analysis |
https://training.galaxyproject.org//topics/epigenetics/tutorials/methylation-seq/tutorial.html |
Epigenomics |
Statistical calculation, Sequence composition calculation, Read mapping, Visualisation, Sequencing quality control |
2017-02-16 |
2025-04-03 |
24 |
True |
False |
False |
True |
bwameth, tp_awk_tool, fastqc, tp_tail_tool, wig_to_bigWig, pileometh, deeptools_compute_matrix, falco, replace_column_with_key_value_file, deeptools_plot_profile, metilene |
|
|
0 |
|
14704 |
24574 |
2.050000 |
0 |
|
Epigenetics |
Hi-C analysis of Drosophila melanogaster cells using HiCExplorer |
https://training.galaxyproject.org//topics/epigenetics/tutorials/hicexplorer/tutorial.html |
|
Read mapping, Visualisation, Formatting |
2018-02-23 |
2025-08-11 |
30 |
True |
False |
False |
True |
hicexplorer_hiccorrectmatrix, hicexplorer_hicfindrestrictionsites, hicexplorer_hicdetectloops, hicexplorer_hicbuildmatrix, hicexplorer_hicpca, pygenomeTracks, hicexplorer_hicfindtads, hicexplorer_hicmergematrixbins, bowtie2, hicexplorer_hicplotmatrix, hicexplorer_hicinfo |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.no, UseGalaxy.org (Main) |
0 |
|
7343 |
12398 |
1.516667 |
0 |
|
Epigenetics |
Infinium Human Methylation BeadChip |
https://training.galaxyproject.org//topics/epigenetics/tutorials/ewas-suite/tutorial.html |
|
|
2018-08-27 |
2024-10-15 |
21 |
True |
True |
False |
True |
clusterprofiler_bitr, clusterprofiler_go, minfi_analysis, Remove beginning1, Cut1, chipeakanno_annopeaks |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no |
|
0 |
|
2846994 |
7532948 |
4.350000 |
0 |
|
Epigenetics |
Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) |
https://training.galaxyproject.org//topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html |
ChIP-seq |
Statistical calculation, Generation, Mapping, Genome indexing, Peak calling, Enrichment analysis, Sequencing quality control, Sequence alignment, Sequence composition calculation, Read mapping, Gene regulatory network analysis |
2016-12-20 |
2025-04-08 |
11 |
True |
False |
False |
True |
deeptools_bam_compare, deeptools_plot_fingerprint, bedtools_intersectbed, deeptools_plot_heatmap, bwa, deeptools_compute_gc_bias, trimmomatic, fastqc, deeptools_compute_matrix, macs2_callpeak, deeptools_plot_correlation, deeptools_correct_gc_bias, deeptools_multi_bam_summary, samtools_idxstats |
UseGalaxy.be, UseGalaxy.fr, UseGalaxy.org (Main) |
Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
7123 |
13060 |
3.300000 |
0 |
|
Epigenetics |
Identification of the binding sites of the Estrogen receptor |
https://training.galaxyproject.org//topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html |
|
Statistical calculation, Sequence trimming, Primer removal, Peak calling, Enrichment analysis, Sequencing quality control, Sequence composition calculation, Read pre-processing, Read mapping, Gene regulatory network analysis |
2017-09-18 |
2025-04-08 |
10 |
True |
False |
False |
True |
deeptools_bam_compare, deeptools_plot_fingerprint, deeptools_plot_heatmap, deeptools_compute_gc_bias, fastqc, bam_to_sam, deeptools_compute_matrix, deeptools_plot_correlation, trim_galore, macs2_callpeak, deeptools_bam_coverage, bowtie2, deeptools_multi_bam_summary, samtools_idxstats |
UseGalaxy.be |
Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
1905 |
2816 |
2.766667 |
0 |
|
Epigenetics |
CUT&RUN data analysis |
https://training.galaxyproject.org//topics/epigenetics/tutorials/cut_and_run/tutorial.html |
|
Sequence alignment analysis, Data handling, Primer removal, Sequence trimming, Validation, Mapping, Peak calling, Sequencing quality control, Enrichment analysis, Formatting, Read pre-processing, Read mapping, Visualisation, Gene regulatory network analysis |
2024-03-06 |
2025-03-19 |
5 |
True |
False |
False |
True |
Extract genomic DNA 1, deeptools_compute_matrix, bowtie2, deeptools_plot_heatmap, multiqc, meme_chip, wig_to_bigWig, bamFilter, falco, pe_histogram, trim_galore, Grep1, picard_MarkDuplicates, deeptools_plot_fingerprint, bedtools_intersectbed, idr, datamash_transpose, bedtools_bamtobed, macs2_callpeak, __FLATTEN__, __EXTRACT_DATASET__ |
|
|
0 |
|
5725 |
7267 |
1.383333 |
0 |
|
Epigenetics |
ATAC-Seq data analysis |
https://training.galaxyproject.org//topics/epigenetics/tutorials/atac-seq/tutorial.html |
|
Statistical calculation, Gene regulatory network analysis, Mapping, Sequence trimming, Primer removal, Sequence alignment analysis, Data handling, Peak calling, Enrichment analysis, Sequencing quality control, Formatting, Sequence composition calculation, Read mapping, Visualisation, Read pre-processing |
2019-09-02 |
2024-08-08 |
23 |
True |
True |
True |
True |
picard_MarkDuplicates, bedtools_intersectbed, deeptools_plot_heatmap, cutadapt, fastqc, wig_to_bigWig, bedtools_bamtobed, bamFilter, pygenomeTracks, Filter1, deeptools_compute_matrix, pe_histogram, Cut1, tp_sort_header_tool, Grep1, macs2_callpeak, bowtie2, samtools_idxstats |
|
|
0 |
|
2908122 |
7643703 |
4.250000 |
0 |
|
Epigenetics |
Introduction to ChIP-Seq data analysis |
https://training.galaxyproject.org//topics/epigenetics/tutorials/introduction-chip-seq/slides.html |
|
|
2017-06-12 |
2024-03-05 |
2 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2844954 |
7529736 |
2.450000 |
0 |
|
Epigenetics |
Introduction to DNA Methylation data analysis |
https://training.galaxyproject.org//topics/epigenetics/tutorials/introduction-dna-methylation/slides.html |
|
|
2016-10-05 |
2024-03-05 |
2 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2844954 |
7529736 |
2.450000 |
0 |
|
Evolution |
Phylogenetics - Back to basics |
https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo/tutorial.html |
|
Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis, Phylogenetic analysis, Phylogenetic tree reconstruction, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation, Sequence analysis, Multiple sequence alignment |
2024-05-10 |
2024-05-10 |
1 |
True |
False |
False |
True |
rbc_mafft, newick_display, fasttree, iqtree |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
4521 |
5834 |
1.950000 |
0 |
|
Evolution |
Tree thinking for tuberculosis evolution and epidemiology |
https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html |
Genomics, Microbiology, Phylogeny, Infectious disease |
Sequence analysis, Phylogenetic tree analysis |
2022-03-16 |
2025-06-04 |
12 |
True |
False |
False |
True |
interactive_tool_rstudio, raxml, upload1 |
UseGalaxy.eu |
|
0 |
|
2167 |
3129 |
2.266667 |
0 |
|
Evolution |
Identifying tuberculosis transmission links: from SNPs to transmission clusters |
https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html |
Genomics, Microbiology, Infectious disease, DNA polymorphism |
Antimicrobial resistance prediction, Phylogenetic tree generation, Phylogenetic tree visualisation, Variant calling |
2022-03-16 |
2025-05-26 |
13 |
True |
False |
False |
True |
tb_variant_filter, tp_sed_tool, tp_replace_in_line, clustering_from_distmat, collapse_dataset, tp_cat, trimmomatic, snp_dists, samtools_view, snippy, snp_sites, bcftools_consensus, tp_easyjoin_tool, Grep1, tp_grep_tool, __MERGE_COLLECTION__, upload1, tb_profiler_profile, addName |
UseGalaxy.eu |
|
0 |
|
2657 |
3823 |
2.833333 |
0 |
|
Evolution |
Phylogenetics - Back to Basics - Introduction |
https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo-intro/slides.html |
|
|
2024-05-10 |
2024-05-10 |
1 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
920649 |
2151039 |
2.283333 |
0 |
|
Evolution |
Phylogenetic analysis for bacterial comparative genomics |
https://training.galaxyproject.org//topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html |
Genomics, Microbiology, Phylogeny |
Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) |
2025-03-14 |
2025-03-14 |
1 |
True |
False |
False |
False |
fasttree, upload1 |
GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) |
Galaxy@AuBi |
0 |
|
81 |
102 |
3.966667 |
0 |
|
Evolution |
Phylogenetics - Back to Basics - Terminology |
https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo-terminology/slides.html |
|
|
2024-05-10 |
2024-05-10 |
1 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
920649 |
2151039 |
2.283333 |
0 |
|
Evolution |
Phylogenetics - Back to Basics - Multiple Sequence Alignment |
https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo-msa/slides.html |
|
|
2024-05-10 |
2024-05-10 |
1 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
920649 |
2151039 |
2.283333 |
0 |
|
Evolution |
Phylogenetics - Back to Basics - Building Trees |
https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo-trees/slides.html |
|
|
2024-05-10 |
2024-05-10 |
1 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
920649 |
2151039 |
2.283333 |
0 |
|
Evolution |
Phylogenetics - Back to Basics - Estimating trees from alignments |
https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo-mle-trees/slides.html |
|
|
2024-05-10 |
2024-05-10 |
1 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
920649 |
2151039 |
2.283333 |
0 |
|
Evolution |
Phylogenetics - Back to Basics - Phylogenetic Networks |
https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo-networks/slides.html |
|
|
2024-05-10 |
2024-05-10 |
1 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
920649 |
2151039 |
2.283333 |
0 |
|
FAIR Data, Workflows, and Research |
Data management in Medicinal Chemistry |
https://training.galaxyproject.org//topics/fair/tutorials/med-chem-data/tutorial.html |
|
|
2025-10-19 |
2025-10-19 |
0 |
True |
False |
True |
True |
ctb_silicos_qed, ctb_im_rxn_maker, openbabel_compound_convert, chembl, md_converter, get_pdb, openbabel_svg_depiction |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.no |
0 |
|
0 |
0 |
0.000000 |
0 |
|
FAIR Data, Workflows, and Research |
An earth-system RO-Crate |
https://training.galaxyproject.org//topics/fair/tutorials/earth_system_rocrate/slides.html |
|
|
2024-12-02 |
2024-12-02 |
1 |
False |
True |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
615064 |
1381342 |
2.083333 |
0 |
|
FAIR Data, Workflows, and Research |
FAIR and its Origins |
https://training.galaxyproject.org//topics/fair/tutorials/fair-origin/tutorial.html |
|
|
2024-03-26 |
2024-03-27 |
2 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
133 |
149 |
0.600000 |
0 |
|
FAIR Data, Workflows, and Research |
Making clinical datasets FAIR |
https://training.galaxyproject.org//topics/fair/tutorials/fair-clinical/tutorial.html |
|
|
2023-10-24 |
2024-09-13 |
5 |
True |
False |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
299 |
396 |
1.750000 |
0 |
|
FAIR Data, Workflows, and Research |
Sequence data submission to ENA |
https://training.galaxyproject.org//topics/fair/tutorials/fair-ena/tutorial.html |
|
|
2023-11-01 |
2024-06-25 |
5 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
508 |
598 |
0.933333 |
0 |
|
FAIR Data, Workflows, and Research |
FAIR in a nutshell |
https://training.galaxyproject.org//topics/fair/tutorials/fair-intro/tutorial.html |
|
|
2023-05-30 |
2024-04-30 |
6 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
819 |
1058 |
1.783333 |
0 |
|
FAIR Data, Workflows, and Research |
RO-Crate - Introduction |
https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-intro/tutorial.html |
|
|
2023-05-23 |
2025-04-08 |
5 |
True |
False |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
571 |
759 |
1.733333 |
0 |
|
FAIR Data, Workflows, and Research |
Introduction to Data Management Plan (DMP) for Peatland Research and PeatDataHub |
https://training.galaxyproject.org//topics/fair/tutorials/data-management-peatlands/tutorial.html |
|
|
2024-09-13 |
2024-09-13 |
1 |
True |
False |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
88 |
117 |
2.316667 |
0 |
|
FAIR Data, Workflows, and Research |
Workflow Run RO-Crate Introduction |
https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-workflow-run-ro-crate/tutorial.html |
|
|
2023-05-11 |
2023-05-11 |
1 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
329 |
421 |
1.433333 |
0 |
|
FAIR Data, Workflows, and Research |
DataPLANT ARCs |
https://training.galaxyproject.org//topics/fair/tutorials/dataplant-arcs/tutorial.html |
|
|
2024-10-22 |
2025-09-17 |
4 |
True |
True |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
675732 |
1525674 |
4.166667 |
0 |
|
FAIR Data, Workflows, and Research |
RO-Crate in Python |
https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-in-python/tutorial.html |
|
|
2023-05-11 |
2025-04-08 |
5 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
232 |
258 |
1.383333 |
0 |
|
FAIR Data, Workflows, and Research |
FAIR data management solutions |
https://training.galaxyproject.org//topics/fair/tutorials/data-management/tutorial.html |
|
|
2023-05-30 |
2025-01-16 |
5 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
354 |
439 |
2.766667 |
0 |
|
FAIR Data, Workflows, and Research |
Exporting Workflow Run RO-Crates from Galaxy |
https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-in-galaxy/tutorial.html |
|
|
2023-05-11 |
2024-08-26 |
8 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
262 |
319 |
2.400000 |
0 |
|
FAIR Data, Workflows, and Research |
Metadata |
https://training.galaxyproject.org//topics/fair/tutorials/fair-metadata/tutorial.html |
|
|
2024-03-26 |
2024-03-27 |
2 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
161 |
196 |
1.400000 |
0 |
|
FAIR Data, Workflows, and Research |
Data Registration |
https://training.galaxyproject.org//topics/fair/tutorials/fair-data-registration/tutorial.html |
|
|
2024-03-26 |
2024-09-27 |
3 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
69 |
73 |
1.600000 |
0 |
|
FAIR Data, Workflows, and Research |
FAIR Galaxy Training Material |
https://training.galaxyproject.org//topics/fair/tutorials/fair-gtn/tutorial.html |
|
|
2023-05-30 |
2024-03-27 |
5 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
135 |
161 |
2.383333 |
0 |
|
FAIR Data, Workflows, and Research |
Best practices for workflows in GitHub repositories |
https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-galaxy-best-practices/tutorial.html |
|
|
2023-05-11 |
2025-04-08 |
6 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
354 |
410 |
1.250000 |
0 |
|
FAIR Data, Workflows, and Research |
Submitting workflows to LifeMonitor |
https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-submitting-life-monitor/tutorial.html |
|
|
2023-05-11 |
2024-09-26 |
4 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
44 |
52 |
4.516667 |
0 |
|
FAIR Data, Workflows, and Research |
Access |
https://training.galaxyproject.org//topics/fair/tutorials/fair-access/tutorial.html |
|
|
2024-03-26 |
2024-03-27 |
2 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
54 |
63 |
2.783333 |
0 |
|
FAIR Data, Workflows, and Research |
FAIR Bioimage Metadata |
https://training.galaxyproject.org//topics/fair/tutorials/bioimage-metadata/tutorial.html |
|
|
2023-09-13 |
2024-10-15 |
4 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
269 |
322 |
2.266667 |
0 |
|
FAIR Data, Workflows, and Research |
REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data |
https://training.galaxyproject.org//topics/fair/tutorials/bioimage-REMBI/tutorial.html |
|
|
2023-09-13 |
2024-10-15 |
6 |
True |
False |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
263 |
298 |
2.283333 |
0 |
|
FAIR Data, Workflows, and Research |
Persistent Identifiers |
https://training.galaxyproject.org//topics/fair/tutorials/fair-persistent-identifiers/tutorial.html |
|
|
2024-03-26 |
2024-03-27 |
2 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
150 |
168 |
0.600000 |
0 |
|
FAIR Data, Workflows, and Research |
FAIRification of an RNAseq dataset |
https://training.galaxyproject.org//topics/fair/tutorials/fair-rna/tutorial.html |
|
|
2024-03-27 |
2024-03-27 |
1 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
231 |
285 |
1.466667 |
0 |
|
Using Galaxy and Managing your Data |
Creating, Editing and Importing Galaxy Workflows |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-editor/tutorial.html |
|
|
2020-07-17 |
2023-11-09 |
12 |
True |
False |
False |
True |
Paste1, Show beginning1, tp_tac |
Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
MISSISSIPPI |
0 |
|
5822 |
7252 |
3.000000 |
0 |
|
Using Galaxy and Managing your Data |
Workflow Reports |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-reports/tutorial.html |
|
Visualisation |
2022-06-02 |
2024-06-14 |
9 |
True |
False |
True |
True |
csv_to_tabular, Grouping1, upload1, tp_sorted_uniq, ggplot2_point, Remove beginning1, Cut1, datamash_ops |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) |
Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz |
0 |
|
844 |
1174 |
2.916667 |
0 |
|
Using Galaxy and Managing your Data |
InterMine integration with Galaxy |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/intermine/tutorial.html |
|
|
2020-12-09 |
2024-02-29 |
9 |
True |
False |
False |
True |
galaxy_intermine_exchange, intermine |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au |
|
0 |
|
176 |
233 |
3.133333 |
0 |
|
Using Galaxy and Managing your Data |
Using Workflow Parameters |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-parameters/tutorial.html |
|
|
2019-06-27 |
2024-06-14 |
15 |
True |
False |
True |
True |
tp_head_tool |
Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
MISSISSIPPI |
0 |
|
1940 |
2481 |
2.316667 |
0 |
|
Using Galaxy and Managing your Data |
Getting data into Galaxy |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/get-data/slides.html |
|
|
2017-05-24 |
2022-10-18 |
4 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2844954 |
7529738 |
2.450000 |
0 |
|
Using Galaxy and Managing your Data |
Galaxy workflows in Dockstore |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/galaxy-on-dockstore/slides.html |
|
|
2022-01-14 |
2022-10-27 |
4 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2297076 |
5693758 |
2.383333 |
0 |
|
Using Galaxy and Managing your Data |
Name tags for following complex histories |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/name-tags/tutorial.html |
|
|
2019-04-08 |
2023-11-09 |
8 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
1598 |
2147 |
2.750000 |
0 |
|
Using Galaxy and Managing your Data |
RStudio in Galaxy |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/rstudio/tutorial.html |
|
|
2019-10-08 |
2025-07-04 |
15 |
True |
False |
False |
False |
interactive_tool_rstudio |
UseGalaxy.eu, UseGalaxy.org.au |
|
0 |
|
5018 |
7805 |
2.166667 |
0 |
|
Using Galaxy and Managing your Data |
Rule Based Uploader: Advanced |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.html |
|
|
2018-05-25 |
2024-06-14 |
11 |
True |
False |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
765 |
1024 |
4.800000 |
0 |
|
Using Galaxy and Managing your Data |
Onedata user-owned storage |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/onedata-byos/tutorial.html |
|
|
2025-03-24 |
2025-04-08 |
3 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
69 |
83 |
4.966667 |
0 |
|
Using Galaxy and Managing your Data |
Group tags for complex experimental designs |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/group-tags/tutorial.html |
|
|
2019-03-06 |
2023-11-09 |
11 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2703 |
3660 |
3.300000 |
0 |
|
Using Galaxy and Managing your Data |
Creating high resolution images of Galaxy Workflows |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-posters/tutorial.html |
|
|
2024-02-05 |
2025-04-08 |
3 |
True |
False |
False |
False |
graphicsmagick_image_convert |
UseGalaxy.eu |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no |
0 |
|
254 |
308 |
2.550000 |
0 |
|
Using Galaxy and Managing your Data |
Importing (uploading) data from Onedata |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/onedata-remote-import/tutorial.html |
|
|
2025-03-24 |
2025-04-08 |
2 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
153 |
176 |
2.616667 |
0 |
|
Using Galaxy and Managing your Data |
Searching Your History |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/search/tutorial.html |
|
|
2020-07-15 |
2023-11-16 |
4 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
400 |
606 |
2.300000 |
0 |
|
Using Galaxy and Managing your Data |
Extracting Workflows from Histories |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history-to-workflow/tutorial.html |
|
|
2017-10-18 |
2024-12-02 |
8 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2968 |
3835 |
3.583333 |
0 |
|
Using Galaxy and Managing your Data |
Getting started with Onedata distributed storage |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/onedata-getting-started/tutorial.html |
|
|
2025-03-24 |
2025-04-08 |
2 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
114 |
155 |
4.166667 |
0 |
|
Using Galaxy and Managing your Data |
Rule Based Uploader |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules/tutorial.html |
|
|
2020-07-04 |
2024-06-14 |
11 |
True |
False |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
4446 |
5883 |
3.116667 |
0 |
|
Using Galaxy and Managing your Data |
Exporting to Onedata remote |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/onedata-remote-export/tutorial.html |
|
|
2025-03-24 |
2025-04-08 |
2 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
30 |
32 |
0.016667 |
0 |
|
Using Galaxy and Managing your Data |
JupyterLab in Galaxy |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/jupyterlab/tutorial.html |
|
|
2020-03-05 |
2025-04-25 |
9 |
True |
False |
False |
False |
interactive_tool_jupyter_notebook |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
2092 |
3360 |
2.816667 |
0 |
|
Using Galaxy and Managing your Data |
Downloading and Deleting Data in Galaxy |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/download-delete-data/tutorial.html |
|
|
2019-10-17 |
2023-11-09 |
6 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
7324 |
9729 |
1.633333 |
0 |
|
Using Galaxy and Managing your Data |
Using dataset collections |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/collections/tutorial.html |
|
Read mapping, Sequence alignment, Generation, Genome indexing |
2016-09-30 |
2024-12-05 |
20 |
True |
False |
True |
False |
bwa_mem, snpSift_extractFields, lofreq_call, collapse_dataset |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
15621 |
21415 |
3.000000 |
0 |
|
Using Galaxy and Managing your Data |
Use Jupyter notebooks in Galaxy |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/galaxy-intro-jupyter/tutorial.html |
|
|
2018-07-02 |
2025-05-11 |
10 |
True |
False |
True |
False |
interactive_tool_jupyter_notebook |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
2347 |
3114 |
2.433333 |
0 |
|
Using Galaxy and Managing your Data |
Annotate, prepare tests and publish Galaxy workflows in workflow registries |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-fairification/tutorial.html |
|
Validation, Read mapping, Visualisation, Sequencing quality control |
2025-05-26 |
2025-05-26 |
1 |
True |
False |
False |
False |
falco, multiqc |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
173 |
206 |
1.733333 |
0 |
|
Using Galaxy and Managing your Data |
Understanding Galaxy history system |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history/tutorial.html |
|
|
2017-02-20 |
2025-04-28 |
12 |
True |
False |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
5445 |
7021 |
2.833333 |
0 |
|
Genome Annotation |
Genome annotation with Prokka |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html |
Genomics, Microbiology, Gene and protein families, Sequence analysis |
Genome annotation, Gene prediction, Coding region prediction, Genome visualisation |
2018-03-06 |
2025-03-19 |
26 |
True |
True |
True |
True |
prokka, jbrowse |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) |
Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
2863372 |
7560948 |
4.366667 |
0 |
|
Genome Annotation |
From small to large-scale genome comparison |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.html |
|
Multiple sequence alignment |
2021-02-08 |
2024-07-31 |
8 |
True |
True |
False |
True |
tp_awk_tool, gecko, chromeister, clustalw |
UseGalaxy.eu, UseGalaxy.org.au |
GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz |
0 |
|
2800247 |
7369288 |
4.633333 |
0 |
|
Genome Annotation |
Comparison of two annotation tools - Helixer and Braker3 |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/comparison-braker-helixer-annotation/tutorial.html |
Sequence assembly, Genomics |
Sequence annotation, Genome visualisation, Genome annotation, Gene prediction, Sequence alignment, Differential protein expression profiling, Sequence assembly validation |
2025-06-20 |
2025-06-25 |
2 |
True |
False |
False |
True |
gffread, jbrowse, busco, rna_star, omark, braker3, helixer |
|
|
0 |
|
266 |
324 |
2.000000 |
0 |
|
Genome Annotation |
Secondary metabolite discovery |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html |
|
Gene prediction, Service invocation, Sequence clustering, Data handling, Differential gene expression analysis |
2024-02-21 |
2024-09-27 |
2 |
True |
False |
False |
True |
ctb_silicos_qed, ncbi_acc_download, edu.tamu.cpt.gff3.customGbkToGff, openbabel_remDuplicates, ctb_simsearch, tp_awk_tool, ctb_np-likeness-calculator, interactive_tool_jupyter_notebook, antismash, Remove beginning1, bp_genbank2gff3, collapse_dataset, ctb_chemfp_mol2fps |
UseGalaxy.eu |
|
0 |
|
618 |
783 |
1.316667 |
0 |
|
Genome Annotation |
Refining Genome Annotations with Apollo (prokaryotes) |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html |
Genomics, Microbiology, Gene and protein families, Sequence analysis |
Genome visualisation |
2021-06-04 |
2025-05-15 |
22 |
True |
True |
True |
True |
create_or_update, jbrowse, iframe, create_account, list_organism |
|
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no |
0 |
|
2619764 |
6752999 |
5.116667 |
0 |
|
Genome Annotation |
Genome annotation with Braker3 |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/braker3/tutorial.html |
Sequence assembly, Genomics, Biodiversity, Zoology, Plant biology |
Genome annotation, Gene prediction, Sequence alignment, Differential protein expression profiling, Sequence annotation, Genome visualisation, Sequence assembly validation |
2025-03-17 |
2025-06-20 |
4 |
True |
False |
False |
True |
gffread, jbrowse, busco, rna_star, fasta-stats, omark, braker3 |
|
|
0 |
|
1167 |
1453 |
2.033333 |
0 |
|
Genome Annotation |
Masking repeats with RepeatMasker |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/repeatmasker/tutorial.html |
Sequence composition, complexity and repeats, Genomics |
Genome annotation, Mapping, RNA-Seq analysis, Repeat sequence detection, Editing |
2021-11-29 |
2025-06-03 |
22 |
True |
False |
True |
True |
bedtools_maskfastabed, red, repeatmodeler, repeatmasker_wrapper |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
9830 |
12553 |
1.383333 |
0 |
|
Genome Annotation |
Identification of AMR genes in an assembled bacterial genome |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html |
Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial resistance |
Antimicrobial resistance prediction, Read mapping, Genome annotation, Genome visualisation |
2024-01-23 |
2025-06-10 |
9 |
True |
False |
True |
True |
jbrowse, upload1, tbl2gff3, staramr_search, Grep1, bakta, bowtie2 |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr |
Galaxy@AuBi, UseGalaxy.org (Main) |
0 |
|
3221 |
4425 |
2.950000 |
0 |
|
Genome Annotation |
Bacterial Genome Annotation |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html |
Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements |
Sequence motif recognition, Genome assembly, Genome visualisation, Protein feature detection, Genome annotation, Nucleic acid feature detection, Multilocus sequence typing, Scaffolding, Structural variation detection |
2024-02-01 |
2024-10-15 |
6 |
True |
False |
True |
True |
Grouping1, jbrowse, upload1, tp_replace_in_column, isescan, tp_tail_tool, tbl2gff3, bakta, integron_finder, plasmidfinder |
UseGalaxy.eu, UseGalaxy.fr |
Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main) |
0 |
|
5939 |
7985 |
2.550000 |
0 |
|
Genome Annotation |
Genome annotation with Helixer |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/helixer/tutorial.html |
Biodiversity, Genomics, Zoology, Plant biology |
Genome annotation, Gene prediction, Differential protein expression profiling, Sequence annotation, Genome visualisation, Sequence assembly validation |
2024-08-21 |
2025-06-04 |
8 |
True |
False |
False |
True |
gffread, jbrowse, busco, jcvi_gff_stats, omark, helixer |
|
|
0 |
|
1111 |
1331 |
1.666667 |
0 |
|
Genome Annotation |
Introduction to Genome Annotation |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/introduction/slides.html |
|
|
2019-05-13 |
2025-04-23 |
5 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2844954 |
7529740 |
2.450000 |
0 |
|
Genome Annotation |
Creating an Official Gene Set |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/official-gene-set/tutorial.html |
|
|
2023-11-02 |
2024-02-29 |
2 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
39 |
45 |
1.683333 |
0 |
|
Genome Annotation |
Bacterial pangenomics |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-pangenomics/tutorial.html |
Genomics, Microbiology |
Essential dynamics, Rarefaction, Genome annotation, Sequence assembly |
2025-03-14 |
2025-03-14 |
1 |
True |
False |
False |
False |
ppanggolin_msa, ppanggolin_all, upload1 |
UseGalaxy.eu, UseGalaxy.fr |
|
0 |
|
78 |
91 |
1.116667 |
0 |
|
Genome Annotation |
Bacterial genome quality control |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html |
Genomics, Microbiology |
Statistical calculation, Sequence composition calculation, Genome comparison, Validation, Sequencing quality control, Sequence assembly validation |
2025-03-14 |
2025-03-14 |
1 |
True |
False |
False |
False |
drep_dereplicate, checkm2, upload1 |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
|
0 |
|
67 |
74 |
2.916667 |
0 |
|
Genome Annotation |
Dataset construction for bacterial comparative genomics |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html |
Genomics, Microbiology |
Sequence database search, Data retrieval, Data handling |
2025-03-14 |
2025-03-14 |
1 |
True |
False |
False |
False |
upload1, Remove beginning1, bg_uniq, cat1, Cut1, datasets_download_genome, sort1 |
UseGalaxy.fr |
UseGalaxy.cz |
0 |
|
67 |
80 |
3.366667 |
0 |
|
Genome Annotation |
Genome Annotation |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/genome-annotation/tutorial.html |
|
|
2015-06-29 |
2025-06-10 |
19 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
34887 |
63639 |
1.450000 |
0 |
|
Genome Annotation |
Comparative gene analysis in unannotated genomes |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html |
Genomics, Gene and protein families, Sequence analysis, Phylogeny, Comparative genomics |
De-novo assembly, Database search, Coding region prediction, Sequence alignment analysis, Transcriptome assembly, Phylogenetic tree generation, Multiple sequence alignment |
2022-09-08 |
2025-06-03 |
10 |
True |
False |
False |
True |
join1, bg_diamond, tp_split_on_column, collapse_dataset, tab2fasta, Filter1, Add_a_column1, regexColumn1, rapidnj, cat1, Cut1, orfipy, gops_intersect_1, rbc_mafft, bg_diamond_makedb, bg_diamond_view |
UseGalaxy.eu, UseGalaxy.org (Main) |
UseGalaxy.cz |
0 |
|
1792 |
2538 |
3.100000 |
0 |
|
Genome Annotation |
Genome annotation with Funannotate |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/funannotate/tutorial.html |
Gene and protein families |
Sequence motif recognition, Information extraction, Sequence annotation, Genome visualisation, Protein feature detection, Genome annotation, Formatting, Homology-based gene prediction, Sequence alignment, Fold recognition, Query and retrieval, Sequence assembly validation |
2021-11-29 |
2025-06-10 |
26 |
True |
False |
True |
True |
aegean_parseval, interproscan, eggnog_mapper, busco, funannotate_compare, jbrowse, funannotate_predict, rna_star, picard_MergeSamFiles, funannotate_annotate |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
10413 |
14798 |
1.966667 |
0 |
|
Genome Annotation |
Genome annotation with Maker (short) |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html |
|
Genome annotation, Sequence annotation, Genome visualisation, Sequence assembly validation |
2021-01-12 |
2024-02-29 |
3 |
True |
False |
False |
True |
gffread, maker, jbrowse, busco, maker_map_ids, jcvi_gff_stats, fasta-stats |
|
UseGalaxy.be |
0 |
|
3878 |
5471 |
2.983333 |
0 |
|
Genome Annotation |
Essential genes detection with Transposon insertion sequencing |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html |
Genomics, Microbiology, Sequence analysis, Mobile genetic elements |
Transposon prediction, Sequence trimming, Primer removal, Read pre-processing |
2019-07-02 |
2024-03-18 |
12 |
True |
True |
False |
True |
cutadapt, tp_easyjoin_tool, gff_to_prot, bowtie_wrapper, Filter1, Add_a_column1, transit_gumbel, Cut1, tp_sort_header_tool, deeptools_bam_coverage, bg_find_subsequences, __EXTRACT_DATASET__ |
UseGalaxy.no, UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.eu |
0 |
|
2852966 |
7544276 |
4.200000 |
0 |
|
Genome Annotation |
Genome annotation with Maker |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html |
|
Sequence annotation, Genome visualisation, Genome annotation, Gene prediction, Homology-based gene prediction, Ab-initio gene prediction, Operation, Sequence assembly validation |
2018-09-24 |
2024-02-29 |
14 |
True |
False |
False |
True |
gffread, maker, jbrowse, busco, maker_map_ids, jcvi_gff_stats, snap_training, fasta-stats, augustus_training |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
13652 |
24222 |
1.866667 |
0 |
|
Genome Annotation |
Functional annotation of protein sequences |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/functional/tutorial.html |
Function analysis, Protein sites, features and motifs |
Sequence motif recognition, Genome annotation, Homology-based gene prediction, Sequence alignment analysis, Information extraction, Fold recognition, Query and retrieval, Protein feature detection |
2022-07-20 |
2025-06-03 |
12 |
True |
False |
False |
True |
interproscan, ncbi_blastp_wrapper, eggnog_mapper, bg_diamond |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.no |
0 |
|
4033 |
5440 |
1.683333 |
0 |
|
Genome Annotation |
Refining Genome Annotations with Apollo (eukaryotes) |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo-euk/tutorial.html |
Genomics |
Genome visualisation |
2022-08-22 |
2025-06-03 |
16 |
True |
False |
False |
False |
iframe, create_or_update, jbrowse |
UseGalaxy.no |
UseGalaxy.cz, UseGalaxy.eu |
0 |
|
1404 |
2162 |
2.450000 |
0 |
|
Genome Annotation |
Long non-coding RNAs (lncRNAs) annotation with FEELnc |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/lncrna/tutorial.html |
|
Annotation, Transcriptome assembly, RNA-Seq analysis, Sequence annotation, Classification |
2022-09-23 |
2024-09-18 |
11 |
True |
False |
True |
True |
gffread, Extract_features1, stringtie, feelnc, tp_cat |
|
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
1847 |
2475 |
2.166667 |
0 |
|
Genome Annotation |
CRISPR screen analysis |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/crispr-screen/tutorial.html |
|
Statistical calculation, Sequence trimming, Primer removal, Genetic variation analysis, Sequencing quality control, Sequence composition calculation, Read pre-processing, Validation |
2021-10-15 |
2024-08-08 |
12 |
True |
True |
True |
True |
mageck_test, multiqc, cutadapt, tp_awk_tool, fastqc, mageck_count, volcanoplot, mageck_mle |
UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no |
0 |
|
2452680 |
6164845 |
4.316667 |
0 |
|
Variant Analysis |
Microbial Variant Calling |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html |
Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation |
Genome visualisation, Phylogenetic tree generation, Phylogenetic tree visualisation, Variant calling |
2018-02-26 |
2025-03-19 |
24 |
True |
False |
False |
True |
snippy, jbrowse |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) |
GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
14933 |
23903 |
2.033333 |
0 |
|
Visualisation |
Genomic Data Visualisation with JBrowse |
https://training.galaxyproject.org//topics/visualisation/tutorials/jbrowse/tutorial.html |
|
Genome visualisation |
2020-01-10 |
2024-10-15 |
17 |
True |
True |
False |
False |
jbrowse |
Galaxy@AuBi, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz |
0 |
|
2850261 |
7536539 |
4.783333 |
0 |
|
Imaging |
Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy |
https://training.galaxyproject.org//topics/imaging/tutorials/omero-suite/tutorial.html |
|
Image analysis |
2024-12-04 |
2025-04-08 |
3 |
True |
False |
False |
False |
omero_get_id, omero_metadata_import, omero_roi_import, omero_get_value, omero_filter, omero_import |
|
|
0 |
|
163 |
210 |
3.283333 |
0 |
|
Imaging |
Training Custom YOLO Models for Segmentation of Bioimages |
https://training.galaxyproject.org//topics/imaging/tutorials/yolo-segmentation-training/tutorial.html |
|
Image annotation, Visualisation, Image analysis, Data handling |
2025-07-25 |
2025-10-14 |
4 |
True |
False |
False |
True |
graphicsmagick_image_convert, interactive_tool_anylabeling, json2yolosegment, yolo_training, unzip, ip_histogram_equalization |
UseGalaxy.eu |
|
0 |
|
178 |
231 |
1.083333 |
0 |
|
Imaging |
Introduction to Image Analysis using Galaxy |
https://training.galaxyproject.org//topics/imaging/tutorials/imaging-introduction/tutorial.html |
|
Image annotation, Image analysis, Data handling, Visualisation |
2019-08-13 |
2025-03-20 |
14 |
True |
False |
False |
True |
ip_binary_to_labelimage, ip_threshold, ip_filter_standard, ip_imageinfo, ip_count_objects, unzip, ip_overlay_images, ip_histogram_equalization |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au |
|
0 |
|
2610 |
3658 |
1.766667 |
0 |
|
Imaging |
Using BioImage.IO models for image analysis in Galaxy |
https://training.galaxyproject.org//topics/imaging/tutorials/process-image-bioimageio/tutorial.html |
|
Image annotation, Image analysis, Data handling, Visualisation |
2025-04-09 |
2025-04-16 |
5 |
True |
False |
False |
True |
bioimage_inference, ip_binary_to_labelimage, ip_threshold, image_math, ip_overlay_images, ip_split_image, __EXTRACT_DATASET__ |
UseGalaxy.eu |
|
0 |
|
157 |
188 |
3.600000 |
0 |
|
Imaging |
Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines |
https://training.galaxyproject.org//topics/imaging/tutorials/2D-spot-detection/tutorial.html |
|
Image annotation, Image analysis, Data handling, Visualisation |
2025-03-20 |
2025-03-20 |
2 |
True |
False |
False |
True |
ip_spot_detection_2d, ip_binary_to_labelimage, idr_download_by_ids, ip_points_to_label, unzip, ip_overlay_images, ip_histogram_equalization |
UseGalaxy.cz, UseGalaxy.eu |
|
0 |
|
144 |
183 |
1.583333 |
0 |
|
Imaging |
Voronoi segmentation |
https://training.galaxyproject.org//topics/imaging/tutorials/voronoi-segmentation/tutorial.html |
|
Image annotation, Image analysis, Data handling, Visualisation |
2025-05-13 |
2025-07-11 |
4 |
True |
False |
False |
True |
colorize_labels, ip_count_objects, ip_binary_to_labelimage, voronoi_tessellation, ip_2d_feature_extraction, ip_threshold, ip_filter_standard, ip_imageinfo, ip_convertimage, unzip, ip_overlay_images, image_math, repeat_channels |
UseGalaxy.eu |
|
0 |
|
231 |
367 |
4.250000 |
0 |
|
Imaging |
Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy |
https://training.galaxyproject.org//topics/imaging/tutorials/parameter-tuning/tutorial.html |
|
Image annotation, Image analysis, Data handling, Visualisation |
2025-04-28 |
2025-04-28 |
1 |
True |
False |
False |
True |
ip_segmetrics, tp_split_on_column, param_value_from_file, collapse_dataset, ip_threshold, ip_filter_standard, ip_histogram_equalization |
UseGalaxy.eu |
UseGalaxy.cz |
0 |
|
66 |
78 |
2.616667 |
0 |
|
Imaging |
Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools |
https://training.galaxyproject.org//topics/imaging/tutorials/electrophoresis-gel-bands-image-analysis/tutorial.html |
|
Image annotation, Image analysis, Data handling, Visualisation |
2025-08-11 |
2025-08-11 |
1 |
True |
False |
False |
True |
graphicsmagick_image_convert, ip_2d_feature_extraction, ip_points_to_label, ip_imageinfo, ip_split_image, interactive_tool_qupath, __EXTRACT_DATASET__ |
UseGalaxy.eu |
|
0 |
|
155 |
191 |
1.466667 |
0 |
|
Imaging |
Analyse HeLa fluorescence siRNA screen |
https://training.galaxyproject.org//topics/imaging/tutorials/hela-screen-analysis/tutorial.html |
|
Image annotation, Image analysis, Data handling, Visualisation |
2019-08-13 |
2024-11-07 |
12 |
True |
False |
False |
True |
ip_2d_filter_segmentation_by_features, ip_binary_to_labelimage, ip_2d_feature_extraction, collapse_dataset, ip_threshold, ip_filter_standard, unzip |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.no |
0 |
|
755 |
974 |
2.216667 |
0 |
|
Imaging |
End-to-End Tissue Microarray Image Analysis with Galaxy-ME |
https://training.galaxyproject.org//topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html |
|
|
2023-02-14 |
2025-03-14 |
6 |
True |
False |
False |
True |
scanpy_compute_graph, vitessce_spatial, squidpy_spatial, unet_coreograph, mesmer, gate_finder, basic_illumination, scimap_mcmicro_to_anndata, palom, scimap_phenotyping, ashlar, ip_convertimage, rename_tiff_channels, celesta, quantification |
|
|
0 |
|
1343 |
1825 |
1.900000 |
0 |
|
Imaging |
Object tracking using CellProfiler |
https://training.galaxyproject.org//topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html |
|
Image analysis, Quantification, Parsing |
2021-03-17 |
2024-10-15 |
8 |
True |
False |
False |
True |
cp_export_to_spreadsheet, cp_measure_object_intensity, cp_track_objects, unzip, cp_measure_object_size_shape, cp_color_to_gray, cp_common, cp_overlay_outlines, cp_cellprofiler, cp_identify_primary_objects, cp_tile, cp_save_images |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
2128 |
2660 |
1.066667 |
0 |
|
Imaging |
Nucleoli segmentation and feature extraction using CellProfiler |
https://training.galaxyproject.org//topics/imaging/tutorials/tutorial-CP/tutorial.html |
|
Image analysis, Quantification, Parsing |
2020-07-01 |
2024-10-15 |
9 |
True |
True |
False |
True |
cp_measure_object_intensity, cp_gray_to_color, cp_display_data_on_image, cp_enhance_or_suppress_features, idr_download_by_ids, cp_identify_primary_objects, cp_save_images, cp_measure_image_intensity, cp_cellprofiler, cp_measure_granularity, cp_measure_texture, cp_export_to_spreadsheet, cp_convert_objects_to_image, cp_measure_object_size_shape, cp_common, cp_measure_image_area_occupied, cp_mask_image, cp_relate_objects, cp_image_math, cp_measure_image_quality |
UseGalaxy.be, UseGalaxy.eu |
Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
2849125 |
7535552 |
3.683333 |
0 |
|
Imaging |
Tracking of mitochondria and capturing mitoflashes |
https://training.galaxyproject.org//topics/imaging/tutorials/detection-of-mitoflashes/tutorial.html |
|
Image analysis |
2024-11-20 |
2024-11-20 |
2 |
True |
False |
False |
True |
ip_points_association_nn, ip_curve_fitting, ip_spot_detection_2d |
UseGalaxy.cz, UseGalaxy.eu |
|
0 |
|
137 |
161 |
0.900000 |
0 |
|
Imaging |
FAIR Bioimage Metadata |
https://training.galaxyproject.org//topics/imaging/tutorials/bioimage-metadata/tutorial.html |
|
|
2025-10-19 |
2025-10-19 |
0 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
0 |
0 |
0.000000 |
0 |
|
Imaging |
REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data |
https://training.galaxyproject.org//topics/imaging/tutorials/bioimage-REMBI/tutorial.html |
|
|
2025-10-19 |
2025-10-19 |
0 |
True |
False |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
0 |
0 |
0.000000 |
0 |
|
Introduction to Galaxy Analyses |
From peaks to genes |
https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html |
|
|
2016-03-29 |
2025-10-04 |
65 |
True |
False |
False |
True |
CONVERTER_interval_to_bed_0, get_flanks1, Grouping1, upload1, tp_replace_in_column, tp_tail_tool, Add_a_column1, Cut1, tp_sort_header_tool, gops_intersect_1 |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.no |
0 |
|
20244 |
33346 |
3.316667 |
0 |
|
Introduction to Galaxy Analyses |
How to reproduce published Galaxy analyses |
https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-reproduce/tutorial.html |
|
Visualisation |
2021-08-25 |
2024-10-15 |
12 |
True |
False |
False |
True |
csv_to_tabular, Grouping1, upload1, tp_sorted_uniq, ggplot2_point, Remove beginning1, Cut1, datamash_ops |
Galaxy@AuBi, UseGalaxy.eu, UseGalaxy.org (Main) |
MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
2156 |
2883 |
4.116667 |
0 |
|
Introduction to Galaxy Analyses |
Data Manipulation Olympics |
https://training.galaxyproject.org//topics/introduction/tutorials/data-manipulation-olympics/tutorial.html |
|
|
2022-07-20 |
2025-05-16 |
15 |
True |
False |
False |
True |
Grouping1, {{version_join}}, tp_sorted_uniq, {{version_count}}, {{version_select_first}}, {{version_cut_advanced}}, {{version_cat}}, Add_a_column1, {{version_sort}}, Count1, {{version_remove_beginning}}, {{version_split}}, tp_cat, {{version_unique}}, join1, {{version_wc}}, {{version_replace_text_line}}, Remove beginning1, tp_sort_header_tool, regexColumn1, {{version_remove_columns_by_header}}, wc_gnu, {{version_paste}}, datamash_ops, tp_split_on_column, upload1, {{version_datamash}}, {{version_replace_text_column}}, Filter1, tabular_to_csv, Show beginning1, Cut1, cat1, {{version_cut_columns}}, {{version_filter}}, {{version_compute}} |
|
|
0 |
|
5825 |
8494 |
3.450000 |
0 |
|
Introduction to Galaxy Analyses |
NGS data logistics |
https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html |
|
Generation, Data handling, Genome indexing, Validation, Sequencing quality control, Formatting, Sequence alignment, SNP detection, Read mapping, Sequence contamination filtering |
2017-02-22 |
2025-07-24 |
38 |
True |
False |
True |
True |
picard_MarkDuplicates, bwa_mem, bwa_mem2, snpEff, multiqc, snpEff_build_gb, lofreq_call, lofreq_indelqual, snpeff_sars_cov_2, samtools_view, Filter1, fasterq_dump, collapse_dataset, snpSift_extractFields, fastp, lofreq_viterbi, bwa, samtools_stats |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
MISSISSIPPI, UseGalaxy.cz |
0 |
|
19674 |
33660 |
3.400000 |
0 |
|
Introduction to Galaxy Analyses |
Introduction to Genomics and Galaxy |
https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-strands/tutorial.html |
|
|
2017-10-18 |
2024-10-15 |
41 |
True |
False |
True |
True |
gene2exon1, Filter1, cat1, gops_intersect_1, tp_cat |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
MISSISSIPPI |
0 |
|
19825 |
31386 |
3.566667 |
0 |
|
Introduction to Galaxy Analyses |
Options for using Galaxy |
https://training.galaxyproject.org//topics/introduction/tutorials/options-for-using-galaxy/slides.html |
|
|
2017-05-24 |
2022-09-23 |
14 |
False |
True |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2845375 |
7530050 |
2.450000 |
0 |
|
Introduction to Galaxy Analyses |
Introduction to Galaxy |
https://training.galaxyproject.org//topics/introduction/tutorials/introduction/slides.html |
|
|
2016-09-30 |
2025-09-23 |
6 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2845375 |
7530050 |
2.450000 |
0 |
|
Introduction to Galaxy Analyses |
Upload data to Galaxy |
https://training.galaxyproject.org//topics/introduction/tutorials/dummy/tutorial.html |
|
|
2022-09-23 |
2023-11-09 |
5 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
427 |
488 |
2.750000 |
0 |
|
Introduction to Galaxy Analyses |
IGV Introduction |
https://training.galaxyproject.org//topics/introduction/tutorials/igv-introduction/tutorial.html |
|
|
2016-03-30 |
2023-02-17 |
11 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
7970 |
11274 |
1.483333 |
0 |
|
Introduction to Galaxy Analyses |
A short introduction to Galaxy |
https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-short/tutorial.html |
|
Sequence composition calculation, Statistical calculation, Sequencing quality control |
2018-08-27 |
2025-09-23 |
43 |
True |
True |
True |
True |
cshl_fastq_quality_filter, fastqc |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) |
Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
2897722 |
7611515 |
7.050000 |
0 |
|
Introduction to Galaxy Analyses |
Galaxy Basics for everyone |
https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html |
|
Visualisation |
2019-11-14 |
2024-12-02 |
34 |
True |
False |
True |
True |
csv_to_tabular, Grouping1, upload1, tp_sorted_uniq, ggplot2_point, Remove beginning1, Cut1, datamash_ops |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) |
Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz |
0 |
|
22174 |
35199 |
3.983333 |
0 |
|
Introduction to Galaxy Analyses |
Galaxy Basics for genomics |
https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-101/tutorial.html |
|
Mapping |
2016-12-19 |
2025-04-22 |
68 |
True |
False |
True |
True |
bedtools_intersectbed, upload1, tp_head_tool, tp_sort_header_tool, datamash_ops, comp1 |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.no |
0 |
|
46700 |
75543 |
3.433333 |
0 |
|
Introduction to Galaxy Analyses |
Very Short Introductions: QC |
https://training.galaxyproject.org//topics/introduction/tutorials/vsi_qc/tutorial.html |
|
Validation, Sequence contamination filtering, Sequencing quality control |
2024-03-26 |
2024-06-25 |
4 |
True |
False |
False |
False |
fastp, multiqc |
Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
MISSISSIPPI, UseGalaxy.no |
0 |
|
294 |
357 |
3.166667 |
0 |
|
Materials Science |
Finding the muon stopping site with pymuon-suite in Galaxy |
https://training.galaxyproject.org//topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.html |
|
|
2024-01-22 |
2024-06-14 |
2 |
True |
False |
True |
True |
pm_muairss_read, pm_uep_opt |
UseGalaxy.cz, UseGalaxy.eu |
|
0 |
|
241 |
321 |
2.166667 |
0 |
|
Metabolomics |
Mass spectrometry imaging: Examining the spatial distribution of analytes |
https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html |
|
|
2019-02-21 |
2024-10-15 |
18 |
True |
False |
False |
True |
cardinal_mz_images, cardinal_quality_report, Filter1, cardinal_filtering, cardinal_data_exporter, cardinal_spectra_plots |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
2971 |
4231 |
1.783333 |
0 |
|
Metabolomics |
Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) |
https://training.galaxyproject.org//topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html |
|
Chromatographic alignment, Chromatogram visualisation, Filtering, Format validation, Spectral library search, Mass spectrum visualisation, Formatting, Label-free quantification, Clustering, Peak detection, Validation, Imputation, Standardisation and normalisation, Data filtering, Correlation |
2023-05-08 |
2023-11-09 |
5 |
True |
False |
False |
True |
msconvert, riassigner, abims_xcms_retcor, waveica, matchms_formatter, abims_xcms_xcmsSet, abims_xcms_group, msnbase_readmsdata, ramclustr_define_experiment, matchms_filtering, ramclustr, matchms_similarity, xcms_merge, abims_xcms_fillPeaks |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au |
0 |
|
2594 |
3351 |
1.533333 |
0 |
|
Metabolomics |
Mass spectrometry imaging: Finding differential analytes |
https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html |
|
|
2019-04-13 |
2023-11-09 |
9 |
True |
False |
False |
True |
Summary_Statistics1, cardinal_mz_images, cardinal_preprocessing, cardinal_segmentations, join_files_on_column_fuzzy, cardinal_quality_report, maldi_quant_peak_detection, cardinal_classification, Filter1, cardinal_combine, maldi_quant_preprocessing, Grep1 |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
1957 |
2810 |
1.850000 |
0 |
|
Metabolomics |
Molecular formula assignment and mass recalibration with MFAssignR package |
https://training.galaxyproject.org//topics/metabolomics/tutorials/mfassignr/tutorial.html |
|
Visualisation |
2025-05-19 |
2025-05-19 |
1 |
True |
False |
False |
True |
mfassignr_isofiltr, mfassignr_findRecalSeries, mfassignr_recal, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_snplot, mfassignr_histnoise, mfassignr_kmdnoise, mfassignr_recallist |
|
|
0 |
|
81 |
99 |
2.500000 |
0 |
|
Metabolomics |
Mass spectrometry: LC-MS analysis |
https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms/tutorial.html |
|
Chromatogram visualisation, Chromatographic alignment, Mass spectrum visualisation, Data filtering, Label-free quantification, Peak detection, Validation |
2019-07-02 |
2025-09-21 |
13 |
True |
False |
False |
True |
xcms_export_samplemetadata, Univariate, abims_xcms_retcor, generic_filter, abims_xcms_xcmsSet, abims_xcms_group, msnbase_readmsdata, xcms_plot_chromatogram, Batch_correction, wsdl_hmdb, quality_metrics, abims_CAMERA_annotateDiffreport, xcms_merge, abims_xcms_fillPeaks |
|
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
12586 |
20605 |
1.600000 |
0 |
|
Metabolomics |
Predicting EI+ mass spectra with QCxMS |
https://training.galaxyproject.org//topics/metabolomics/tutorials/qcxms-predictions/tutorial.html |
|
|
2024-10-01 |
2024-10-01 |
1 |
True |
True |
False |
True |
tp_cut_tool, qcxms_getres, openbabel_compound_convert, param_value_from_file, qcxms_neutral_run, split_file_to_collection, xtb_molecular_optimization, __FILTER_FAILED_DATASETS__, ctb_im_conformers, tp_cat, qcxms_production_run |
UseGalaxy.eu |
UseGalaxy.org.au |
0 |
|
713662 |
1641087 |
3.166667 |
0 |
|
Metabolomics |
Mass spectrometry: LC-MS preprocessing with XCMS |
https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html |
|
Chromatogram visualisation, Chromatographic alignment, Mass spectrum visualisation, Data filtering, Label-free quantification, Peak detection, Validation |
2020-02-04 |
2024-10-15 |
14 |
True |
True |
False |
False |
xcms_export_samplemetadata, abims_xcms_retcor, intens_check, abims_xcms_xcmsSet, abims_xcms_group, msnbase_readmsdata, xcms_plot_chromatogram, idchoice, abims_xcms_summary, abims_CAMERA_annotateDiffreport, xcms_merge, abims_xcms_fillPeaks |
UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no |
0 |
|
2851391 |
7539529 |
4.750000 |
0 |
|
Metabolomics |
Introduction to Metabolomics |
https://training.galaxyproject.org//topics/metabolomics/tutorials/introduction/slides.html |
|
|
2018-11-20 |
2023-01-12 |
1 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2845375 |
7530055 |
2.450000 |
0 |
|
Metabolomics |
Mass spectrometry: GC-MS analysis with the metaMS package |
https://training.galaxyproject.org//topics/metabolomics/tutorials/gcms/tutorial.html |
|
Chromatogram visualisation, Chromatographic alignment, Mass spectrum visualisation, Data filtering, Label-free quantification, Peak detection, Validation |
2021-09-22 |
2025-10-01 |
8 |
True |
False |
False |
False |
xcms_export_samplemetadata, abims_xcms_xcmsSet, abims_xcms_group, msnbase_readmsdata, xcms_plot_chromatogram, metams_runGC, xcms_merge, abims_xcms_fillPeaks |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.no |
0 |
|
1485 |
2399 |
1.666667 |
0 |
|
Metabolomics |
Mass spectrometry: LC-MS data processing |
https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html |
|
|
2021-12-14 |
2024-10-15 |
8 |
True |
False |
False |
False |
Multivariate, generic_filter, normalization, intens_check, Batch_correction, quality_metrics |
UseGalaxy.fr |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no |
0 |
|
2752 |
3727 |
1.966667 |
0 |
|
Microbiome |
Introduction to Microbiome Analysis |
https://training.galaxyproject.org//topics/microbiome/tutorials/introduction/slides.html |
|
|
2017-06-22 |
2024-08-08 |
5 |
False |
True |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2845375 |
7530055 |
2.450000 |
0 |
|
Microbiome |
Analyses of metagenomics data - The global picture |
https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html |
Metagenomics, Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding |
Phylogenetic analysis, DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Sequence clustering, Visualisation |
2017-06-22 |
2024-08-09 |
4 |
True |
False |
False |
True |
mothur_screen_seqs, mothur_make_group, mothur_classify_otu, metaphlan2, mothur_unique_seqs, mothur_summary_seqs, mothur_count_seqs, metaphlan2krona, mothur_merge_files, mothur_align_seqs, humann2_renorm_table, humann2, mothur_make_shared, krona-text, mothur_pre_cluster, mothur_make_biom, mothur_classify_seqs, humann2_regroup_table, taxonomy_krona_chart, mothur_cluster_split, mothur_filter_seqs |
|
UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
7951 |
10780 |
2.716667 |
0 |
|
Microbiome |
Metatranscriptomics analysis using microbiome RNA-seq data (short) |
https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html |
Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis |
Statistical calculation, Phylogenetic tree editing, Sequence alignment analysis, Phylogenetic analysis, Phylogenetic tree visualisation, Primer removal, Sequence trimming, Sequencing quality control, Taxonomic classification, Conversion, Sequence composition calculation, Read pre-processing, Validation, Visualisation, Species frequency estimation, Sequence similarity search, Sequence comparison, Phylogenetic inference |
2020-02-13 |
2025-06-16 |
6 |
True |
False |
True |
True |
metaphlan, bg_sortmerna, humann_unpack_pathways, tp_find_and_replace, fastq_paired_end_interlacer, humann_rename_table, multiqc, graphlan_annotate, tp_sort_header_tool, humann_renorm_table, humann_regroup_table, humann, combine_metaphlan2_humann2, Grep1, humann_split_stratified_table, graphlan, cutadapt, fastqc, taxonomy_krona_chart, Cut1, export2graphlan |
UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.no |
0 |
|
691 |
881 |
2.300000 |
0 |
|
Microbiome |
Building an amplicon sequence variant (ASV) table from 16S data using DADA2 |
https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html |
Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding |
Analysis, Visualisation, Deposition, DNA barcoding, Variant calling |
2024-06-05 |
2025-07-03 |
11 |
True |
False |
True |
True |
dada2_makeSequenceTable, Grouping1, tp_replace_in_line, dada2_filterAndTrim, Add_a_column1, tp_replace_in_column, phyloseq_from_dada2, __SORTLIST__, dada2_plotQualityProfile, interactive_tool_phyloseq, dada2_dada, dada2_removeBimeraDenovo, dada2_learnErrors, dada2_assignTaxonomyAddspecies, __UNZIP_COLLECTION__, dada2_mergePairs, collection_element_identifiers, tp_head_tool, dada2_seqCounts, cat1 |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
6280 |
8875 |
2.383333 |
0 |
|
Microbiome |
Taxonomic Profiling and Visualization of Metagenomic Data |
https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html |
Metagenomics, Microbial ecology, Taxonomy, Sequence analysis |
Statistical calculation, Genome annotation, Aggregation, Visualisation, Taxonomic classification |
2023-05-03 |
2025-04-24 |
6 |
True |
False |
True |
True |
interactive_tool_pavian, metaphlan, interactive_tool_phinch, krakentools_kreport2krona, taxonomy_krona_chart, kraken2, est_abundance, __UNZIP_COLLECTION__, kraken_biom |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
11417 |
15283 |
2.016667 |
0 |
|
Microbiome |
16S Microbial analysis with Nanopore data |
https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html |
Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding |
Statistical calculation, Sequence contamination filtering, Sequence composition calculation, Validation, Visualisation, Sequencing quality control, Taxonomic classification |
2020-11-24 |
2024-07-31 |
5 |
True |
False |
False |
True |
multiqc, fastqc, tp_replace_in_line, porechop, datamash_reverse, Remove beginning1, taxonomy_krona_chart, kraken2, fastp |
UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr |
0 |
|
7623 |
10518 |
2.600000 |
0 |
|
Microbiome |
Clinical Metaproteomics 1: Database-Generation |
https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-1-database-generation/tutorial.html |
|
Tag-based peptide identification, Protein identification, Expression analysis, de Novo sequencing, Target-Decoy |
2025-10-19 |
2025-10-19 |
0 |
True |
False |
True |
True |
metanovo, dbbuilder, uniprotxml_downloader, fasta_merge_files_and_filter_unique_sequences |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.org (Main) |
0 |
|
0 |
0 |
0.000000 |
0 |
|
Microbiome |
MGnify v5.0 Amplicon Pipeline |
https://training.galaxyproject.org//topics/microbiome/tutorials/mgnify-amplicon/tutorial.html |
Metagenomics, Taxonomy, Sequence analysis |
Comparison, Alignment, Formatting, Validation, Visualisation, Nucleic acid design, Read pre-processing, Sequence feature detection, Statistical calculation, Analysis, k-mer counting, Mapping, Sequence trimming, DNA barcoding, Sequencing quality control, Nucleic acid feature detection, Sequence composition calculation, Sequence contamination filtering |
2025-07-30 |
2025-07-30 |
2 |
True |
False |
False |
True |
bedtools_maskfastabed, cmsearch_deoverlap, Grouping1, param_value_from_file, collapse_dataset, Add_a_column1, tp_find_and_replace, ampvis2_heatmap, trimmomatic, multiqc, bedtools_getfastabed, infernal_cmsearch, biom_convert, query_tabular, gops_concat_1, filter_tabular, ampvis2_load, prinseq, tp_awk_tool, seqprep, __FILTER_FROM_FILE__, fastq_filter, mapseq, wc_gnu, fastq_dl, __UNZIP_COLLECTION__, __MERGE_COLLECTION__, mgnify_seqprep, collection_element_identifiers, cshl_fasta_formatter, fastqc, CONVERTER_gz_to_uncompressed, taxonomy_krona_chart, CONVERTER_uncompressed_to_gz, lotus2, fastp, collection_column_join, __FILTER_EMPTY_DATASETS__, fastq_to_fasta_python |
|
|
0 |
|
102 |
124 |
3.116667 |
0 |
|
Microbiome |
Clinical Metaproteomics 4: Quantitation |
https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-4-quantitation/tutorial.html |
|
Statistical calculation, Visualisation, Heat map generation, Standardisation and normalisation, Clustering, Protein quantification, Principal component plotting, Imputation |
2025-10-19 |
2025-10-19 |
0 |
True |
False |
True |
True |
Grep1, maxquant, Cut1, Grouping1 |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
0 |
0 |
0.000000 |
0 |
|
Microbiome |
Clinical Metaproteomics 3: Verification |
https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html |
|
|
2025-10-19 |
2025-10-19 |
0 |
True |
False |
True |
True |
dbbuilder, Grouping1, uniprotxml_downloader, query_tabular, Remove beginning1, collapse_dataset, Filter1, Cut1, fasta_merge_files_and_filter_unique_sequences, pepquery2, tp_cat |
UseGalaxy.cz, UseGalaxy.eu |
UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
0 |
0 |
0.000000 |
0 |
|
Microbiome |
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition |
https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html |
Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis |
Genome assembly, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Sequence assembly visualisation, Box-Whisker plot plotting, Data handling, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation, Variant calling, Taxonomic classification, Scatter plot plotting, Aggregation, Phylogenetic tree reconstruction, Validation, Visualisation, De-novo assembly, Mapping assembly, Sequence assembly, Statistical calculation, Mapping, Sequence alignment analysis, Antimicrobial resistance prediction, Sequencing quality control, Multiple sequence alignment, Base-calling, Phylogenetic tree analysis, Multilocus sequence typing, Sequence composition calculation, Cross-assembly, Pairwise sequence alignment, Sequence contamination filtering |
2023-01-26 |
2024-09-27 |
11 |
True |
False |
True |
True |
Grouping1, tp_sorted_uniq, param_value_from_file, porechop, snpSift_filter, tp_multijoin_tool, collapse_dataset, tab2fasta, Add_a_column1, split_file_to_collection, snpSift_extractFields, tp_find_and_replace, fasta_merge_files_and_filter_unique_sequences, flye, __FILTER_FAILED_DATASETS__, Count1, tp_cut_tool, barchart_gnuplot, bcftools_norm, medaka_consensus_pipeline, multiqc, bedtools_getfastabed, tp_replace_in_column, bamtools_split_mapped, table_compute, abricate, Remove beginning1, kraken2, minimap2, nanoplot, samtools_coverage, samtools_fastx, fasttree, compose_text_param, bcftools_consensus, regex1, krakentools_kreport2krona, regexColumn1, clair3, Grep1, Paste1, __BUILD_LIST__, clustalw, newick_display, __FILTER_EMPTY_DATASETS__, krakentools_extract_kraken_reads, mlst, tp_split_on_column, collection_element_identifiers, fastqc, tp_head_tool, CONVERTER_gz_to_uncompressed, samtools_depth, taxonomy_krona_chart, ggplot2_heatmap, fastp, Cut1, collection_column_join, bandage_image, add_line_to_file, fasta2tab |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
4630 |
6981 |
3.416667 |
0 |
|
Microbiome |
Metatranscriptomics analysis using microbiome RNA-seq data |
https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html |
Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis |
Phylogenetic tree editing, Taxonomic classification, Aggregation, Validation, Visualisation, Read pre-processing, Statistical calculation, Phylogenetic tree visualisation, Sequence alignment analysis, Phylogenetic analysis, Primer removal, Sequence trimming, Sequencing quality control, Conversion, Sequence composition calculation, Species frequency estimation, Sequence similarity search, Sequence comparison, Phylogenetic inference |
2019-11-21 |
2025-06-16 |
6 |
True |
True |
True |
True |
metaphlan, Grouping1, bg_sortmerna, humann_unpack_pathways, tp_find_and_replace, fastq_paired_end_interlacer, humann_rename_table, multiqc, graphlan_annotate, tp_sort_header_tool, humann_renorm_table, humann_regroup_table, humann, combine_metaphlan_humann, Grep1, humann_split_stratified_table, graphlan, cutadapt, fastqc, taxonomy_krona_chart, Cut1, export2graphlan |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.eu |
0 |
|
2851586 |
7538037 |
4.316667 |
0 |
|
Microbiome |
Calculating α and β diversity from microbiome taxonomic data |
https://training.galaxyproject.org//topics/microbiome/tutorials/diversity/tutorial.html |
|
Visualisation, Aggregation |
2024-08-01 |
2025-06-17 |
7 |
True |
False |
True |
True |
krakentools_alpha_diversity, krakentools_beta_diversity |
Galaxy@Pasteur, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi |
0 |
|
6010 |
7237 |
1.250000 |
0 |
|
Microbiome |
Assembly of metagenomic sequencing data |
https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html |
Metagenomics, Sequence assembly |
Genome assembly, Sequence assembly visualisation, Data handling, Variant calling, Local alignment, Formatting, Read mapping, Visualisation, Sequence file editing, Read pre-processing, Statistical calculation, Sequence alignment analysis, Sequence trimming, Primer removal, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering, Sequence assembly validation |
2022-12-05 |
2025-06-16 |
6 |
True |
False |
True |
True |
coverm_contig, filter_tabular, random_lines1, cutadapt, fastqc, megahit_contig2fastg, ngsutils_bam_filter, megahit, bg_uniq, bandage_info, collection_column_join, seqtk_subseq, bandage_image, metaspades, bowtie2, quast, bamtools, tp_cat |
|
UseGalaxy.cz, UseGalaxy.eu |
0 |
|
4120 |
5765 |
3.033333 |
0 |
|
Microbiome |
Identification of the micro-organisms in a beer using Nanopore sequencing |
https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html |
Metagenomics, Microbial ecology, Taxonomy, Sequence analysis |
Statistical calculation, Sequence contamination filtering, Aggregation, Sequence composition calculation, Visualisation, Sequencing quality control, Taxonomic classification |
2022-09-29 |
2024-11-29 |
5 |
True |
False |
True |
True |
fastqc, porechop, krakentools_kreport2krona, Filter1, taxonomy_krona_chart, kraken2, fastp |
GalaxyTrakr, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
2502 |
3630 |
2.833333 |
0 |
|
Microbiome |
Antibiotic resistance detection |
https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html |
Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial resistance |
Genome assembly, Sequence assembly visualisation, Box-Whisker plot plotting, Antimicrobial resistance prediction, Sequence analysis, De-novo assembly, Scatter plot plotting, Aggregation, Pairwise sequence alignment, Mapping assembly |
2019-06-25 |
2024-06-14 |
4 |
True |
False |
True |
True |
unicycler, miniasm, racon, nanoplot, minimap2, staramr_search, bandage_image, gfa_to_fa, PlasFlow |
UseGalaxy.eu |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
3096 |
4347 |
2.950000 |
0 |
|
Microbiome |
Clinical Metaproteomics 2: Discovery |
https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html |
|
Statistical calculation, Heat map generation, Standardisation and normalisation, Filtering, Imputation, Formatting, Clustering, Protein quantification, Principal component plotting, Visualisation |
2025-10-19 |
2025-10-19 |
0 |
True |
False |
True |
True |
dbbuilder, msconvert, filter_tabular, Grouping1, fasta_cli, query_tabular, Remove beginning1, maxquant, Filter1, peptide_shaker, search_gui, Cut1, fasta_merge_files_and_filter_unique_sequences, Grep1, ident_params, fasta2tab, tp_cat |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
0 |
0 |
0.000000 |
0 |
|
Microbiome |
Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data |
https://training.galaxyproject.org//topics/microbiome/tutorials/metaplasmidome_query/tutorial.html |
Genomics, Microbiology, Sequence analysis, Mobile genetic elements |
Visualisation, Pairwise sequence alignment |
2025-01-07 |
2025-01-07 |
1 |
True |
False |
False |
True |
join1, CONVERTER_fasta_to_tabular, ggplot2_histogram, Grouping1, tp_replace_in_column, tp_sorted_uniq, tp_tail_tool, count_gff_features, histogram_rpy, tab2fasta, Filter1, Add_a_column1, minimap2, cat1, Cut1, add_column_headers, sort1, MQoutputfilter |
UseGalaxy.fr |
|
0 |
|
271 |
311 |
0.916667 |
0 |
|
Microbiome |
Clinical Metaproteomics 5: Data Interpretation |
https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-5-data-interpretation/tutorial.html |
|
Visualisation, Prediction and recognition |
2025-10-19 |
2025-10-19 |
0 |
True |
False |
True |
True |
Grep1, msstatstmt, unipept |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
0 |
0 |
0.000000 |
0 |
|
Microbiome |
Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2 |
https://training.galaxyproject.org//topics/microbiome/tutorials/lotus2-identifying-fungi/tutorial.html |
|
DNA barcoding, Sequence feature detection |
2024-09-30 |
2024-09-30 |
2 |
True |
False |
False |
True |
lotus2 |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au |
|
0 |
|
622 |
785 |
1.600000 |
0 |
|
Microbiome |
QIIME 2 Moving Pictures |
https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html |
Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding |
|
2024-03-14 |
2024-03-14 |
1 |
external |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
520 |
812 |
2.916667 |
0 |
|
Microbiome |
Binning of metagenomic sequencing data |
https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html |
Metagenomics, Sequence assembly |
Statistical calculation, Genome assembly, Sequence composition calculation, Validation, Sequencing quality control, Sequence assembly validation |
2023-12-05 |
2025-05-15 |
6 |
True |
False |
True |
False |
checkm_lineage_wf, megahit |
GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr |
UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
5215 |
6400 |
1.533333 |
0 |
|
Microbiome |
Indexing and profiling microbes with MetaSBT |
https://training.galaxyproject.org//topics/microbiome/tutorials/metasbt/tutorial.html |
Microbial ecology, Taxonomy |
|
2025-08-25 |
2025-08-25 |
7 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
26 |
32 |
4.183333 |
0 |
|
Microbiome |
QIIME 2 Cancer Microbiome Intervention |
https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html |
Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding |
|
2024-02-12 |
2024-03-14 |
3 |
external |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
380 |
611 |
3.233333 |
0 |
|
Microbiome |
16S Microbial Analysis with mothur (short) |
https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html |
Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding |
Phylogenetic analysis, DNA barcoding, Phylogenetic tree generation, Sequencing quality control, Sequence read processing, Taxonomic classification, Sequence clustering, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Visualisation |
2019-05-13 |
2024-06-14 |
5 |
True |
False |
True |
True |
mothur_screen_seqs, mothur_remove_lineage, mothur_classify_otu, collapse_dataset, mothur_unique_seqs, mothur_sub_sample, mothur_heatmap_sim, mothur_summary_seqs, mothur_count_seqs, mothur_venn, mothur_rarefaction_single, mothur_cluster, mothur_chimera_vsearch, mothur_make_shared, mothur_remove_groups, mothur_tree_shared, mothur_dist_shared, mothur_summary_single, mothur_count_groups, newick_display, mothur_remove_seqs, mothur_pre_cluster, mothur_classify_seqs, mothur_dist_seqs, mothur_cluster_split, XY_Plot_1, mothur_filter_seqs |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr |
0 |
|
4951 |
8234 |
4.600000 |
0 |
|
Microbiome |
16S Microbial Analysis with mothur (extended) |
https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html |
Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding |
Phylogenetic analysis, DNA barcoding, Phylogenetic tree generation, Sequencing quality control, Sequence read processing, Taxonomic classification, Sequence clustering, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Visualisation |
2017-02-12 |
2024-03-14 |
4 |
True |
False |
False |
True |
mothur_screen_seqs, mothur_remove_lineage, mothur_taxonomy_to_krona, mothur_get_groups, mothur_classify_otu, mothur_unique_seqs, mothur_make_contigs, mothur_sub_sample, mothur_heatmap_sim, mothur_summary_seqs, mothur_count_seqs, mothur_venn, mothur_rarefaction_single, mothur_cluster, mothur_align_seqs, mothur_seq_error, mothur_chimera_vsearch, mothur_make_shared, mothur_remove_groups, mothur_tree_shared, mothur_dist_shared, mothur_summary_single, mothur_count_groups, newick_display, mothur_remove_seqs, mothur_pre_cluster, mothur_make_biom, mothur_classify_seqs, mothur_dist_seqs, taxonomy_krona_chart, mothur_cluster_split, XY_Plot_1, mothur_filter_seqs |
UseGalaxy.be, UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
11419 |
16756 |
2.766667 |
0 |
|
Variant Analysis |
Pox virus genome analysis from tiled-amplicon sequencing data |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html |
|
Generation, Sequence alignment analysis, Genome indexing, Primer removal, Sequence analysis, Sequencing quality control, Multiple sequence alignment, Local alignment, Sequence alignment, Global alignment, Read mapping, Sequence contamination filtering |
2023-05-15 |
2024-03-20 |
4 |
True |
False |
False |
True |
ivar_consensus, param_value_from_file, Add_a_column1, __ZIP_COLLECTION__, qualimap_bamqc, EMBOSS: maskseq51, samtools_view, mimodd_info, fatovcf, __APPLY_RULES__, bwa_mem, compose_text_param, fasta_regex_finder, samtools_merge, Grep1, ivar_trim, datamash_ops, upload1, rbc_mafft, fastp, Cut1, fasta_compute_length |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.org (Main) |
0 |
|
990 |
1178 |
2.400000 |
0 |
|
Variant Analysis |
M. tuberculosis Variant Analysis |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html |
Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease |
Statistical calculation, Phylogenetic tree visualisation, Sequence alignment analysis, Antimicrobial resistance prediction, Phylogenetic tree generation, Sequencing quality control, Taxonomic classification, Variant calling, Sequence analysis, Genome visualisation, Local alignment, Sequence alignment, Global alignment, Sequence composition calculation, Validation, Sequence contamination filtering |
2020-07-25 |
2024-07-26 |
30 |
True |
False |
True |
True |
tb_variant_filter, tp_sed_tool, mosdepth, samtools_stats, qualimap_bamqc, multiqc, kraken2, jvarkit_wgscoverageplotter, snippy, bcftools_consensus, EMBOSS:%20seqret84, tp_awk_tool, EMBOSS: seqret84, tbvcfreport, jbrowse, upload1, fastqc, tb_profiler_profile, fastp, __FLATTEN__ |
|
|
0 |
|
7388 |
11435 |
3.016667 |
0 |
|
Variant Analysis |
Avian influenza viral strain analysis from gene segment sequencing data |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/aiv-analysis/tutorial.html |
|
Generation, Data retrieval, Phylogenetic analysis, Genome indexing, Primer removal, Sequence alignment analysis, Data handling, Sequence file editing, Sequence analysis, Sequencing quality control, Multiple sequence alignment, Sequence alignment, Read mapping, De-novo assembly, Sequence contamination filtering |
2022-11-21 |
2024-10-04 |
10 |
True |
False |
False |
False |
qualimap_bamqc, bwa_mem, ivar_consensus, iqtree, upload1, __RELABEL_FROM_FILE__, vapor, samtools_view, bamtools_split_ref, collapse_dataset, rbc_mafft, Show beginning1, tp_find_and_replace, fastp, Grep1, seqtk_subseq |
UseGalaxy.eu, UseGalaxy.org (Main) |
UseGalaxy.cz |
0 |
|
1937 |
2727 |
2.516667 |
0 |
|
Transcriptomics |
Whole transcriptome analysis of Arabidopsis thaliana |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html |
|
Sequence trimming, Primer removal, Validation, Sequencing quality control, Differential gene expression analysis, Gene expression analysis, RNA-Seq analysis, Sequence composition calculation, Read mapping, Visualisation, RNA-Seq quantification, Read pre-processing |
2021-04-08 |
2025-08-10 |
18 |
True |
True |
True |
True |
__MERGE_COLLECTION__, multiqc, rbc_mirdeep2_mapper, sample_seqs, targetfinder, deseq2, Filter1, falco, salmon, trim_galore, cat1, Cut1, rbc_mirdeep2_quantifier, filter_by_fasta_ids, sort1 |
UseGalaxy.cz |
|
0 |
|
2705748 |
7026573 |
5.016667 |
0 |
|
Sequence analysis |
Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants |
https://training.galaxyproject.org//topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html |
|
Phylogenetic inference (from molecular sequences), Phylogenetic tree editing, Phylogenetic analysis, Sequence analysis, Multiple sequence alignment |
2025-03-26 |
2025-04-27 |
2 |
True |
False |
True |
True |
iqtree, ete_treeviewer, Remove beginning1, trimal, Filter1, quicktree, rbc_mafft, Cut1, filter_by_fasta_ids, tapscan_classify |
UseGalaxy.eu |
|
0 |
|
200 |
250 |
1.283333 |
0 |
|
Sequence analysis |
NCBI BLAST+ against the MAdLand |
https://training.galaxyproject.org//topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.html |
|
Sequence alignment analysis |
2023-01-16 |
2024-07-31 |
9 |
True |
False |
False |
False |
ncbi_blastx_wrapper, ncbi_blastp_wrapper, bg_diamond |
Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
GalaxyTrakr, UseGalaxy.no |
0 |
|
1570 |
1985 |
2.933333 |
0 |
|
Single Cell |
Analysis of plant scRNA-Seq Data with Scanpy |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-plant/tutorial.html |
|
Principal component visualisation, Differential gene expression analysis, Expression profile clustering |
2021-04-08 |
2025-02-13 |
7 |
True |
False |
True |
True |
scanpy_cluster_reduce_dimension, anndata_manipulate, scanpy_remove_confounders, anndata_import, scanpy_inspect, scanpy_plot, scanpy_normalize, scanpy_filter |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
2646 |
3312 |
1.533333 |
0 |
|
Proteomics |
Statistical analysis of DIA data |
https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.html |
|
Differential protein expression profiling, Tag-based peptide identification, Spectrum calculation |
2020-12-02 |
2023-11-09 |
9 |
True |
False |
False |
True |
Grep1, Filter1, histogram_rpy, msstats |
UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
1308 |
1840 |
2.650000 |
0 |
|
Proteomics |
Annotating a protein list identified by LC-MS/MS experiments |
https://training.galaxyproject.org//topics/proteomics/tutorials/proteome_annotation/tutorial.html |
|
|
2019-09-12 |
2024-06-14 |
11 |
True |
False |
True |
True |
IDconverter, retrieve_from_hpa, Jvenn, reactome_analysis, cluter_profiler, rna_abbased_data, MQoutputfilter |
|
UseGalaxy.be, UseGalaxy.fr |
0 |
|
3041 |
4425 |
2.783333 |
0 |
|
Proteomics |
Library Generation for DIA Analysis |
https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html |
|
Statistical calculation, Visualisation, Heat map generation, Standardisation and normalisation, Clustering, Protein quantification, Principal component plotting, Imputation |
2020-12-02 |
2025-06-02 |
12 |
True |
False |
False |
True |
OpenSwathDecoyGenerator, diapysef, maxquant, Filter1, OpenSwathAssayGenerator, TargetedFileConverter |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
4501 |
5876 |
1.366667 |
0 |
|
Proteomics |
Detection and quantitation of N-termini (degradomics) via N-TAILS |
https://training.galaxyproject.org//topics/proteomics/tutorials/ntails/tutorial.html |
Proteomics |
|
2017-02-14 |
2025-04-08 |
16 |
True |
False |
False |
True |
FileFilter, HighResPrecursorMassCorrector, PeptideIndexer, FileMerger, ConsensusID, IDMapper, IDMerger, MSGFPlusAdapter, IDFilter, FeatureFinderMultiplex, MzTabExporter, IDConflictResolver, FalseDiscoveryRate |
|
|
0 |
|
835 |
1156 |
1.433333 |
0 |
|
Proteomics |
Mass spectrometry imaging: Loading and exploring MSI data |
https://training.galaxyproject.org//topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.html |
Proteomics |
|
2018-11-27 |
2025-04-08 |
18 |
True |
False |
False |
True |
Grep1, cardinal_quality_report, cardinal_data_exporter, tp_sort_header_tool |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
2689 |
4173 |
1.683333 |
0 |
|
Proteomics |
Label-free data analysis using MaxQuant |
https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-label-free/tutorial.html |
|
Statistical calculation, Visualisation, Tag-based peptide identification, Heat map generation, Differential protein expression profiling, Standardisation and normalisation, Spectrum calculation, Clustering, Protein quantification, Principal component plotting, Imputation |
2020-04-29 |
2025-05-21 |
14 |
True |
False |
False |
True |
histogram_rpy, maxquant, Filter1, Add_a_column1, Cut1, tp_sort_header_tool, Grep1, msstats |
UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
19700 |
28781 |
1.766667 |
0 |
|
Proteomics |
metaQuantome 3: Taxonomy |
https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html |
Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy |
Functional clustering, Heat map generation, Filtering, Indexing, Principal component visualisation, Visualisation, Statistical inference, Differential protein expression analysis, Quantification, Query and retrieval |
2020-10-29 |
2024-03-15 |
14 |
True |
False |
False |
True |
metaquantome_sample, metaquantome_expand, metaquantome_stat, metaquantome_db, metaquantome_viz, metaquantome_filter |
UseGalaxy.be, UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
438 |
576 |
2.366667 |
0 |
|
Proteomics |
metaQuantome 1: Data creation |
https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html |
Proteomics, Proteogenomics, Biodiversity, Taxonomy |
Formatting, Label-free quantification, Visualisation, Filtering, Prediction and recognition |
2020-10-16 |
2024-03-14 |
20 |
True |
False |
False |
True |
msconvert, tp_replace_in_column, tp_replace_in_line, regex1, query_tabular, Remove beginning1, Filter1, peptide_shaker, unipept, flashlfq, Cut1, search_gui, Grep1 |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
879 |
1492 |
3.800000 |
0 |
|
Proteomics |
Biomarker candidate identification |
https://training.galaxyproject.org//topics/proteomics/tutorials/biomarker_selection/tutorial.html |
|
|
2019-06-13 |
2023-11-09 |
9 |
True |
False |
False |
True |
tp_cut_tool, IDconverter, retrieve_from_hpa, retr_pepatlas1, prot_features, Jvenn, rna_abbased_data, MQoutputfilter |
|
UseGalaxy.be, UseGalaxy.fr |
0 |
|
1621 |
2203 |
2.533333 |
0 |
|
Proteomics |
Neoantigen 1a: Fusion-Database-Generation |
https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-fusion-database-generation/tutorial.html |
|
Sequence alignment |
2025-01-14 |
2025-07-02 |
1 |
True |
False |
False |
True |
arriba, arriba_get_filters, tp_awk_tool, regex1, rna_star, CONVERTER_gz_to_uncompressed, query_tabular, tab2fasta |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
107 |
134 |
1.016667 |
0 |
|
Proteomics |
Peptide and Protein ID using OpenMS tools |
https://training.galaxyproject.org//topics/proteomics/tutorials/protein-id-oms/tutorial.html |
|
Formatting, Filtering |
2017-10-16 |
2025-04-08 |
32 |
True |
False |
False |
True |
msconvert, XTandemAdapter, PeakPickerHiRes, PeptideIndexer, TextExporter, FidoAdapter, ConsensusID, IDMerger, MSGFPlusAdapter, IDFilter, IDScoreSwitcher, Grep1, FalseDiscoveryRate, IDPosteriorErrorProbability, FileInfo |
|
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
3376 |
5669 |
2.933333 |
0 |
|
Proteomics |
metaQuantome 2: Function |
https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html |
Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics |
Functional clustering, Heat map generation, Filtering, Indexing, Principal component visualisation, Visualisation, Statistical inference, Differential protein expression analysis, Quantification, Query and retrieval |
2020-10-29 |
2024-03-15 |
14 |
True |
False |
False |
True |
metaquantome_sample, metaquantome_expand, metaquantome_stat, metaquantome_db, metaquantome_viz, metaquantome_filter |
UseGalaxy.eu |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
408 |
579 |
4.233333 |
0 |
|
Proteomics |
Peptide and Protein ID using SearchGUI and PeptideShaker |
https://training.galaxyproject.org//topics/proteomics/tutorials/protein-id-sg-ps/tutorial.html |
|
|
2017-06-12 |
2025-04-08 |
28 |
True |
False |
False |
True |
PeakPickerHiRes, FileConverter, peptide_shaker, search_gui, Grep1 |
|
|
0 |
|
3028 |
4887 |
1.900000 |
0 |
|
Proteomics |
Proteogenomics 1: Database Creation |
https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html |
|
Statistical calculation, Sequence alignment, Transcriptome assembly, RNA-Seq analysis, Sequence annotation, Variant calling |
2018-11-20 |
2025-05-08 |
29 |
True |
False |
True |
True |
custom_pro_db, bed_to_protein_map, cat_multi_datasets, hisat2, tp_replace_in_column, translate_bed, stringtie, query_tabular, tab2fasta, regexColumn1, gffcompare, sqlite_to_tabular, fasta_merge_files_and_filter_unique_sequences, filter_tabular, freebayes, gffcompare_to_bed, fasta2tab |
UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
5755 |
9458 |
2.633333 |
0 |
|
Proteomics |
Peptide Library Data Analysis |
https://training.galaxyproject.org//topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.html |
|
|
2021-01-22 |
2023-11-09 |
5 |
True |
False |
False |
True |
pdaug_fishers_plot, pdaug_peptide_data_access, pdaug_peptide_sequence_analysis, pdaug_addclasslabel, pdaug_sequence_property_based_descriptors, pdaug_tsvtofasta, pdaug_merge_dataframes, pdaug_basic_plots |
UseGalaxy.be |
|
0 |
|
715 |
977 |
2.433333 |
0 |
|
Proteomics |
Clinical Metaproteomics 1: Database-Generation |
https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.html |
|
Tag-based peptide identification, Protein identification, Expression analysis, de Novo sequencing, Target-Decoy |
2024-02-06 |
2025-07-30 |
7 |
True |
False |
True |
True |
metanovo, dbbuilder, uniprotxml_downloader, fasta_merge_files_and_filter_unique_sequences |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.org (Main) |
0 |
|
553 |
848 |
4.483333 |
0 |
|
Proteomics |
Peptide and Protein Quantification via Stable Isotope Labelling (SIL) |
https://training.galaxyproject.org//topics/proteomics/tutorials/protein-quant-sil/tutorial.html |
|
|
2017-03-17 |
2025-04-08 |
32 |
True |
False |
False |
True |
Summary_Statistics1, XTandemAdapter, PeptideIndexer, histogram_rpy, TextExporter, tp_tail_tool, IDScoreSwitcher, MultiplexResolver, FidoAdapter, IDMapper, ProteinQuantifier, FeatureFinderMultiplex, Grep1, IDConflictResolver, FalseDiscoveryRate, IDPosteriorErrorProbability, FileInfo |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
1333 |
1872 |
1.583333 |
0 |
|
Proteomics |
Neoantigen 5a: Predicting HLA Binding |
https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-predicting-hla-binding/tutorial.html |
|
Genetic variation analysis, Read mapping |
2025-01-14 |
2025-07-02 |
1 |
True |
False |
False |
True |
optitype, tp_awk_tool, query_tabular, seq2hla |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
44 |
49 |
0.050000 |
0 |
|
Proteomics |
Proteogenomics 3: Novel peptide analysis |
https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.html |
|
|
2018-11-20 |
2025-05-15 |
20 |
True |
False |
True |
True |
pep_pointer, peptide_genomic_coordinate, ncbi_blastp_wrapper, query_tabular |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no |
0 |
|
1604 |
2292 |
2.700000 |
0 |
|
Proteomics |
Clinical Metaproteomics 4: Quantitation |
https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.html |
|
Statistical calculation, Visualisation, Heat map generation, Standardisation and normalisation, Clustering, Protein quantification, Principal component plotting, Imputation |
2024-02-06 |
2025-08-10 |
5 |
True |
False |
True |
True |
Grep1, maxquant, Cut1, Grouping1 |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
173 |
239 |
3.666667 |
0 |
|
Proteomics |
Clinical Metaproteomics 3: Verification |
https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html |
|
|
2024-02-06 |
2025-08-10 |
7 |
True |
False |
True |
True |
dbbuilder, Grouping1, uniprotxml_downloader, query_tabular, Remove beginning1, collapse_dataset, Filter1, Cut1, fasta_merge_files_and_filter_unique_sequences, pepquery2, tp_cat |
UseGalaxy.cz, UseGalaxy.eu |
UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
186 |
252 |
5.416667 |
0 |
|
Proteomics |
Machine Learning Modeling of Anticancer Peptides |
https://training.galaxyproject.org//topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.html |
|
|
2021-01-22 |
2023-11-09 |
8 |
True |
False |
False |
True |
pdaug_addclasslabel, pdaug_sequence_property_based_descriptors, pdaug_merge_dataframes, pdaug_basic_plots, pdaug_ml_models |
UseGalaxy.be |
|
0 |
|
1013 |
1515 |
2.233333 |
0 |
|
Proteomics |
Protein FASTA Database Handling |
https://training.galaxyproject.org//topics/proteomics/tutorials/database-handling/tutorial.html |
Proteomics |
|
2017-02-14 |
2025-04-08 |
30 |
True |
False |
False |
True |
dbbuilder, addValue, tab2fasta, DecoyDatabase, fasta_merge_files_and_filter_unique_sequences, fasta2tab |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) |
0 |
|
4627 |
7370 |
2.133333 |
0 |
|
Proteomics |
DIA Analysis using OpenSwathWorkflow |
https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html |
|
Formatting, Filtering |
2020-12-02 |
2025-05-20 |
12 |
True |
False |
False |
True |
msconvert, pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, OpenSwathWorkflow, pyprophet_score, Grep1 |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
3014 |
4242 |
2.400000 |
0 |
|
Proteomics |
Metaproteomics tutorial |
https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html |
Proteomics, Proteogenomics, Biodiversity, Taxonomy |
Visualisation, Prediction and recognition |
2017-06-28 |
2024-06-14 |
41 |
True |
False |
True |
True |
query_tabular, sqlite_to_tabular, unipept, search_gui, peptide_shaker |
UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz |
0 |
|
2867 |
4572 |
2.716667 |
0 |
|
Proteomics |
Single Cell Proteomics data analysis with bioconductor-scp |
https://training.galaxyproject.org//topics/proteomics/tutorials/bioconductor-scp/tutorial.html |
|
Expression analysis, Visualisation |
2025-02-07 |
2025-02-10 |
2 |
True |
False |
False |
False |
bioconductor_scp, Grouping1 |
UseGalaxy.eu, UseGalaxy.org.au |
|
0 |
|
173 |
226 |
1.200000 |
0 |
|
Proteomics |
Neoantigen 2: Database merge and FragPipe discovery |
https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.html |
|
|
2025-01-14 |
2025-07-02 |
1 |
True |
False |
False |
True |
fragpipe, query_tabular, Remove beginning1, collapse_dataset, fasta_merge_files_and_filter_unique_sequences, Grep1, validate_fasta_database |
UseGalaxy.eu, UseGalaxy.org (Main) |
UseGalaxy.org.au |
0 |
|
125 |
150 |
1.500000 |
0 |
|
Proteomics |
Secretome Prediction |
https://training.galaxyproject.org//topics/proteomics/tutorials/secretome-prediction/tutorial.html |
|
|
2017-04-13 |
2025-04-08 |
15 |
True |
False |
False |
True |
term_id_vs_term_name, tp_cut_tool, wolf_psort, tp_easyjoin_tool, uniprot, tp_sorted_uniq, Filter1, get_subontology_from, bg_uniq, Grep1, Convert characters1, comp1 |
|
|
0 |
|
636 |
955 |
1.500000 |
0 |
|
Proteomics |
Neoantigen 4: Variant Annotation |
https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-variant-annotation/tutorial.html |
|
|
2025-01-14 |
2025-07-02 |
1 |
True |
False |
False |
True |
query_tabular, tab2fasta, regexColumn1, pep_pointer, Convert characters1 |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no |
0 |
|
58 |
72 |
1.683333 |
0 |
|
Proteomics |
Proteogenomics 2: Database Search |
https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html |
|
Conversion, Peptide database search |
2018-11-20 |
2025-05-08 |
24 |
True |
False |
True |
True |
query_tabular, tab2fasta, mz_to_sqlite, search_gui, ident_params, peptide_shaker |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
1514 |
2256 |
4.800000 |
0 |
|
Proteomics |
Neoantigen 3: PepQuery2 Verification |
https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-peptide-verification/tutorial.html |
|
Formatting, Filtering |
2025-01-14 |
2025-07-02 |
1 |
True |
False |
False |
True |
msconvert, ncbi_blastp_wrapper, query_tabular, tab2fasta, pepquery2 |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
46 |
54 |
2.483333 |
0 |
|
Proteomics |
MaxQuant and MSstats for the analysis of TMT data |
https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.html |
|
Statistical calculation, Visualisation, Heat map generation, Standardisation and normalisation, Clustering, Protein quantification, Principal component plotting, Imputation |
2021-08-13 |
2025-01-08 |
11 |
True |
False |
False |
True |
maxquant, msstatstmt |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.org (Main) |
0 |
|
4196 |
5618 |
1.650000 |
0 |
|
Proteomics |
Multiomics data analysis using MultiGSEA |
https://training.galaxyproject.org//topics/proteomics/tutorials/multiGSEA-tutorial/tutorial.html |
|
Pathway analysis, Gene-set enrichment analysis, Aggregation |
2025-03-10 |
2025-03-11 |
2 |
True |
False |
False |
True |
Filter1, multigsea, tp_grep_tool |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
225 |
247 |
1.833333 |
0 |
|
Proteomics |
Clinical Metaproteomics 2: Discovery |
https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html |
|
Statistical calculation, Heat map generation, Standardisation and normalisation, Filtering, Imputation, Formatting, Clustering, Protein quantification, Principal component plotting, Visualisation |
2024-02-06 |
2025-08-10 |
5 |
True |
False |
True |
True |
dbbuilder, msconvert, filter_tabular, Grouping1, fasta_cli, query_tabular, Remove beginning1, maxquant, Filter1, peptide_shaker, search_gui, Cut1, fasta_merge_files_and_filter_unique_sequences, Grep1, ident_params, fasta2tab, tp_cat |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
329 |
442 |
7.366667 |
0 |
|
Proteomics |
Neoantigen 1b: Non-Reference-Database-Generation |
https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html |
|
Statistical calculation, Sequence alignment, Transcriptome assembly, RNA-Seq analysis, Sequence annotation, Variant calling |
2025-01-14 |
2025-07-02 |
1 |
True |
False |
False |
True |
custom_pro_db, bed_to_protein_map, hisat2, translate_bed, stringtie, CONVERTER_gz_to_uncompressed, query_tabular, tab2fasta, regexColumn1, gffcompare, sqlite_to_tabular, fasta_merge_files_and_filter_unique_sequences, filter_tabular, freebayes, gffcompare_to_bed, fasta2tab, tp_cat |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no |
0 |
|
59 |
67 |
0.533333 |
0 |
|
Proteomics |
Clinical Metaproteomics 5: Data Interpretation |
https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-5-data-interpretation/tutorial.html |
|
Visualisation, Prediction and recognition |
2024-02-06 |
2025-08-10 |
4 |
True |
False |
True |
True |
Grep1, msstatstmt, unipept |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
267 |
356 |
2.900000 |
0 |
|
Proteomics |
MaxQuant and MSstats for the analysis of label-free data |
https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html |
|
Statistical calculation, Visualisation, Tag-based peptide identification, Heat map generation, Differential protein expression profiling, Standardisation and normalisation, Spectrum calculation, Clustering, Protein quantification, Principal component plotting, Imputation |
2021-02-17 |
2025-09-22 |
19 |
True |
False |
True |
True |
Summary_Statistics1, tp_easyjoin_tool, tp_replace_in_column, uniprot, maxquant, Filter1, datamash_ops, ggplot2_heatmap2, Cut1, Grep1, fasta2tab, msstats |
|
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
8401 |
13564 |
2.666667 |
0 |
|
Proteomics |
Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides |
https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-hla-binding-novel-peptides/tutorial.html |
|
|
2025-01-14 |
2025-07-02 |
1 |
True |
False |
False |
True |
table_compute, iedb_api, query_tabular, Remove beginning1, Filter1, Cut1, pepquery2 |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
36 |
38 |
1.016667 |
0 |
|
Proteomics |
EncyclopeDIA |
https://training.galaxyproject.org//topics/proteomics/tutorials/encyclopedia/tutorial.html |
|
Formatting, Filtering |
2021-06-21 |
2025-05-19 |
12 |
True |
False |
True |
True |
msconvert, encyclopedia_searchtolib, encyclopedia_quantify |
|
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
1957 |
2672 |
1.766667 |
0 |
|
Proteomics |
Introduction to proteomics, protein identification, quantification and statistical modelling |
https://training.galaxyproject.org//topics/proteomics/tutorials/introduction/slides.html |
|
|
2017-12-01 |
2024-08-08 |
3 |
False |
True |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2845375 |
7530066 |
2.450000 |
0 |
|
Proteomics |
Label-free versus Labelled - How to Choose Your Quantitation Method |
https://training.galaxyproject.org//topics/proteomics/tutorials/labelfree-vs-labelled/tutorial.html |
|
|
2017-03-17 |
2025-05-27 |
18 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
7613 |
12321 |
0.900000 |
0 |
|
Sequence analysis |
Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes |
https://training.galaxyproject.org//topics/sequence-analysis/tutorials/viral_primer_design/tutorial.html |
|
PCR primer design, Local alignment, Sequence alignment, Sequence alignment analysis, Global alignment, Sequence analysis, Multiple sequence alignment |
2025-03-20 |
2025-03-20 |
2 |
True |
False |
False |
True |
varvamp, rbc_mafft, split_file_to_collection, ncbi_makeblastdb, EMBOSS: degapseq20, fasta_compute_length |
UseGalaxy.eu |
|
0 |
|
473 |
555 |
1.083333 |
0 |
|
Sequence analysis |
Screening assembled genomes for contamination using NCBI FCS |
https://training.galaxyproject.org//topics/sequence-analysis/tutorials/ncbi-fcs/tutorial.html |
|
Sequence contamination filtering, Sequence trimming, Sequence assembly validation |
2024-04-16 |
2024-04-16 |
2 |
True |
False |
False |
True |
ncbi_fcs_gx, ncbi_fcs_adaptor |
GalaxyTrakr, UseGalaxy.org (Main) |
|
0 |
|
1735 |
2361 |
2.316667 |
0 |
|
Sequence analysis |
Mapping |
https://training.galaxyproject.org//topics/sequence-analysis/tutorials/mapping/tutorial.html |
Mapping |
Statistical calculation, Read mapping, Sequence alignment analysis, Data handling, Primer removal, Sequence trimming, Genome visualisation, Sequencing quality control, Sequence composition calculation, Validation, Read pre-processing |
2016-10-04 |
2025-03-31 |
43 |
True |
True |
True |
True |
jbrowse, multiqc, fastqc, bamFilter, trim_galore, bowtie2, samtools_stats |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
2909813 |
7638513 |
5.166667 |
0 |
|
Sequence analysis |
Quality and contamination control in bacterial isolate using Illumina MiSeq Data |
https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html |
Whole genome sequencing, Genomics, Microbiology, Microbial ecology |
Statistical calculation, Expression analysis, Sequencing quality control, Taxonomic classification, Cross-assembly, Read mapping, Visualisation, Sequence contamination filtering |
2024-07-15 |
2025-03-20 |
4 |
True |
False |
True |
True |
upload1, falco, kraken2, fastp, est_abundance, recentrifuge |
UseGalaxy.eu, UseGalaxy.fr |
UseGalaxy.cz, UseGalaxy.org (Main) |
0 |
|
1487 |
1934 |
2.850000 |
0 |
|
Sequence analysis |
Clean and manage Sanger sequences from raw files to aligned consensus |
https://training.galaxyproject.org//topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html |
|
Data handling, Phylogenetic analysis, Demultiplexing, DNA barcoding, Sequencing quality control, Taxonomic classification, Sequence read processing, Sequence clustering, Visualisation, Sequence file editing |
2024-01-08 |
2024-03-05 |
2 |
True |
False |
False |
True |
seqtk_trimfq, tab2fasta, ab1_fastq_converter, fastq_groomer, fastq_to_tabular, ncbi_blastn_wrapper, fastq_masker_by_quality, unzip, mothur_merge_files, seqtk_mergepe, filter_by_fasta_ids, __SORTLIST__, aligned_to_consensus, regex1, cshl_fastq_to_fasta, __FILTER_FROM_FILE__, qiime_align_seqs, cshl_fastx_reverse_complement, collection_element_identifiers, mothur_degap_seqs |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr |
|
0 |
|
3137 |
3947 |
1.750000 |
0 |
|
Sequence analysis |
Quality Control |
https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-control/tutorial.html |
|
Statistical calculation, Box-Whisker plot plotting, Sequence trimming, Primer removal, Sequencing quality control, Scatter plot plotting, Sequence composition calculation, Validation, Read pre-processing |
2016-10-04 |
2025-03-29 |
48 |
True |
True |
True |
True |
fastqe, multiqc, cutadapt, fastqc, pycoqc, nanoplot |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr |
0 |
|
2950164 |
7721541 |
5.483333 |
0 |
|
Single Cell |
Bulk RNA Deconvolution with MuSiC |
https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music/tutorial.html |
|
|
2022-02-11 |
2025-02-14 |
10 |
True |
False |
True |
True |
music_deconvolution, music_construct_eset, music_inspect_eset |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
3816 |
4836 |
1.616667 |
0 |
|
Single Cell |
Generating a single cell matrix using Alevin |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin/tutorial.html |
|
Sequence composition calculation, RNA-Seq quantification, Gene expression analysis |
2021-03-03 |
2025-05-07 |
24 |
True |
False |
True |
True |
join1, sceasy_convert, anndata_manipulate, alevin, dropletutils_empty_drops, dropletutils_read_10x, anndata_inspect, _ensembl_gtf2gene_list, _salmon_kallisto_mtx_to_10x, Cut1, _dropletBarcodePlot |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
3384 |
5158 |
3.516667 |
0 |
|
Single Cell |
GO Enrichment Analysis on Single-Cell RNA-Seq Data |
https://training.galaxyproject.org//topics/single-cell/tutorials/GO-enrichment/tutorial.html |
|
Gene-set enrichment analysis |
2024-09-17 |
2025-04-08 |
8 |
True |
True |
False |
True |
goenrichment, gprofiler_gost, Cut1, tp_split_on_column |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) |
|
0 |
|
738970 |
1703907 |
3.000000 |
0 |
|
Single Cell |
Pseudobulk Analysis with Decoupler and EdgeR |
https://training.galaxyproject.org//topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html |
|
Differential gene expression analysis, Principal component visualisation, Expression profile clustering |
2025-02-12 |
2025-05-09 |
8 |
True |
False |
True |
True |
column_remove_by_header, decoupler_pseudobulk, anndata_manipulate, tp_awk_tool, tp_replace_in_column, tp_replace_in_line, anndata_inspect, edger, volcanoplot, __EXTRACT_DATASET__, scanpy_filter |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
1366 |
1586 |
0.650000 |
0 |
|
Single Cell |
Pre-processing of 10X Single-Cell RNA Datasets |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html |
|
Sequence alignment, Loading, Validation, Community profiling, Sequencing quality control |
2019-09-11 |
2025-04-29 |
13 |
True |
False |
True |
True |
rna_starsolo, dropletutils, multiqc |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
12085 |
15601 |
1.866667 |
0 |
|
Single Cell |
Pre-processing of Single-Cell RNA Data |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing/tutorial.html |
|
Sequence alignment, Sequencing quality control, Sequence alignment analysis, Data handling, Read summarisation, Validation, RNA-Seq quantification |
2019-02-22 |
2025-04-08 |
5 |
True |
True |
False |
True |
umi_tools_extract, featurecounts, tp_sed_tool, multiqc, rna_star, umi_tools_count, bamFilter, collection_column_join, __FLATTEN__, samtools_stats |
UseGalaxy.eu |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
2851580 |
7538145 |
4.716667 |
0 |
|
Single Cell |
Single-cell quality control with scater |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scater-qc/tutorial.html |
|
Read pre-processing, Sequence visualisation, Sequencing quality control |
2019-10-23 |
2025-02-14 |
6 |
True |
False |
False |
True |
scater_plot_pca, scater_create_qcmetric_ready_sce, scater_plot_dist_scatter, scater_filter |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
683 |
773 |
0.750000 |
0 |
|
Single Cell |
Pre-processing of 10X Single-Cell ATAC-seq Datasets |
https://training.galaxyproject.org//topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html |
|
Statistical calculation, Generation, Visualisation, Mapping, Genome indexing, Peak calling, Enrichment analysis, Sequencing quality control, Differential gene expression analysis, Expression profile clustering, Sequence alignment, Principal component visualisation, Sequence composition calculation, Read mapping, Imputation, Gene regulatory network analysis |
2023-04-24 |
2025-10-16 |
10 |
True |
False |
False |
True |
bwa_mem, tp_sorted_uniq, fastqc, sinto_barcode, anndata_inspect, episcanpy_preprocess, scanpy_plot, episcanpy_build_matrix, falco, macs2_callpeak, sinto_fragments, bedtools_sortbed |
UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
5855 |
6903 |
1.100000 |
0 |
|
Single Cell |
Converting between common single cell data formats |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-data-ingest/tutorial.html |
|
Community profiling, Loading |
2024-02-13 |
2025-03-11 |
4 |
True |
False |
False |
True |
join1, tp_cut_tool, tabular_to_fastq, anndata_ops, sceasy_convert, monocle3_create, dropletutils, tp_tail_tool, dropletutils_read_10x, datamash_transpose, anndata_inspect, regexColumn1, Filter1, seurat_read10x, Cut1, scanpy_filter_cells, fastq_to_tabular |
|
UseGalaxy.org (Main) |
0 |
|
2375 |
2832 |
1.316667 |
0 |
|
Single Cell |
An introduction to scRNA-seq data analysis |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-intro/slides.html |
|
|
2021-01-29 |
2025-02-13 |
8 |
False |
True |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2812957 |
7416028 |
2.450000 |
0 |
|
Single Cell |
Generating a single cell matrix using Alevin and combining datasets (bash + R) |
https://training.galaxyproject.org//topics/single-cell/tutorials/alevin-commandline/tutorial.html |
|
|
2023-12-08 |
2025-04-22 |
5 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
593 |
829 |
3.800000 |
0 |
|
Single Cell |
Importing files from public atlases |
https://training.galaxyproject.org//topics/single-cell/tutorials/EBI-retrieval/tutorial.html |
|
|
2023-11-14 |
2025-03-11 |
8 |
True |
False |
True |
True |
sceasy_convert, anndata_ops, retrieve_scxa, hca_matrix_downloader, regexColumn1, scanpy_read_10x, seurat_read10x, tp_find_and_replace, tp_grep_tool |
|
|
0 |
|
536 |
709 |
3.950000 |
0 |
|
Single Cell |
Understanding Barcodes |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-umis/tutorial.html |
|
Sequence composition calculation, Statistical calculation, Sequencing quality control |
2019-02-20 |
2025-02-14 |
11 |
True |
False |
True |
True |
umi_tools_extract, fastqc, seq_filter_by_id |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, UseGalaxy.no |
0 |
|
6197 |
7721 |
1.233333 |
0 |
|
Single Cell |
Downstream Single-cell RNA analysis with RaceID |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-raceid/tutorial.html |
|
Molecular dynamics, Expression analysis, Expression profile clustering |
2019-03-25 |
2025-02-14 |
7 |
True |
False |
False |
True |
tp_sed_tool, raceid_inspecttrajectory, raceid_trajectory, tp_head_tool, datamash_transpose, raceid_clustering, raceid_filtnormconf, datamash_ops, raceid_inspectclusters |
UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
1051 |
1242 |
1.300000 |
0 |
|
Single Cell |
Clustering 3K PBMCs with Scanpy |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html |
|
Principal component visualisation, Differential gene expression analysis, Expression profile clustering |
2019-12-19 |
2025-04-29 |
16 |
True |
True |
True |
True |
scanpy_cluster_reduce_dimension, anndata_manipulate, scanpy_remove_confounders, anndata_import, scanpy_inspect, anndata_inspect, scanpy_plot, scanpy_normalize, datamash_ops, scanpy_filter |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
2853222 |
7541271 |
4.466667 |
0 |
|
Single Cell |
Filter, plot, and explore single cell RNA-seq data with Seurat (R) |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRStudio/tutorial.html |
|
|
2023-10-02 |
2025-03-11 |
11 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
3157 |
3612 |
0.966667 |
0 |
|
Single Cell |
Combining single cell datasets after pre-processing |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html |
|
|
2022-09-08 |
2025-04-22 |
22 |
True |
False |
True |
True |
anndata_ops, anndata_manipulate, tp_replace_in_column, anndata_inspect, Cut1, Paste1 |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.org (Main) |
0 |
|
2452 |
3434 |
2.516667 |
0 |
|
Single Cell |
Removing the effects of the cell cycle |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html |
|
Principal component visualisation, Differential gene expression analysis, Expression profile clustering |
2023-01-25 |
2025-03-11 |
14 |
True |
False |
False |
True |
scanpy_cluster_reduce_dimension, anndata_manipulate, tp_easyjoin_tool, table_compute, addValue, scanpy_regress_variable, anndata_inspect, scanpy_inspect, scanpy_plot, cat1, sort1 |
|
|
0 |
|
2050 |
2419 |
0.783333 |
0 |
|
Single Cell |
Single-cell ATAC-seq standard processing with SnapATAC2 |
https://training.galaxyproject.org//topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html |
|
Generation, Essential dynamics, Genome indexing, Differential gene expression analysis, Expression profile clustering, Sequence alignment, Dimensionality reduction, Principal component visualisation, Read mapping, Gene expression profiling |
2024-07-11 |
2025-07-02 |
5 |
True |
False |
False |
True |
anndata_ops, bwa_mem, anndata_manipulate, snapatac2_preprocessing, scanpy_filter, snapatac2_plotting, snapatac2_peaks_and_motif, scanpy_inspect, anndata_inspect, scanpy_plot, Cut1, replace_column_with_key_value_file, snapatac2_clustering, scanpy_normalize, fasta_compute_length |
|
|
0 |
|
1439 |
1749 |
1.100000 |
0 |
|
Single Cell |
Comparing inferred cell compositions using MuSiC deconvolution |
https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music-4-compare/tutorial.html |
|
|
2023-01-20 |
2025-02-13 |
10 |
True |
False |
False |
True |
music_compare |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
269 |
412 |
1.033333 |
0 |
|
Single Cell |
Filter, plot and explore single-cell RNA-seq data with Scanpy (Python) |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case-jupyter_basic-pipeline/tutorial.html |
|
|
2023-08-25 |
2025-03-11 |
13 |
True |
False |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
3181 |
3775 |
1.500000 |
0 |
|
Single Cell |
Converting NCBI Data to the AnnData Format |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html |
|
|
2023-12-13 |
2025-03-11 |
7 |
True |
False |
True |
True |
anndata_ops, anndata_manipulate, tp_replace_in_column, unzip, anndata_import, anndata_inspect, Cut1, Paste1, scanpy_filter_cells |
UseGalaxy.org.au |
|
0 |
|
420 |
497 |
1.766667 |
0 |
|
Single Cell |
Scanpy Parameter Iterator |
https://training.galaxyproject.org//topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.html |
|
|
2023-07-19 |
2025-02-13 |
8 |
True |
False |
False |
True |
scanpy_compute_graph, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_find_cluster, scanpy_run_tsne, scanpy_run_umap |
UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
268 |
302 |
1.166667 |
0 |
|
Single Cell |
Multi-sample batch correction with Harmony and SnapATAC2 |
https://training.galaxyproject.org//topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html |
|
Essential dynamics, Dimensionality reduction, Gene expression profiling |
2025-02-28 |
2025-07-02 |
2 |
True |
False |
False |
True |
anndata_manipulate, snapatac2_preprocessing, snapatac2_plotting, collection_element_identifiers, snapatac2_peaks_and_motif, __FILTER_FROM_FILE__, anndata_inspect, Show beginning1, snapatac2_clustering, __EXTRACT_DATASET__, fasta_compute_length |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
421 |
476 |
0.933333 |
0 |
|
Single Cell |
Evaluating Reference Data for Bulk RNA Deconvolution |
https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html |
|
Visualisation, Annotation |
2025-02-02 |
2025-03-11 |
3 |
True |
False |
False |
True |
music_deconvolution, tp_sed_tool, tp_multijoin_tool, collapse_dataset, Add_a_column1, Count1, join1, tp_cut_tool, music_construct_eset, table_compute, Remove beginning1, __DUPLICATE_FILE_TO_COLLECTION__, ggplot2_violin, tp_easyjoin_tool, tp_awk_tool, ggplot2_point, Paste1, annotatemyids, datamash_transpose, Cut1, collection_column_join, bg_column_arrange_by_header |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
97 |
117 |
1.050000 |
0 |
|
Single Cell |
Filter, plot, and explore single cell RNA-seq data with Seurat |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html |
|
|
2024-04-09 |
2025-03-11 |
10 |
True |
False |
False |
True |
seurat_run_pca, seurat_filter_cells, retrieve_scxa, seurat_normalise_data, seurat_run_umap, seurat_find_clusters, seurat_scale_data, seurat_find_neighbours, seurat_read10x, seurat_find_markers, seurat_plot, seurat_find_variable_genes |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
1769 |
2160 |
1.350000 |
0 |
|
Single Cell |
Clustering 3K PBMCs with Seurat |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-seurat-pbmc3k/tutorial.html |
|
|
2025-01-23 |
2025-05-09 |
5 |
True |
False |
True |
True |
csv_to_tabular, seurat_reduce_dimension, seurat_preprocessing, Filter1, Cut1, seurat_data, seurat_clustering, seurat_plot, seurat_create |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
MISSISSIPPI |
0 |
|
1100 |
1301 |
1.216667 |
0 |
|
Single Cell |
Filter, plot and explore single-cell RNA-seq data with Scanpy |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html |
|
Principal component visualisation, Differential gene expression analysis, Expression profile clustering |
2021-03-24 |
2025-04-23 |
24 |
True |
False |
True |
True |
scanpy_cluster_reduce_dimension, anndata_ops, anndata_manipulate, scanpy_plot_embed, join1, scanpy_find_markers, interactive_tool_cellxgene_vip, scanpy_inspect, anndata_inspect, scanpy_plot, scanpy_normalise_data, scanpy_compute_graph, retrieve_scxa, scanpy_run_pca, scanpy_find_variable_genes, scanpy_scale_data, scanpy_filter_genes, Cut1, scanpy_normalize, scanpy_filter_cells, scanpy_find_cluster, scanpy_run_tsne, scanpy_run_umap, scanpy_filter |
|
|
0 |
|
5175 |
7894 |
2.616667 |
0 |
|
Single Cell |
Plates, Batches, and Barcodes |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-plates-batches-barcodes/slides.html |
|
|
2019-02-16 |
2025-02-13 |
4 |
False |
True |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2845375 |
7530072 |
2.450000 |
0 |
|
Single Cell |
Inferring single cell trajectories with Scanpy (Python) |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_JUPYTER-trajectories/tutorial.html |
|
|
2021-04-07 |
2025-03-11 |
20 |
True |
False |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
4436 |
5252 |
1.300000 |
0 |
|
Single Cell |
Inferring single cell trajectories with Scanpy |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_trajectories/tutorial.html |
|
|
2023-12-08 |
2025-03-11 |
13 |
True |
False |
False |
True |
scanpy_compute_graph, scanpy_run_diffmap, scanpy_run_fdg, anndata_manipulate, scanpy_run_dpt, scanpy_run_paga, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_find_cluster |
|
UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
1226 |
1558 |
2.250000 |
0 |
|
Single Cell |
Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution |
https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html |
|
Annotation |
2023-01-20 |
2024-02-13 |
8 |
True |
False |
False |
True |
join1, tp_cut_tool, music_construct_eset, tp_sed_tool, tp_easyjoin_tool, tp_awk_tool, retrieve_scxa, regex1, annotatemyids, datamash_transpose, music_manipulate_eset, anndata_inspect, table_compute, scanpy_read_10x, Cut1, sort1, add_line_to_file |
|
UseGalaxy.cz |
0 |
|
725 |
1223 |
2.216667 |
0 |
|
Single Cell |
Single-cell Formats and Resources |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-data-formats/slides.html |
|
|
2024-07-26 |
2025-02-13 |
4 |
False |
True |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
808191 |
1874843 |
2.233333 |
0 |
|
Single Cell |
Inferring single cell trajectories with Monocle3 (R) |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_monocle3-rstudio/tutorial.html |
|
|
2023-04-12 |
2025-03-11 |
13 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
6192 |
7048 |
0.800000 |
0 |
|
Single Cell |
Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution |
https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.html |
|
Annotation |
2023-01-20 |
2024-02-13 |
8 |
True |
False |
False |
True |
tp_cut_tool, column_remove_by_header, music_construct_eset, tp_sed_tool, tp_easyjoin_tool, tp_awk_tool, annotatemyids, regex1, table_compute, music_manipulate_eset, sort1 |
|
UseGalaxy.cz |
0 |
|
672 |
1078 |
1.633333 |
0 |
|
Single Cell |
Inferring single cell trajectories with Monocle3 |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html |
|
|
2022-09-30 |
2025-04-23 |
24 |
True |
False |
True |
True |
join1, tp_cut_tool, monocle3_reduceDim, monocle3_create, monocle3_partition, monocle3_topmarkers, datamash_transpose, monocle3_learnGraph, monocle3_preprocess, anndata_inspect, regexColumn1, Filter1, monocle3_plotCells, Cut1, monocle3_orderCells, monocle3_diffExp |
UseGalaxy.eu, UseGalaxy.org (Main) |
|
0 |
|
3858 |
4794 |
1.500000 |
0 |
|
Single Cell |
Trajectory analysis |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-trajectories/slides.html |
|
|
2022-09-30 |
2025-02-13 |
4 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
1890484 |
4443758 |
2.316667 |
0 |
|
Single Cell |
Automated Cell Annotation |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html |
|
|
2023-09-04 |
2025-02-27 |
7 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
1288280 |
2995750 |
2.316667 |
0 |
|
Statistics and machine learning |
Machine learning: classification and regression |
https://training.galaxyproject.org//topics/statistics/tutorials/classification_regression/tutorial.html |
|
|
2019-03-07 |
2025-04-08 |
13 |
True |
False |
False |
True |
sklearn_svm_classifier, plotly_ml_performance_plots, sklearn_ensemble, plotly_regression_performance_plots |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
5665 |
10201 |
0.766667 |
0 |
|
Statistics and machine learning |
Clustering in Machine Learning |
https://training.galaxyproject.org//topics/statistics/tutorials/clustering_machinelearning/tutorial.html |
|
Visualisation |
2020-05-08 |
2025-04-08 |
14 |
True |
False |
False |
True |
sklearn_numeric_clustering, csv_to_tabular, ggplot2_point |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr |
0 |
|
8420 |
13986 |
0.933333 |
0 |
|
Statistics and machine learning |
Image classification in Galaxy with fruit 360 dataset |
https://training.galaxyproject.org//topics/statistics/tutorials/fruit_360/tutorial.html |
|
|
2021-12-01 |
2024-07-09 |
8 |
True |
True |
True |
True |
tp_cut_tool, keras_model_config, keras_model_builder, model_prediction, ml_visualization_ex, sklearn_to_categorical, keras_train_and_eval |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
2364098 |
5901172 |
3.116667 |
0 |
|
Statistics and machine learning |
Train and Test a Deep learning image classifier with Galaxy-Ludwig |
https://training.galaxyproject.org//topics/statistics/tutorials/galaxy-ludwig/tutorial.html |
|
|
2024-10-28 |
2024-12-11 |
2 |
True |
False |
False |
True |
ludwig_experiment |
|
|
0 |
|
161 |
204 |
2.066667 |
0 |
|
Statistics and machine learning |
Text-mining with the SimText toolset |
https://training.galaxyproject.org//topics/statistics/tutorials/text-mining_simtext/tutorial.html |
|
|
2021-04-05 |
2025-05-07 |
8 |
True |
False |
False |
True |
pubmed_by_queries, pmids_to_pubtator_matrix, interactive_tool_simtext_app |
UseGalaxy.eu |
|
0 |
|
467 |
643 |
2.633333 |
0 |
|
Statistics and machine learning |
Introduction to deep learning |
https://training.galaxyproject.org//topics/statistics/tutorials/intro_deep_learning/tutorial.html |
|
|
2020-03-26 |
2025-04-08 |
9 |
True |
False |
False |
True |
keras_model_config, keras_model_builder, model_prediction, ml_visualization_ex, keras_train_and_eval |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
2413 |
3092 |
1.666667 |
0 |
|
Statistics and machine learning |
Prepare Data from CbioPortal for Flexynesis Integration |
https://training.galaxyproject.org//topics/statistics/tutorials/flexynesis_cbio_import/tutorial.html |
|
|
2025-08-10 |
2025-08-13 |
2 |
True |
False |
False |
True |
tp_cut_tool, flexynesis_cbioportal_import, table_compute, flexynesis_utils, tp_sort_header_tool, __EXTRACT_DATASET__ |
UseGalaxy.eu |
|
0 |
|
25 |
25 |
1.300000 |
0 |
|
Statistics and machine learning |
Unsupervised Analysis of Bone Marrow Cells with Flexynesis |
https://training.galaxyproject.org//topics/statistics/tutorials/flexynesis_unsupervised/tutorial.html |
|
|
2025-08-10 |
2025-08-13 |
2 |
True |
False |
False |
True |
flexynesis, flexynesis_utils, flexynesis_plot, __EXTRACT_DATASET__ |
UseGalaxy.eu |
|
0 |
|
21 |
25 |
6.933333 |
0 |
|
Statistics and machine learning |
Deep Learning (Part 2) - Recurrent neural networks (RNN) |
https://training.galaxyproject.org//topics/statistics/tutorials/RNN/tutorial.html |
|
|
2021-02-23 |
2025-05-10 |
15 |
True |
True |
True |
True |
keras_model_config, keras_model_builder, model_prediction, ml_visualization_ex, keras_train_and_eval |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.no |
0 |
|
2778439 |
7279707 |
3.233333 |
0 |
|
Statistics and machine learning |
Regression in Machine Learning |
https://training.galaxyproject.org//topics/statistics/tutorials/regression_machinelearning/tutorial.html |
|
|
2020-01-25 |
2025-05-14 |
19 |
True |
True |
True |
True |
sklearn_generalized_linear, Remove beginning1, sklearn_searchcv, sklearn_ensemble, sklearn_build_pipeline, plotly_regression_performance_plots |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.no |
0 |
|
2848584 |
7534126 |
3.733333 |
0 |
|
Statistics and machine learning |
Identifing Survival Markers of Brain tumor with Flexynesis |
https://training.galaxyproject.org//topics/statistics/tutorials/flexynesis_survival/tutorial.html |
|
|
2025-08-13 |
2025-08-13 |
2 |
True |
False |
False |
True |
flexynesis, tp_replace_in_column, Add_a_column1, flexynesis_plot, __EXTRACT_DATASET__, datamash_ops |
UseGalaxy.eu |
|
0 |
|
22 |
25 |
1.933333 |
0 |
|
Statistics and machine learning |
Classification in Machine Learning |
https://training.galaxyproject.org//topics/statistics/tutorials/classification_machinelearning/tutorial.html |
|
|
2020-04-30 |
2025-05-14 |
18 |
True |
True |
True |
True |
sklearn_generalized_linear, Remove beginning1, sklearn_searchcv, sklearn_ensemble, sklearn_svm_classifier, sklearn_nn_classifier, plotly_ml_performance_plots, sklearn_build_pipeline |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.no |
0 |
|
2848108 |
7534082 |
4.700000 |
0 |
|
Statistics and machine learning |
Modeling Breast Cancer Subtypes with Flexynesis |
https://training.galaxyproject.org//topics/statistics/tutorials/flexynesis_classification/tutorial.html |
|
|
2025-08-13 |
2025-09-02 |
3 |
True |
False |
False |
True |
join1, tabpfn, flexynesis, tp_cut_tool, tp_easyjoin_tool, table_compute, datamash_transpose, Show beginning1, tp_sort_header_tool, pick_value, flexynesis_plot, __EXTRACT_DATASET__ |
UseGalaxy.eu |
|
0 |
|
49 |
74 |
2.350000 |
0 |
|
Statistics and machine learning |
Building the LORIS LLR6 PanCancer Model Using PyCaret |
https://training.galaxyproject.org//topics/statistics/tutorials/loris_model/tutorial.html |
|
|
2024-12-13 |
2025-05-08 |
2 |
True |
True |
True |
True |
PyCaret_Model_Comparison |
|
|
0 |
|
596722 |
1334355 |
4.350000 |
0 |
|
Statistics and machine learning |
A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy |
https://training.galaxyproject.org//topics/statistics/tutorials/gpu_jupyter_lab/tutorial.html |
|
|
2022-04-06 |
2025-04-08 |
9 |
True |
False |
False |
True |
Filter1, interactive_tool_ml_jupyter_notebook, Cut1 |
UseGalaxy.eu |
|
0 |
|
1180 |
1501 |
1.500000 |
0 |
|
Statistics and machine learning |
Interval-Wise Testing for omics data |
https://training.galaxyproject.org//topics/statistics/tutorials/iwtomics/tutorial.html |
|
Comparison, Peak calling, Differential gene expression analysis, Differentially-methylated region identification, Genome annotation |
2018-06-14 |
2023-11-09 |
17 |
True |
False |
False |
True |
iwtomics_testandplot, iwtomics_plotwithscale, iwtomics_loadandplot |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
366 |
488 |
2.950000 |
0 |
|
Statistics and machine learning |
PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis |
https://training.galaxyproject.org//topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html |
|
|
2021-05-06 |
2023-11-09 |
7 |
True |
False |
False |
True |
pancancer_targene_cell_line_predictions, pancancer_external_sample_status_prediction, pancancer_targene_summary_figures, pancancer_alternative_genes_pathwaymapper, pancancer_pathway_count_heatmaps, pancancer_targene_pharmacology, pancancer_compare_within_models, pancancer_classifier, pancancer_within_disease_analysis, pancancer_map_mutation_class, pancancer_apply_weights, pancancer_visualize_decisions |
|
|
0 |
|
773 |
1212 |
3.183333 |
0 |
|
Statistics and machine learning |
Deep Learning (Part 3) - Convolutional neural networks (CNN) |
https://training.galaxyproject.org//topics/statistics/tutorials/CNN/tutorial.html |
|
|
2021-04-19 |
2025-05-09 |
19 |
True |
True |
True |
True |
keras_model_config, keras_model_builder, model_prediction, ml_visualization_ex, sklearn_to_categorical, keras_train_and_eval |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
2703474 |
6998340 |
3.333333 |
0 |
|
Statistics and machine learning |
Basics of machine learning |
https://training.galaxyproject.org//topics/statistics/tutorials/machinelearning/tutorial.html |
|
|
2018-11-05 |
2025-05-13 |
15 |
True |
True |
True |
True |
sklearn_svm_classifier |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.fr, UseGalaxy.no |
0 |
|
2848088 |
7533746 |
5.416667 |
0 |
|
Statistics and machine learning |
Age prediction using machine learning |
https://training.galaxyproject.org//topics/statistics/tutorials/age-prediction-with-ml/tutorial.html |
|
|
2019-01-25 |
2025-04-08 |
12 |
True |
False |
False |
True |
sklearn_searchcv, plotly_parallel_coordinates_plot, sklearn_ensemble, sklearn_build_pipeline, plotly_regression_performance_plots |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.no |
0 |
|
13134 |
21199 |
0.683333 |
0 |
|
Statistics and machine learning |
Deep Learning (Part 1) - Feedforward neural networks (FNN) |
https://training.galaxyproject.org//topics/statistics/tutorials/FNN/tutorial.html |
|
|
2021-04-28 |
2024-06-14 |
12 |
True |
True |
True |
True |
keras_model_config, keras_model_builder, model_prediction, keras_train_and_eval, plotly_regression_performance_plots |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.no |
0 |
|
2707899 |
6987342 |
3.183333 |
0 |
|
Statistics and machine learning |
Fine tune large protein model (ProtTrans) using HuggingFace |
https://training.galaxyproject.org//topics/statistics/tutorials/fine_tuning_protTrans/tutorial.html |
|
|
2024-06-17 |
2025-04-08 |
4 |
True |
True |
True |
False |
interactive_tool_ml_jupyter_notebook |
UseGalaxy.eu |
|
0 |
|
866406 |
2016594 |
3.316667 |
0 |
|
Statistics and machine learning |
Supervised Learning with Hyperdimensional Computing |
https://training.galaxyproject.org//topics/statistics/tutorials/hyperdimensional_computing/tutorial.html |
|
|
2023-04-28 |
2023-11-09 |
2 |
True |
False |
False |
False |
chopin2 |
UseGalaxy.org (Main) |
|
0 |
|
428 |
532 |
0.716667 |
0 |
|
Statistics and machine learning |
Introduction to Machine Learning using R |
https://training.galaxyproject.org//topics/statistics/tutorials/intro-to-ml-with-r/tutorial.html |
|
|
2021-05-21 |
2024-10-15 |
15 |
True |
False |
True |
False |
interactive_tool_rstudio |
UseGalaxy.eu, UseGalaxy.org.au |
|
0 |
|
4014 |
6011 |
1.083333 |
0 |
|
Synthetic Biology |
Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools |
https://training.galaxyproject.org//topics/synthetic-biology/tutorials/retrosynthesis_analysis/tutorial.html |
|
|
2022-06-23 |
2024-06-14 |
8 |
True |
False |
True |
True |
retropath2, get_sbml_model, rp2paths, rpcompletion, rrparser, rpextractsink |
|
|
0 |
|
562 |
828 |
2.633333 |
0 |
|
Synthetic Biology |
Designing plasmids encoding predicted pathways by using the BASIC assembly method |
https://training.galaxyproject.org//topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.html |
|
|
2022-05-12 |
2024-06-14 |
8 |
True |
False |
True |
True |
dnabot, rpbasicdesign, selenzy-wrapper |
|
|
0 |
|
998 |
1556 |
2.750000 |
0 |
|
Synthetic Biology |
Evaluating and ranking a set of pathways based on multiple metrics |
https://training.galaxyproject.org//topics/synthetic-biology/tutorials/pathway_analysis/tutorial.html |
|
|
2022-09-26 |
2024-06-14 |
7 |
True |
False |
True |
True |
rpthermo, rpranker, rpfba, rpscore |
|
|
0 |
|
629 |
936 |
3.000000 |
0 |
|
Teaching and Hosting Galaxy training |
Workshop Kickoff |
https://training.galaxyproject.org//topics/teaching/tutorials/workshop-intro/slides.html |
|
|
2019-06-04 |
2024-02-20 |
5 |
False |
True |
False |
False |
|
|
|
0 |
|
2845375 |
7530082 |
2.450000 |
0 |
|
Teaching and Hosting Galaxy training |
Overview of the Galaxy Training Material for Instructors |
https://training.galaxyproject.org//topics/teaching/tutorials/gtn-for-instructors/slides.html |
|
|
2022-09-23 |
2024-08-08 |
3 |
False |
True |
True |
False |
|
|
|
0 |
|
1899927 |
4470799 |
2.316667 |
0 |
|
Teaching and Hosting Galaxy training |
Teaching experiences |
https://training.galaxyproject.org//topics/teaching/tutorials/experiences/tutorial.html |
|
|
2022-09-23 |
2022-09-23 |
1 |
True |
False |
False |
False |
|
|
|
0 |
|
277 |
498 |
2.750000 |
0 |
|
Teaching and Hosting Galaxy training |
Asynchronous training |
https://training.galaxyproject.org//topics/teaching/tutorials/gallantries-async/tutorial.html |
|
|
2023-11-02 |
2023-11-02 |
1 |
True |
False |
False |
False |
|
|
|
0 |
|
7 |
7 |
0.000000 |
0 |
|
Teaching and Hosting Galaxy training |
Hybrid training |
https://training.galaxyproject.org//topics/teaching/tutorials/hybrid-training/tutorial.html |
|
|
2022-09-23 |
2024-06-25 |
7 |
True |
False |
False |
False |
|
|
|
0 |
|
21 |
23 |
0.016667 |
0 |
|
Teaching and Hosting Galaxy training |
Course Builder |
https://training.galaxyproject.org//topics/teaching/tutorials/gallantries-coursebuilder/tutorial.html |
|
|
2023-11-02 |
2023-11-02 |
1 |
True |
False |
False |
False |
|
|
|
0 |
|
126 |
147 |
2.183333 |
0 |
|
Teaching and Hosting Galaxy training |
Running a workshop as instructor |
https://training.galaxyproject.org//topics/teaching/tutorials/running-workshop/tutorial.html |
|
|
2018-11-15 |
2025-04-08 |
6 |
True |
False |
False |
False |
|
|
|
0 |
|
156 |
285 |
1.383333 |
0 |
|
Teaching and Hosting Galaxy training |
Training Infrastructure as a Service |
https://training.galaxyproject.org//topics/teaching/tutorials/setup-tiaas-for-training/tutorial.html |
|
|
2018-11-15 |
2023-12-20 |
4 |
True |
False |
False |
False |
|
|
|
0 |
|
217 |
408 |
6.466667 |
0 |
|
Teaching and Hosting Galaxy training |
Galaxy Admin Training |
https://training.galaxyproject.org//topics/teaching/tutorials/galaxy-admin-training/tutorial.html |
|
|
2020-11-04 |
2024-09-17 |
5 |
True |
False |
False |
False |
|
|
|
0 |
|
147 |
160 |
2.766667 |
0 |
|
Teaching and Hosting Galaxy training |
Set up a Galaxy for Training |
https://training.galaxyproject.org//topics/teaching/tutorials/setup-galaxy-for-training/tutorial.html |
|
|
2018-06-04 |
2023-11-09 |
5 |
True |
False |
False |
False |
|
|
|
0 |
|
306 |
352 |
4.083333 |
0 |
|
Teaching and Hosting Galaxy training |
Teaching online |
https://training.galaxyproject.org//topics/teaching/tutorials/teaching-online/tutorial.html |
|
|
2022-09-23 |
2023-10-23 |
4 |
True |
False |
False |
False |
|
|
|
0 |
|
21 |
21 |
0.083333 |
0 |
|
Teaching and Hosting Galaxy training |
Live Coding is a Skill |
https://training.galaxyproject.org//topics/teaching/tutorials/live-coding/tutorial.html |
|
|
2022-09-23 |
2023-11-09 |
6 |
True |
False |
False |
False |
|
|
|
0 |
|
84 |
88 |
0.283333 |
0 |
|
Teaching and Hosting Galaxy training |
Organizing a workshop |
https://training.galaxyproject.org//topics/teaching/tutorials/organize-workshop/tutorial.html |
|
|
2018-11-15 |
2023-11-09 |
4 |
True |
False |
False |
False |
|
|
|
0 |
|
250 |
272 |
1.066667 |
0 |
|
Transcriptomics |
3: RNA-seq genes to pathways |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html |
|
Gene functional annotation, Gene set testing, Gene-set enrichment analysis |
2018-12-31 |
2023-11-09 |
13 |
True |
False |
False |
True |
join1, tp_cut_tool, fgsea, Add_a_column1, goseq, Cut1, tp_sort_header_tool, egsea |
UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
25961 |
41683 |
1.933333 |
0 |
|
Transcriptomics |
RNA-RNA interactome data analysis |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-interactome/tutorial.html |
|
Statistical calculation, Sequence composition calculation, Sequence trimming, Primer removal, Sequencing quality control, Read pre-processing |
2020-03-23 |
2023-11-09 |
12 |
True |
False |
False |
True |
cutadapt, fastqc, chira_merge, query_tabular, chira_map, chira_quantify, chira_collapse, chira_extract |
UseGalaxy.be, UseGalaxy.no, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au |
0 |
|
1455 |
2209 |
2.816667 |
0 |
|
Transcriptomics |
2: RNA-seq counts to genes |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html |
|
RNA-Seq analysis, Annotation |
2018-12-31 |
2024-04-10 |
21 |
True |
False |
False |
True |
tp_cut_tool, annotatemyids, tp_replace_in_line, limma_voom, mergeCols1 |
UseGalaxy.be, UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au |
0 |
|
43157 |
73033 |
2.266667 |
0 |
|
Transcriptomics |
Differential abundance testing of small RNAs |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/srna/tutorial.html |
|
Statistical calculation, Sequence trimming, Primer removal, Differential gene expression analysis, Sequencing quality control, Gene expression analysis, Sequence alignment, RNA-Seq analysis, Sequence composition calculation, RNA-Seq quantification, Read pre-processing |
2017-06-29 |
2023-11-09 |
26 |
True |
False |
False |
True |
samtool_filter2, hisat2, fastq_manipulation, fastqc, deseq2, Filter1, salmon, trim_galore, bedtools_bamtofastq |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
6889 |
12104 |
2.100000 |
0 |
|
Transcriptomics |
Small Non-coding RNA Clustering using BlockClust |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.html |
|
|
2018-12-14 |
2023-11-09 |
8 |
True |
False |
False |
True |
blockbuster, samtools_sort, blockclust, tp_sort_header_tool |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
1022 |
1394 |
2.983333 |
0 |
|
Transcriptomics |
Genome-wide alternative splicing analysis |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html |
|
Statistical calculation, Data handling, Transcriptome assembly, Sequence annotation, Sequencing quality control, Sequence analysis, Protein sequence analysis, Formatting, Sequence alignment, RNA-Seq analysis, Sequence composition calculation, Validation, Visualisation, De-novo assembly, Sequence contamination filtering, Sequence comparison, Sequence assembly validation |
2023-05-17 |
2025-03-28 |
11 |
True |
True |
False |
True |
stringtie_merge, Add_a_column1, pfamscan, rseqc_geneBody_coverage, cpat, tp_cat, rseqc_infer_experiment, multiqc, gtftobed12, Remove beginning1, gffcompare, gffread, rseqc_read_distribution, rseqc_junction_saturation, tp_awk_tool, rseqc_inner_distance, __FILTER_FROM_FILE__, gene2exon1, pygenomeTracks, rna_quast, tp_uniq_tool, tp_grep_tool, collection_element_identifiers, fastqc, rna_star, addValue, isoformswitchanalyzer, stringtie, Filter1, rseqc_junction_annotation, cat1, Cut1, fastp, __FLATTEN__, sort1 |
|
UseGalaxy.cz, UseGalaxy.fr |
0 |
|
1492096 |
3435873 |
4.200000 |
0 |
|
Transcriptomics |
Visualization of RNA-Seq results with heatmap2 |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html |
|
|
2018-12-31 |
2023-11-09 |
13 |
True |
False |
False |
True |
join1, ggplot2_heatmap2, datamash_transpose, Cut1 |
UseGalaxy.eu, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
77292 |
127370 |
1.366667 |
0 |
|
Transcriptomics |
1: RNA-Seq reads to counts |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html |
|
Statistical calculation, Data handling, Sequence trimming, Primer removal, Sequencing quality control, Sequence composition calculation, Formatting, Sequence alignment, Read summarisation, Validation, RNA-Seq quantification, Read pre-processing |
2018-09-23 |
2024-08-09 |
33 |
True |
False |
False |
True |
picard_MarkDuplicates, rseqc_geneBody_coverage, rseqc_infer_experiment, rseqc_read_distribution, featurecounts, hisat2, multiqc, cutadapt, fastqc, collection_column_join, samtools_idxstats |
UseGalaxy.eu |
MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
77499 |
141130 |
2.583333 |
0 |
|
Transcriptomics |
Visualization of RNA-Seq results with Volcano Plot |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.html |
|
|
2018-12-31 |
2025-04-17 |
16 |
True |
False |
True |
True |
volcanoplot |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.no |
0 |
|
152290 |
250219 |
1.333333 |
0 |
|
Transcriptomics |
CLIP-Seq data analysis from pre-processing to motif detection |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/clipseq/tutorial.html |
|
Statistical calculation, Sequence composition calculation, Sequence alignment, Mapping, Sequence trimming, Primer removal, Sequencing quality control, Read pre-processing |
2018-08-17 |
2023-11-09 |
23 |
True |
False |
False |
True |
umi_tools_extract, peakachu, Extract genomic DNA 1, bctools_extract_alignment_ends, umi_tools_dedup, deeptools_plot_correlation, __SORTLIST__, bedtools_genomecoveragebed_bedgraph, rcas, meme_chip, tp_awk_tool, wig_to_bigWig, __MERGE_COLLECTION__, deeptools_plot_fingerprint, bedtools_slopbed, cutadapt, fastqc, rna_star, sort1, deeptools_multi_bam_summary |
|
UseGalaxy.no |
0 |
|
8175 |
16164 |
1.883333 |
0 |
|
Transcriptomics |
De novo transcriptome assembly, annotation, and differential expression analysis |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/full-de-novo/tutorial.html |
|
Statistical calculation, Coding region prediction, Transcriptome assembly, Sequencing quality control, Gene functional annotation, Sequence composition calculation, Validation, De-novo assembly, de Novo sequencing |
2020-02-13 |
2023-11-09 |
8 |
True |
False |
False |
True |
trimmomatic, trinity_samples_qccheck, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity, multiqc, trinity_define_clusters_by_cutting_tree, fastqc, trinity_run_de_analysis, transdecoder, trinotate, trinity_contig_exn50_statistic, trinity_filter_low_expr_transcripts, describe_samples, trinity_abundance_estimates_to_matrix |
UseGalaxy.eu |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no |
0 |
|
14409 |
26163 |
2.433333 |
0 |
|
Transcriptomics |
GO Enrichment Analysis |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/goenrichment/tutorial.html |
|
Gene-set enrichment analysis |
2019-01-23 |
2024-03-05 |
12 |
True |
False |
False |
True |
Filter1, goslimmer, goenrichment |
Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
23013 |
37418 |
1.333333 |
0 |
|
Transcriptomics |
Network analysis with Heinz |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html |
|
Differential gene expression analysis, Pathway or network analysis, RNA-Seq analysis |
2018-10-11 |
2024-01-15 |
16 |
True |
True |
False |
True |
heinz_visualization, deseq2, heinz_scoring, Cut1, heinz_bum, heinz |
UseGalaxy.be, UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
2847403 |
7533247 |
5.700000 |
0 |
|
Transcriptomics |
RNA-Seq data analysis, clustering and visualisation tutorial |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html |
|
RNA-Seq analysis, Gene functional annotation, Differential gene expression analysis |
2025-05-28 |
2025-06-16 |
5 |
True |
False |
False |
True |
Multivariate, Grouping1, tp_easyjoin_tool, table_compute, deseq2, Filter1, tp_sort_header_tool, Add_a_column1, ggplot2_heatmap2, cat1, Show beginning1, Cut1, goseq, deg_annotate, length_and_gc_content, volcanoplot |
UseGalaxy.eu, UseGalaxy.fr |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) |
0 |
|
732 |
927 |
1.616667 |
0 |
|
Transcriptomics |
RNA-Seq analysis with AskOmics Interactive Tool |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-analysis-with-askomics-it/tutorial.html |
|
|
2020-07-09 |
2023-11-09 |
13 |
True |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2846374 |
7531362 |
6.166667 |
0 |
|
Transcriptomics |
Introduction to Transcriptomics |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/introduction/slides.html |
|
|
2016-10-05 |
2025-04-08 |
3 |
False |
True |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2845375 |
7530085 |
2.450000 |
0 |
|
Transcriptomics |
Visualization of RNA-Seq results with CummeRbund |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-cummerbund/tutorial.html |
|
|
2017-10-16 |
2023-11-09 |
16 |
True |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2847918 |
7533927 |
4.200000 |
0 |
|
Transcriptomics |
Visualization of RNA-Seq results with Volcano Plot in R |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot-r/tutorial.html |
|
|
2021-06-14 |
2024-06-14 |
8 |
True |
False |
True |
False |
interactive_tool_rstudio, volcanoplot |
UseGalaxy.eu, UseGalaxy.org.au |
|
0 |
|
30817 |
42112 |
1.683333 |
0 |
|
Transcriptomics |
RNA Seq Counts to Viz in R |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.html |
|
|
2019-10-08 |
2024-10-15 |
21 |
True |
False |
True |
False |
interactive_tool_rstudio |
UseGalaxy.eu, UseGalaxy.org.au |
|
0 |
|
4222 |
5412 |
1.933333 |
0 |
|
Transcriptomics |
RNA-seq Alignment with STAR |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.html |
|
|
2023-05-15 |
2023-11-09 |
6 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
10509 |
12897 |
1.450000 |
0 |
|
Transcriptomics |
Reference-based RNAseq data analysis (long) |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/rb-rnaseq/tutorial.html |
|
|
2017-02-22 |
2023-02-17 |
12 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
21968 |
34443 |
2.183333 |
0 |
|
Transcriptomics |
Reference-based RNA-Seq data analysis |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/ref-based/tutorial.html |
|
Data handling, Pathway or network visualisation, Differential gene expression analysis, Exonic splicing enhancer prediction, Formatting, Sequence alignment, Read summarisation, Read mapping, Gene functional annotation, Validation, Visualisation, Sequence trimming, Primer removal, Enrichment analysis, Sequencing quality control, Pathway or network analysis, RNA-Seq analysis, Read pre-processing, RNA-Seq quantification |
2016-10-05 |
2025-10-04 |
104 |
True |
False |
True |
True |
Grouping1, tp_replace_in_line, Add_a_column1, pathview, rseqc_geneBody_coverage, deg_annotate, tp_cat, samtools_idxstats, join1, rseqc_infer_experiment, __TAG_FROM_FILE__, multiqc, table_compute, gtftobed12, deseq2, samtools_view, dexseq_count, tp_sort_header_tool, rseqc_read_distribution, ChangeCase, featurecounts, __FILTER_FROM_FILE__, pygenomeTracks, falco, ggplot2_heatmap2, goseq, tp_grep_tool, __MERGE_COLLECTION__, picard_MarkDuplicates, cutadapt, collection_element_identifiers, dexseq, tp_tail_tool, rna_star, Filter1, length_and_gc_content, cat1, Cut1, __FLATTEN__, __EXTRACT_DATASET__ |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
184001 |
346150 |
2.800000 |
0 |
|
Transcriptomics |
Pathway analysis with the MINERVA Platform |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/minerva-pathways/tutorial.html |
|
Statistical calculation, Read summarisation, Data handling, Sequence trimming, Primer removal, Sequencing quality control, Sequence composition calculation, Sequence alignment, RNA-Seq analysis, Gene functional annotation, Validation, RNA-Seq quantification, Read pre-processing, Annotation |
2024-03-28 |
2024-07-26 |
3 |
True |
False |
False |
True |
tp_sorted_uniq, tp_replace_in_line, limma_voom, Add_a_column1, rseqc_geneBody_coverage, join1, multiqc, fasterq_dump, tp_sort_header_tool, rseqc_read_distribution, featurecounts, goseq, Grep1, hisat2, cutadapt, annotatemyids, fastqc, Cut1, collection_column_join, __EXTRACT_DATASET__ |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) |
0 |
|
592 |
709 |
1.666667 |
0 |
|
Transcriptomics |
De novo transcriptome reconstruction with RNA-Seq |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/de-novo/tutorial.html |
|
Statistical calculation, Read summarisation, Transcriptome assembly, Sequence annotation, Sequencing quality control, Differential gene expression analysis, Sequence alignment, RNA-Seq analysis, Sequence composition calculation, RNA-Seq quantification |
2017-02-19 |
2024-06-14 |
36 |
True |
False |
True |
True |
trimmomatic, featurecounts, hisat2, stringtie_merge, fastqc, stringtie, deseq2, gffcompare, Filter1, deeptools_bam_coverage |
Galaxy@AuBi, UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
16548 |
28564 |
2.666667 |
0 |
|
Variant Analysis |
Introduction to Variant analysis |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/introduction/slides.html |
|
|
2016-08-19 |
2023-03-05 |
2 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2845375 |
7530086 |
2.450000 |
0 |
|
Variant Analysis |
Calling very rare variants |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/dunovo/tutorial.html |
|
Statistical calculation, Generation, Genome indexing, Sequencing quality control, Variant calling, Sequence alignment, Sequence composition calculation, Read mapping |
2017-02-22 |
2024-12-09 |
21 |
True |
False |
False |
True |
bwa_mem, fastqc, bamleftalign, Filter1, make_families, sequence_content_trimmer, allele_counts_1, correct_barcodes, align_families, naive_variant_caller, dunovo |
UseGalaxy.org (Main) |
|
0 |
|
1951 |
3054 |
1.766667 |
0 |
|
Variant Analysis |
Calling variants in non-diploid systems |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html |
Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation |
Statistical calculation, Generation, Sequence alignment analysis, Genome indexing, Data handling, Sequencing quality control, Variant calling, Formatting, Sequence alignment, Sequence composition calculation, Read mapping |
2017-02-16 |
2024-03-15 |
23 |
True |
False |
False |
True |
picard_MarkDuplicates, bwa_mem, fastqc, bamleftalign, vcffilter2, bamFilter, vcf2tsv, picard_MergeSamFiles, Cut1, freebayes |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
8501 |
15358 |
2.150000 |
0 |
|
Variant Analysis |
Identification of somatic and germline variants from tumor and normal sample pairs |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/somatic-variants/tutorial.html |
|
Statistical calculation, Generation, Sequence alignment analysis, Genome indexing, Data handling, Validation, Sequencing quality control, Variant calling, Sequence alignment, Sequence composition calculation, Read mapping, Visualisation |
2019-03-13 |
2025-03-20 |
16 |
True |
False |
False |
True |
bwa_mem, gemini_query, snpEff, trimmomatic, multiqc, tp_easyjoin_tool, fastqc, bamleftalign, samtools_rmdup, bamFilter, falco, samtools_calmd, gemini_annotate, gemini_load, varscan_somatic, bg_column_arrange_by_header |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr |
0 |
|
14265 |
25688 |
2.500000 |
0 |
|
Variant Analysis |
Exome sequencing data analysis for diagnosing a genetic disease |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/exome-seq/tutorial.html |
|
Statistical calculation, Generation, Genome indexing, Genetic variation analysis, Validation, Sequencing quality control, Sequence analysis, Variant calling, Sequence alignment, Sequence composition calculation, Read mapping |
2016-08-19 |
2025-05-11 |
29 |
True |
False |
True |
True |
gemini_inheritance, snpEff_download, bwa_mem, bcftools_norm, snpEff, trimmomatic, multiqc, fastqc, samtools_rmdup, samtools_view, gemini_load, freebayes |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
34742 |
63322 |
2.750000 |
0 |
|
Variant Analysis |
Mapping and molecular identification of phenotype-causing mutations |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html |
|
|
2018-03-07 |
2023-11-09 |
16 |
True |
False |
False |
True |
snpEff_download, snpEff, mimodd_varextract, mimodd_map, tp_find_and_replace, mimodd_varcall, mimodd_vcf_filter, mimodd_varreport |
UseGalaxy.be, UseGalaxy.eu |
GalaxyTrakr, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
4297 |
6325 |
2.716667 |
0 |
|
Variant Analysis |
Trio Analysis using Synthetic Datasets from RD-Connect GPAP |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/trio-analysis/tutorial.html |
|
Genetic variation analysis, Sequence analysis |
2022-05-19 |
2024-09-17 |
13 |
True |
False |
True |
True |
gemini_inheritance, bcftools_norm, snpEff, bcftools_merge, pyega3, CONVERTER_gz_to_uncompressed, regexColumn1, Filter1, CONVERTER_uncompressed_to_gz, gene_iobio_display_generation_iframe, gemini_load, tp_grep_tool |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
1917 |
3403 |
3.666667 |
0 |
|
Variant Analysis |
Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html |
|
Generation, Data handling, Genome indexing, Primer removal, Sequence trimming, Sequence alignment, Read pre-processing, Read mapping, Visualisation |
2025-02-24 |
2025-02-24 |
1 |
True |
False |
False |
True |
ncbi_acc_download, bwa_mem, fastq_dump, bcftools_call, tp_awk_tool, tp_replace_in_column, tp_replace_in_line, bcftools_mpileup, ggplot2_point, collapse_dataset, vcf2tsv, Filter1, trim_galore |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
235 |
326 |
1.033333 |
0 |
|
Variant Analysis |
Calling variants in diploid systems |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/dip/tutorial.html |
|
Statistical calculation, Genetic variation analysis, Sequence analysis, Variant calling |
2017-02-20 |
2025-04-28 |
17 |
True |
False |
False |
True |
gemini_query, snpEff, gemini_db_info, vcfallelicprimitives, gemini_load, freebayes |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr |
UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
15224 |
26193 |
3.233333 |
0 |
|
Variant Analysis |
Somatic Variant Discovery from WES Data Using Control-FREEC |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html |
|
Statistical calculation, Generation, Genome indexing, Validation, Copy number estimation, Sequencing quality control, Variant calling, Sequence visualisation, Sequence alignment, Sequence composition calculation, Read mapping, Visualisation, Genome alignment |
2022-10-05 |
2025-03-20 |
14 |
True |
False |
False |
True |
bwa_mem, trimmomatic, multiqc, fastqc, tp_replace_in_line, tp_text_file_with_recurring_lines, __RELABEL_FROM_FILE__, bamleftalign, samtools_rmdup, falco, samtools_calmd, samtools_view, Grep1, __BUILD_LIST__, control_freec, __EXTRACT_DATASET__, circos |
|
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au |
0 |
|
1819 |
2336 |
2.033333 |
0 |
|
Variant Analysis |
Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs) |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/beacon_cnv_query/tutorial.html |
|
Genetic variation analysis, Database search, Service discovery |
2024-08-06 |
2024-09-27 |
3 |
True |
False |
False |
False |
beacon2_cnv |
|
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au |
0 |
|
161 |
198 |
2.616667 |
0 |
|
Variant Analysis |
Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/beaconise_1000hg/tutorial.html |
|
Database search, Genetic variation analysis, Service discovery |
2024-08-06 |
2024-09-27 |
3 |
True |
False |
False |
False |
beacon2_import, beacon2_cnv, cnv_vcf2json, cnv_phenopacket |
|
UseGalaxy.eu |
0 |
|
296 |
335 |
0.516667 |
0 |
|
Visualisation |
Ploting a Microbial Genome with Circos |
https://training.galaxyproject.org//topics/visualisation/tutorials/circos-microbial/tutorial.html |
|
Sequence visualisation |
2023-11-08 |
2024-09-17 |
3 |
True |
False |
False |
True |
gff2bed1, circos_wiggle_to_scatter, Cut1, circos_gc_skew, deeptools_bam_coverage, circos_interval_to_tile, circos_interval_to_text, circos |
UseGalaxy.cz, UseGalaxy.fr |
Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
1379 |
1753 |
1.933333 |
0 |
|
Visualisation |
Visualisation with Circos |
https://training.galaxyproject.org//topics/visualisation/tutorials/circos/tutorial.html |
|
Sequence visualisation |
2020-01-10 |
2024-10-15 |
22 |
True |
True |
True |
True |
random_lines1, upload1, Remove beginning1, Cut1, Grep1, circos |
Galaxy@AuBi, Galaxy@Pasteur, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.no |
0 |
|
2875486 |
7578211 |
4.116667 |
0 |
|
Visualisation |
Friends Don't Let Friends Make Bad Graphs |
https://training.galaxyproject.org//topics/visualisation/tutorials/bad-graphs/slides.html |
|
|
2023-11-20 |
2023-11-20 |
2 |
False |
True |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
1204088 |
2811787 |
2.316667 |
0 |
|
Visualisation |
Visualisations in Galaxy |
https://training.galaxyproject.org//topics/visualisation/tutorials/introduction/slides.html |
|
|
2020-01-10 |
2023-01-12 |
1 |
False |
True |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
2845375 |
7530089 |
2.450000 |
0 |