|
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 |
|
3032563 |
7822753 |
2.350000 |
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 |
|
3034363 |
7825321 |
5.750000 |
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 |
2025-11-22 |
106 |
True |
True |
True |
False |
|
|
|
0 |
|
3058121 |
7870277 |
4.083333 |
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 |
2025-11-22 |
63 |
True |
True |
True |
False |
|
|
|
0 |
|
3036646 |
7829777 |
5.616667 |
0 |
|
Galaxy Server administration |
Galaxy Monitoring with gxadmin |
https://training.galaxyproject.org//topics/admin/tutorials/gxadmin/tutorial.html |
|
|
2019-01-28 |
2025-11-13 |
27 |
True |
True |
True |
False |
|
|
|
0 |
|
3033454 |
7824141 |
4.983333 |
0 |
|
Galaxy Server administration |
Reference Data with CVMFS |
https://training.galaxyproject.org//topics/admin/tutorials/cvmfs/tutorial.html |
|
|
2019-01-27 |
2025-11-22 |
53 |
True |
True |
True |
False |
|
|
|
0 |
|
3034700 |
7825909 |
5.433333 |
0 |
|
Galaxy Server administration |
Galaxy Monitoring with Telegraf and Grafana |
https://training.galaxyproject.org//topics/admin/tutorials/monitoring/tutorial.html |
|
|
2019-01-31 |
2025-11-22 |
52 |
True |
True |
True |
False |
|
|
|
0 |
|
3035455 |
7828102 |
3.216667 |
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 |
|
3032563 |
7822753 |
2.350000 |
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 |
|
3033914 |
7824869 |
3.883333 |
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 |
|
3034868 |
7826219 |
5.016667 |
0 |
|
Galaxy Server administration |
Gearing towards production |
https://training.galaxyproject.org//topics/admin/tutorials/production/slides.html |
|
|
2019-01-28 |
2025-11-20 |
11 |
False |
True |
True |
False |
|
|
|
0 |
|
3032563 |
7822753 |
2.350000 |
0 |
|
Galaxy Server administration |
Data Libraries |
https://training.galaxyproject.org//topics/admin/tutorials/data-library/tutorial.html |
|
|
2021-01-14 |
2025-11-22 |
34 |
True |
True |
True |
False |
|
|
|
0 |
|
3016335 |
7759580 |
4.383333 |
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 |
2025-11-22 |
9 |
True |
True |
True |
False |
|
|
|
0 |
|
3033145 |
7823526 |
11.133333 |
0 |
|
Galaxy Server administration |
Running Jobs on Remote Resources with Pulsar |
https://training.galaxyproject.org//topics/admin/tutorials/pulsar/tutorial.html |
|
|
2019-01-28 |
2025-11-22 |
53 |
True |
True |
True |
False |
|
|
|
0 |
|
3035120 |
7826959 |
5.183333 |
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 |
|
3039020 |
7834289 |
4.033333 |
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 |
|
3032563 |
7822754 |
2.350000 |
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 |
|
3032563 |
7822754 |
2.350000 |
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 |
|
3032563 |
7822754 |
2.350000 |
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 |
|
3032563 |
7822754 |
2.350000 |
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 |
|
3033270 |
7823863 |
3.150000 |
0 |
|
Galaxy Server administration |
Galactic Database |
https://training.galaxyproject.org//topics/admin/tutorials/database/slides.html |
|
|
2019-01-28 |
2025-11-20 |
6 |
False |
True |
True |
False |
|
|
|
0 |
|
3032563 |
7822754 |
2.350000 |
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 |
|
3032563 |
7822754 |
2.350000 |
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 |
|
3032563 |
7822754 |
2.350000 |
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 |
|
1016645 |
2226839 |
2.000000 |
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 |
|
3032563 |
7822754 |
2.350000 |
0 |
|
Galaxy Server administration |
Reference Data with Data Managers |
https://training.galaxyproject.org//topics/admin/tutorials/reference-genomes/tutorial.html |
|
Generation, Read mapping, Genome indexing, Sequence alignment |
2019-01-28 |
2023-04-21 |
7 |
True |
True |
False |
False |
bwa, data_manager_fetch_genome_all_fasta_dbkey, bwa_mem_index_builder_data_manager |
|
|
0 |
|
3033134 |
7823496 |
6.650000 |
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 |
|
3032563 |
7822754 |
2.350000 |
0 |
|
Galaxy Server administration |
Setting up Celery Workers for Galaxy |
https://training.galaxyproject.org//topics/admin/tutorials/celery/tutorial.html |
|
|
2022-07-16 |
2025-11-22 |
17 |
True |
True |
False |
False |
|
|
|
0 |
|
2177379 |
5002241 |
3.783333 |
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 |
|
3032563 |
7822755 |
2.350000 |
0 |
|
Galaxy Server administration |
Deploying a Beacon v1 in Galaxy |
https://training.galaxyproject.org//topics/admin/tutorials/beacon/tutorial.html |
|
|
2023-04-16 |
2025-11-22 |
7 |
True |
False |
False |
False |
|
|
|
0 |
|
153 |
171 |
1.900000 |
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 |
|
45 |
50 |
3.916667 |
0 |
|
Galaxy Server administration |
Enable upload via FTP |
https://training.galaxyproject.org//topics/admin/tutorials/ftp/tutorial.html |
|
|
2021-06-18 |
2025-11-22 |
26 |
True |
False |
False |
False |
|
|
|
0 |
|
1249 |
1710 |
1.633333 |
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 |
|
709 |
1089 |
2.866667 |
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 |
|
40 |
45 |
3.066667 |
0 |
|
Galaxy Server administration |
Performant Uploads with TUS |
https://training.galaxyproject.org//topics/admin/tutorials/tus/tutorial.html |
|
|
2022-03-01 |
2025-11-22 |
22 |
True |
False |
True |
False |
|
|
|
0 |
|
871 |
1268 |
5.183333 |
0 |
|
Galaxy Server administration |
Monitoring Galaxy and Pulsar with Sentry |
https://training.galaxyproject.org//topics/admin/tutorials/sentry/tutorial.html |
|
|
2023-04-19 |
2025-11-22 |
10 |
True |
False |
False |
False |
|
|
|
0 |
|
220 |
265 |
1.133333 |
0 |
|
Galaxy Server administration |
Galaxy Monitoring with Reports |
https://training.galaxyproject.org//topics/admin/tutorials/reports/tutorial.html |
|
|
2019-01-31 |
2025-11-22 |
46 |
True |
False |
False |
False |
|
|
|
0 |
|
505 |
672 |
2.700000 |
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 |
|
682 |
785 |
0.616667 |
0 |
|
Galaxy Server administration |
Training Infrastructure as a Service (TIaaS) |
https://training.galaxyproject.org//topics/admin/tutorials/tiaas/tutorial.html |
|
|
2020-02-12 |
2025-11-22 |
42 |
True |
False |
True |
False |
|
|
|
0 |
|
555 |
740 |
3.200000 |
0 |
|
Galaxy Server administration |
Mapping Jobs to Destinations using TPV |
https://training.galaxyproject.org//topics/admin/tutorials/job-destinations/tutorial.html |
|
|
2021-01-17 |
2025-11-22 |
40 |
True |
False |
True |
False |
|
|
|
0 |
|
1692 |
2648 |
3.383333 |
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 |
|
200 |
239 |
2.083333 |
0 |
|
Galaxy Server administration |
Customizing the look of Galaxy |
https://training.galaxyproject.org//topics/admin/tutorials/customization/tutorial.html |
|
|
2023-04-16 |
2025-11-22 |
8 |
True |
False |
False |
False |
|
|
|
0 |
|
590 |
719 |
4.450000 |
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 |
|
65 |
71 |
2.783333 |
0 |
|
Galaxy Server administration |
Use Apptainer containers for running Galaxy jobs |
https://training.galaxyproject.org//topics/admin/tutorials/apptainer/tutorial.html |
|
|
2021-01-08 |
2025-11-22 |
17 |
True |
False |
True |
False |
|
|
|
0 |
|
1083 |
1377 |
2.583333 |
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 |
|
3035 |
4960 |
1.066667 |
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 |
|
56 |
74 |
2.833333 |
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 |
|
8288 |
16404 |
0.700000 |
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 |
|
402 |
539 |
2.400000 |
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 |
|
1617 |
2668 |
2.266667 |
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 |
|
672 |
982 |
2.116667 |
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 |
|
74 |
93 |
1.716667 |
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 |
|
62 |
70 |
0.616667 |
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 |
|
1107 |
1261 |
0.333333 |
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 |
|
2368 |
3051 |
0.433333 |
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 |
|
3048587 |
7852895 |
3.300000 |
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 |
|
1669818 |
3714608 |
2.150000 |
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 |
|
1684082 |
3746984 |
2.150000 |
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 |
|
1731035 |
3850380 |
2.150000 |
0 |
|
Assembly |
An Introduction to Genome Assembly |
https://training.galaxyproject.org//topics/assembly/tutorials/general-introduction/tutorial.html |
|
Sequence composition calculation, Formatting, Sequencing quality control, Visualisation, De-novo assembly, Sequence assembly validation, Validation, Statistical calculation |
2017-05-23 |
2024-09-12 |
29 |
True |
True |
True |
True |
multiqc, velvetg, quast, fastq_paired_end_interlacer, fastqc, velveth |
Galaxy@AuBi, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr |
0 |
|
3068359 |
7881376 |
5.200000 |
0 |
|
Assembly |
Genome Assembly Quality Control |
https://training.galaxyproject.org//topics/assembly/tutorials/assembly-quality-control/tutorial.html |
Biodiversity, Sequence assembly, Data quality management |
Phasing, Genome assembly, Visualisation, De-novo assembly, k-mer counting, Sequence assembly validation, Scaffolding |
2022-08-26 |
2025-06-04 |
6 |
True |
True |
False |
True |
merqury, meryl, chromeister, busco, quast |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
2131904 |
4868891 |
4.400000 |
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 |
Sequence assembly visualisation, Filtering, Mapping assembly, Cross-assembly, Read mapping, Scatter plot plotting, Sequence composition calculation, Box-Whisker plot plotting, Sequence alignment, Genome assembly, Sequence contamination filtering, Sequencing quality control, Visualisation, De-novo assembly, Sequence assembly validation, Sequencing error detection, Statistical calculation |
2021-03-24 |
2024-11-29 |
15 |
True |
False |
False |
True |
nanoplot, polypolish, CONVERTER_bz2_to_uncompressed, flye, fastp, bwa_mem2, quast, bandage_image, porechop, upload1, fastqc, filtlong |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr |
0 |
|
10456 |
15680 |
3.416667 |
0 |
|
Assembly |
Large genome assembly and polishing |
https://training.galaxyproject.org//topics/assembly/tutorials/largegenome/tutorial.html |
Genomics, Sequence assembly, Biodiversity |
Sequence assembly visualisation, Mapping assembly, Cross-assembly, Sequence assembly, Scatter plot plotting, Sequence composition calculation, Box-Whisker plot plotting, Pairwise sequence alignment, Variant calling, Base-calling, Genome assembly, Sequencing quality control, Visualisation, De-novo assembly, Sequence assembly validation, Sequence contamination filtering, Validation, Statistical calculation |
2023-03-06 |
2025-06-04 |
14 |
True |
False |
True |
True |
minimap2, nanoplot, fastqc, medaka_consensus_pipeline, multiqc, barchart_gnuplot, flye, fastp, busco, meryl, racon, quast, genomescope, fasta-stats, bandage_image |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
7411 |
9616 |
2.000000 |
0 |
|
Assembly |
Hybrid genome assembly - Nanopore and Illumina |
https://training.galaxyproject.org//topics/assembly/tutorials/hybrid_denovo_assembly/tutorial.html |
|
Aggregation, Mapping assembly, Cross-assembly, Sequence assembly, Read mapping, Generation, Genome indexing, Genome assembly, Sequencing quality control, Analysis, Read alignment, Visualisation, De-novo assembly, Sequence assembly validation, Sequence alignment, Validation |
2025-11-03 |
2025-11-06 |
2 |
True |
False |
False |
True |
bwa_mem, multiqc, flye, busco, pilon, unicycler, quast |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
GalaxyTrakr, UseGalaxy.be, UseGalaxy.no |
0 |
|
105 |
143 |
3.133333 |
0 |
|
Assembly |
ERGA post-assembly QC |
https://training.galaxyproject.org//topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html |
Genomics, Sequence assembly, Biodiversity |
Sequence assembly visualisation, Sequence alignment analysis, Scaffolding, Pairwise sequence alignment, Data handling, Phasing, Genome assembly, Data parsing, Visualisation, Genotyping, De-novo assembly, k-mer counting, Sequence assembly validation, Data deposition, Sequence alignment, Sequence trimming |
2023-06-23 |
2025-06-04 |
8 |
True |
False |
True |
True |
gfastats, merqury, samtools_stats, bg_diamond, meryl, CONVERTER_gz_to_uncompressed, interactive_tool_blobtoolkit, pretext_map, pretext_snapshot, minimap2, blobtoolkit, bandage_image, bellerophon, bwa_mem2, smudgeplot, genomescope, __EXTRACT_DATASET__, collapse_dataset, busco, tp_find_and_replace |
UseGalaxy.eu |
UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
1974 |
2549 |
2.033333 |
0 |
|
Assembly |
Chloroplast genome assembly |
https://training.galaxyproject.org//topics/assembly/tutorials/chloroplast-assembly/tutorial.html |
|
Mapping assembly, Cross-assembly, Read mapping, Scatter plot plotting, Generation, Genome indexing, Genome assembly, Analysis, De-novo assembly, Coding region prediction, Sequence assembly visualisation, Genome visualisation, Sequence assembly, Gene prediction, Box-Whisker plot plotting, Genome annotation, Read alignment, Sequence alignment |
2020-12-04 |
2025-05-15 |
21 |
True |
False |
True |
True |
bwa_mem, nanoplot, flye, fasta-stats, pilon, prokka, bandage_info, upload1, jbrowse, bandage_image |
UseGalaxy.eu |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) |
0 |
|
8026 |
12480 |
2.816667 |
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 |
|
873 |
1062 |
1.900000 |
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_dustmasker_wrapper, tp_cat, Filter1, Cut1, gfastats, parse_mito_blast, tp_sed_tool, kraken2, ncbi_blastn_wrapper |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
1665 |
2058 |
2.466667 |
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 |
Sequence assembly visualisation, Read mapping, Sequence composition calculation, Genome assembly, Sequencing quality control, Visualisation, Sequence contamination filtering, Sequence assembly validation, Statistical calculation |
2021-03-24 |
2025-11-18 |
17 |
True |
False |
True |
True |
fastqc, fastp, quast, falco, shovill, bandage_info, upload1, bandage_image |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
|
0 |
|
10199 |
15673 |
3.566667 |
0 |
|
Assembly |
Assembly of metagenomic sequencing data |
https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html |
Metagenomics, Sequence assembly |
Read mapping, Sequence alignment analysis, Sequence file editing, Sequence composition calculation, Data handling, Genome assembly, Sequencing quality control, Read pre-processing, Sequence contamination filtering, Sequence trimming, Sequence assembly visualisation, Variant calling, Primer removal, Formatting, Visualisation, Local alignment, Sequence assembly validation, Statistical calculation |
2025-11-23 |
2025-11-23 |
0 |
True |
False |
True |
True |
tp_cat, filter_tabular, collection_column_join, cutadapt, megahit, coverm_contig, seqtk_subseq, metaspades, megahit_contig2fastg, random_lines1, ngsutils_bam_filter, quast, bandage_image, bandage_info, bg_uniq, bowtie2, bamtools, fastqc |
|
UseGalaxy.cz, UseGalaxy.eu |
0 |
|
2 |
2 |
0.000000 |
0 |
|
Assembly |
De Bruijn Graph Assembly |
https://training.galaxyproject.org//topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html |
|
Sequence assembly, Genome assembly, Optimisation and refinement |
2017-05-24 |
2024-02-01 |
25 |
True |
True |
False |
True |
velvetoptimiser, fasta-stats, spades |
Galaxy@AuBi, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
3039091 |
7833098 |
4.983333 |
0 |
|
Assembly |
Unicycler Assembly |
https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html |
Sequence assembly, Genomics, Microbiology |
Aggregation, Sequence composition calculation, Gene prediction, Genome assembly, Sequencing quality control, Genome annotation, Visualisation, Sequence assembly validation, Coding region prediction, Validation, Statistical calculation |
2017-10-11 |
2025-05-15 |
24 |
True |
True |
False |
True |
multiqc, prokka, unicycler, quast, fastqc |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
3045552 |
7844958 |
4.416667 |
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 |
|
Sequence assembly visualisation, Aggregation, Scatter plot plotting, Read mapping, Sequence file editing, Box-Whisker plot plotting, Pairwise sequence alignment, Data handling, Genome assembly, Sequencing quality control, Sequence contamination filtering, Validation |
2020-04-21 |
2025-05-15 |
14 |
True |
True |
True |
True |
fasta_filter_by_length, minimap2, nanoplot, __ZIP_COLLECTION__, samtools_stats, multiqc, samtools_fastx, fasterq_dump, collapse_dataset, fastp, seqtk_sample, unicycler, samtools_view, bandage_info, bowtie2, bandage_image |
UseGalaxy.eu, UseGalaxy.org.au |
Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) |
0 |
|
3038626 |
7832742 |
5.550000 |
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 |
Mapping, Scaffolding, Pairwise sequence alignment, Data handling, Primer removal, Phasing, Genome assembly, Read pre-processing, Visualisation, Read binning, De-novo assembly, k-mer counting, Sequence assembly validation, Sequence alignment, Sequence trimming |
2021-06-04 |
2025-06-04 |
57 |
True |
False |
True |
True |
cat1, gfastats, collection_column_join, merqury, cutadapt, meryl, Convert characters1, salsa, pretext_map, pretext_snapshot, minimap2, bionano_scaffold, gfa_to_fa, sort1, hifiasm, bellerophon, yahs, tp_grep_tool, Add_a_column1, bwa_mem2, tp_cut_tool, quast, purge_dups, genomescope, collapse_dataset, busco, tp_find_and_replace, bedtools_bamtobed |
|
UseGalaxy.cz |
0 |
|
15910 |
24005 |
1.966667 |
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 |
flye, gfa_to_fa, busco, quast, fasta-stats, hifiasm |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.no |
0 |
|
834 |
982 |
1.516667 |
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 |
Sequence assembly validation, Visualisation |
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.no, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
3528 |
4870 |
2.666667 |
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 visualisation, Genome visualisation, Mapping, Read mapping, Sequence alignment |
2018-06-14 |
2024-06-24 |
29 |
True |
False |
False |
True |
fasta_filter_by_length, cat1, bedtools_intersectbed, circos_interval_to_tiles, tp_replace_in_column, tp_sort_header_tool, addValue, bedtools_sortbed, upload1, tp_cat, circos_aln_to_links, Filter1, Cut1, tp_replace_in_line, mergeCols1, datamash_ops, lastz_wrapper_2, join1, random_lines1, tp_grep_tool, Grep1, tp_sed_tool, collapse_dataset, bedtools_complementbed, circos, fasta_compute_length, jbrowse |
|
|
0 |
|
6755 |
13007 |
2.933333 |
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 |
|
570631 |
1113779 |
1.516667 |
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 |
|
3011912 |
7754223 |
2.350000 |
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 |
|
2551138 |
6197705 |
2.283333 |
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 |
|
301 |
347 |
0.500000 |
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 |
|
2426098 |
5798350 |
4.216667 |
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 |
xarray_metadata_info, argo_getdata, timeseries_extraction, xarray_coords_info, interactive_tool_odv |
UseGalaxy.eu |
|
0 |
|
313 |
374 |
1.083333 |
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 |
xarray_metadata_info, __EXTRACT_DATASET__, __MERGE_COLLECTION__, xarray_mapplot, xarray_netcdf2netcdf, graphicsmagick_image_montage, regexColumn1, ggplot2_point, xarray_coords_info, xarray_select, climate_stripes |
UseGalaxy.eu, UseGalaxy.org (Main) |
UseGalaxy.cz |
0 |
|
2425873 |
5797837 |
5.033333 |
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 |
divand_full_analysis, interactive_tool_odv, interactive_tool_divand |
UseGalaxy.eu |
|
0 |
|
229 |
276 |
1.716667 |
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 |
tool_biogeochemical_calibration, harmonize_insitu_to_netcdf, tool_odv_history, tool_odv, interactive_tool_odv |
UseGalaxy.eu |
|
0 |
|
44 |
55 |
1.816667 |
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 |
interactive_tool_panoply, xarray_metadata_info, __EXTRACT_DATASET__, ctsm_fates, tp_find_and_replace, ggplot2_point, xarray_select |
UseGalaxy.eu, UseGalaxy.org (Main) |
|
0 |
|
3034134 |
7825098 |
4.150000 |
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 |
interactive_tool_panoply, datamash_ops, tp_awk_tool, cds_essential_variability, Grep1, ggplot2_point, psy_maps, climate_stripes |
UseGalaxy.eu |
|
0 |
|
1075 |
1483 |
1.266667 |
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 |
|
3032649 |
7822760 |
2.350000 |
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 |
|
415 |
500 |
1.150000 |
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 |
|
557 |
964 |
1.766667 |
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 |
obis_data, spocc_occ, argo_getdata, c3s |
UseGalaxy.eu |
|
0 |
|
108 |
142 |
2.133333 |
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 |
|
184 |
230 |
0.900000 |
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 |
|
6343 |
10318 |
0.800000 |
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 |
2025-11-04 |
3 |
True |
False |
False |
False |
|
|
|
0 |
|
33 |
35 |
0.250000 |
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 |
|
62 |
76 |
0.533333 |
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 |
2025-10-28 |
2 |
True |
False |
False |
False |
|
|
|
0 |
|
11 |
12 |
0.033333 |
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 |
|
46 |
61 |
7.966667 |
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 |
2025-10-28 |
5 |
True |
False |
False |
False |
|
|
|
0 |
|
94 |
118 |
2.333333 |
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 |
2025-10-28 |
2 |
True |
False |
False |
False |
|
|
|
0 |
|
19 |
21 |
2.550000 |
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 |
|
96 |
130 |
2.783333 |
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 |
|
121 |
134 |
1.866667 |
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 |
tp_cat, ctb_alignit, openbabel_addh, rdconf, split_file_to_collection, sort1 |
UseGalaxy.cz |
|
0 |
|
1263 |
1822 |
2.383333 |
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, chembl, ctb_im_rxn_maker, get_pdb, md_converter, openbabel_compound_convert, openbabel_svg_depiction |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.no |
0 |
|
458 |
548 |
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 |
chembl, get_pdb, prepare_box, fpocket, ctb_obgrep, ctb_filter, ctb_chemfp_nxn_clustering, ctb_compound_convert, ctb_remDuplicates, openbabel_svg_depiction, tp_cat, ctb_chemfp_mol2fps, tp_grep_tool, ctb_change_title, sdf_to_tab, ctb_remIons, ctb_chemfp_butina_clustering, collapse_dataset, openbabel_compound_convert, ctb_online_data_fetch, docking, tp_find_and_replace, prepare_receptor, ctb_np-likeness-calculator |
|
UseGalaxy.org (Main) |
0 |
|
19732 |
33650 |
1.600000 |
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_pca, bio3d_rmsd, bio3d_rmsf, mdanalysis_ramachandran_plot, mdanalysis_rdf, mdanalysis_distance, mdanalysis_cosine_analysis, mdanalysis_dihedral |
UseGalaxy.eu, UseGalaxy.org (Main) |
Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
32427 |
57453 |
1.233333 |
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 |
rdock_rbcavity, ctb_frankenstein_ligand, rdock_rbdock, enumerate_charges, sucos_max_score, collapse_dataset, rxdock_rbdock, openbabel_compound_convert, xchem_transfs_scoring, split_file_to_collection, rxdock_rbcavity, xchem_pose_scoring |
|
|
0 |
|
3194 |
5247 |
3.033333 |
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_editconf, gmx_em, get_pdb, gmx_setup, tp_grep_tool, gmx_solvate, gmx_sim |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no |
0 |
|
26776 |
47897 |
1.433333 |
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_pca, gmx_editconf, gmx_em, bio3d_rmsd, gmx_energy, bio3d_rmsf, get_pdb, md_converter, openbabel_compound_convert, gmx_merge_topology_files, gmx_setup, vmd_hbonds, tp_grep_tool, gmx_solvate, ambertools_acpype, gmx_sim, mdanalysis_cosine_analysis, bio3d_pca_visualize |
UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no |
0 |
|
10882 |
19083 |
2.416667 |
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_npt, namd_nvt, minimizer |
|
|
0 |
|
4225 |
7073 |
1.216667 |
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 |
|
1805 |
2430 |
1.633333 |
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 |
|
3032757 |
7822884 |
3.866667 |
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 |
|
3032649 |
7822761 |
2.350000 |
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 |
|
5421 |
6456 |
0.783333 |
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 |
|
288 |
585 |
1.066667 |
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 |
|
275 |
357 |
3.566667 |
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 |
|
686 |
1037 |
2.383333 |
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 |
|
80 |
97 |
2.300000 |
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 |
|
368 |
503 |
4.666667 |
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 |
|
300 |
458 |
2.383333 |
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 |
|
269 |
356 |
2.766667 |
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 |
|
66 |
108 |
0.700000 |
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 |
|
556 |
747 |
1.666667 |
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 |
|
1241 |
1699 |
0.550000 |
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 |
|
584 |
774 |
2.766667 |
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 |
|
39 |
44 |
0.583333 |
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 |
|
110 |
124 |
0.283333 |
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, Primer removal, Read pre-processing, Read mapping, Sequence file editing, Sequence trimming |
2018-06-20 |
2025-11-20 |
33 |
True |
False |
True |
True |
tp_cat, Filter1, Cut1, cutadapt, tp_sorted_uniq, bam_to_sam, seqtk_subseq, c3s, random_lines1, tp_sed_tool, tp_cut_tool, fastq_to_tabular, bowtie2 |
|
|
0 |
|
1796 |
2655 |
4.950000 |
0 |
|
Contributing to the Galaxy Training Material |
FAIR Galaxy Training Material |
https://training.galaxyproject.org//topics/contributing/tutorials/fair-gtn/tutorial.html |
|
|
2025-11-23 |
2025-11-23 |
0 |
True |
False |
False |
False |
|
|
|
0 |
|
0 |
0 |
0.000000 |
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 |
|
47 |
49 |
0.600000 |
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 |
|
44 |
44 |
0.083333 |
0 |
|
Contributing to the Galaxy Training Material |
Creating content in Markdown |
https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-content/tutorial.html |
|
Sequencing quality control, Validation |
2017-06-25 |
2025-04-08 |
85 |
True |
False |
False |
False |
upload1, multiqc |
|
|
0 |
|
3726 |
9735 |
2.083333 |
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 |
|
3032649 |
7822763 |
2.350000 |
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 |
|
106 |
125 |
3.816667 |
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 |
|
Sequencing quality control, Variant classification, Visualisation, Sequence contamination filtering, Read mapping, Tree-based sequence alignment, Validation |
2021-06-08 |
2025-11-21 |
10 |
True |
False |
True |
True |
compose_text_param, multiqc, bcftools_consensus, collapse_dataset, snpSift_filter, falco, pangolin, fastp |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr |
0 |
|
2889 |
3498 |
2.033333 |
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 |
|
2711857 |
6732283 |
3.666667 |
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 |
|
Variant calling, Tree-based sequence alignment, Methylation analysis, Variant classification |
2021-06-30 |
2025-03-28 |
18 |
True |
False |
True |
False |
fasta_regex_finder, Filter1, datamash_ops, nextclade, upload1, pangolin |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) |
|
0 |
|
7381 |
13208 |
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 |
|
Read mapping, Generation, Genome indexing, Sequence alignment, Data handling, Formatting, Sequencing quality control, Sequence contamination filtering, SNP detection, Validation |
2020-06-24 |
2024-06-14 |
16 |
True |
False |
True |
True |
bwa_mem, Filter1, lofreq_call, samtools_stats, multiqc, lofreq_viterbi, lofreq_indelqual, snpeff_sars_cov_2, Grep1, picard_MarkDuplicates, tp_cut_tool, snpSift_extractFields, fasterq_dump, fastp |
UseGalaxy.eu, UseGalaxy.org (Main) |
MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
13712 |
20617 |
2.883333 |
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 |
|
Data handling, Read mapping, Generation, Genome indexing, Sequence alignment, Sequence file editing |
2021-08-04 |
2023-11-09 |
5 |
True |
False |
False |
True |
__UNZIP_COLLECTION__, bwa_mem, samtools_fastx, trimmomatic, tp_replace_in_line, seqtk_subseq, Grep1, __ZIP_COLLECTION__ |
UseGalaxy.fr, UseGalaxy.org (Main) |
Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
4073 |
5778 |
2.416667 |
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 |
|
Data handling, SNP detection |
2021-05-31 |
2024-06-14 |
12 |
True |
True |
True |
False |
fastq_dump, tp_cat, query_tabular, jq, snpeff_sars_cov_2, fastq_to_fasta_python, fasterq_dump |
UseGalaxy.be, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no |
0 |
|
2813295 |
7068225 |
4.016667 |
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 |
|
Sequencing quality control, Genome visualisation, Read mapping, Generation, Sequence composition calculation, Genome indexing, Sequence alignment, Statistical calculation |
2023-07-10 |
2024-02-29 |
2 |
True |
False |
False |
False |
bwa_mem, jbrowse, fastqc |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz |
0 |
|
1265 |
1645 |
4.016667 |
0 |
|
Foundations of Data Science |
Data Manipulation Olympics |
https://training.galaxyproject.org//topics/data-science/tutorials/data-manipulation-olympics/tutorial.html |
|
|
2025-11-23 |
2025-11-23 |
0 |
True |
False |
False |
True |
cat1, {{version_paste}}, {{version_replace_text_line}}, {{version_filter}}, {{version_unique}}, tp_sort_header_tool, {{version_replace_text_column}}, tabular_to_csv, tp_split_on_column, Remove beginning1, {{version_split}}, Count1, {{version_cut_advanced}}, {{version_cut_columns}}, upload1, {{version_sort}}, tp_cat, Filter1, Cut1, {{version_join}}, tp_sorted_uniq, datamash_ops, {{version_datamash}}, join1, {{version_count}}, Add_a_column1, wc_gnu, {{version_wc}}, {{version_select_first}}, {{version_cat}}, {{version_remove_beginning}}, Grouping1, Show beginning1, {{version_compute}}, regexColumn1, {{version_remove_columns_by_header}} |
|
|
0 |
|
1 |
1 |
13.583333 |
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 |
|
1311925 |
2921735 |
2.716667 |
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, PhagePromotor, UseGalaxy.no |
0 |
|
1467595 |
3272102 |
4.783333 |
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 |
|
296 |
527 |
0.583333 |
0 |
|
Foundations of Data Science |
Python - Warm-up for statistics and machine learning |
https://training.galaxyproject.org//topics/data-science/tutorials/python-warmup-stat-ml/tutorial.html |
|
|
2025-03-11 |
2025-03-11 |
1 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
126 |
146 |
0.950000 |
0 |
|
Foundations of Data Science |
SQL with Python |
https://training.galaxyproject.org//topics/data-science/tutorials/sql-python/tutorial.html |
|
|
2021-10-11 |
2023-11-16 |
7 |
True |
False |
False |
False |
|
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Foundations of Data Science |
SQL Educational Game - Murder Mystery |
https://training.galaxyproject.org//topics/data-science/tutorials/sql-game/tutorial.html |
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2023-11-23 |
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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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2022-07-07 |
2023-10-23 |
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Foundations of Data Science |
Advanced CLI in Galaxy |
https://training.galaxyproject.org//topics/data-science/tutorials/cli-advanced/tutorial.html |
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2021-09-30 |
2024-10-15 |
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Foundations of Data Science |
Introduction to SQL |
https://training.galaxyproject.org//topics/data-science/tutorials/sql-basic/tutorial.html |
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2024-12-13 |
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Foundations of Data Science |
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https://training.galaxyproject.org//topics/data-science/tutorials/python-basics/tutorial.html |
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Foundations of Data Science |
CLI basics |
https://training.galaxyproject.org//topics/data-science/tutorials/cli-basics/tutorial.html |
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Foundations of Data Science |
One protein along the UniProt page |
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2024-12-05 |
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Foundations of Data Science |
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https://training.galaxyproject.org//topics/data-science/tutorials/python-math/tutorial.html |
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2023-02-13 |
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Foundations of Data Science |
Make & Snakemake |
https://training.galaxyproject.org//topics/data-science/tutorials/snakemake/tutorial.html |
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Foundations of Data Science |
CLI Educational Game - Bashcrawl |
https://training.galaxyproject.org//topics/data-science/tutorials/cli-bashcrawl/tutorial.html |
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2021-09-30 |
2024-10-15 |
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UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
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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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2022-06-16 |
2023-11-16 |
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Foundations of Data Science |
R basics in Galaxy |
https://training.galaxyproject.org//topics/data-science/tutorials/r-basics/tutorial.html |
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2019-10-08 |
2024-06-14 |
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Foundations of Data Science |
Advanced SQL |
https://training.galaxyproject.org//topics/data-science/tutorials/sql-advanced/tutorial.html |
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2021-10-11 |
2024-12-13 |
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UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
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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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2021-10-11 |
2023-11-16 |
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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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2023-06-16 |
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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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2024-10-15 |
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Foundations of Data Science |
Python - Functions |
https://training.galaxyproject.org//topics/data-science/tutorials/python-functions/tutorial.html |
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2022-04-25 |
2023-02-13 |
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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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2024-01-23 |
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UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
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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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2021-11-08 |
2024-10-15 |
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UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
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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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UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
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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 |
2024-02-20 |
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UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
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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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UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
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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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UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
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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 |
2024-05-07 |
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UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
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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 |
2024-05-07 |
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UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
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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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2024-02-06 |
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UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
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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 |
2024-06-25 |
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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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2024-02-13 |
2024-02-20 |
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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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2022-04-25 |
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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2022-04-25 |
2023-02-13 |
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Foundations of Data Science |
Data manipulation with Pandas |
https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture6/tutorial.html |
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2025-02-27 |
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Foundations of Data Science |
Versioning your code and data with git |
https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture7/tutorial.html |
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2024-03-12 |
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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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2022-04-25 |
2023-02-13 |
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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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2022-10-19 |
2023-05-18 |
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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 - Type annotations |
https://training.galaxyproject.org//topics/data-science/tutorials/python-typing/tutorial.html |
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2022-10-19 |
2023-02-13 |
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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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2022-10-19 |
2023-02-13 |
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UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
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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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527 |
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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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UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
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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 |
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3032649 |
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Galaxy Code Architecture |
https://training.galaxyproject.org//topics/dev/tutorials/architecture/slides.html |
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2017-06-20 |
2024-06-14 |
34 |
False |
True |
False |
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3032649 |
7822765 |
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Development in Galaxy |
Scripting Galaxy using the API and BioBlend |
https://training.galaxyproject.org//topics/dev/tutorials/bioblend-api/tutorial.html |
|
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2017-01-17 |
2023-11-16 |
22 |
True |
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True |
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3033382 |
7823721 |
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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 |
20 |
True |
True |
False |
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3033361 |
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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 |
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3032649 |
7822765 |
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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 |
14 |
False |
True |
False |
False |
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3032649 |
7822765 |
2.350000 |
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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 |
6 |
False |
True |
False |
False |
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3032649 |
7822765 |
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Development in Galaxy |
Generic plugins |
https://training.galaxyproject.org//topics/dev/tutorials/visualization-generic/tutorial.html |
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2016-09-30 |
2023-11-09 |
21 |
True |
True |
False |
False |
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3033003 |
7823270 |
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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 |
10 |
True |
True |
True |
False |
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0 |
|
2821015 |
7093516 |
4.700000 |
0 |
|
Development in Galaxy |
Galaxy Webhooks |
https://training.galaxyproject.org//topics/dev/tutorials/webhooks/tutorial.html |
|
|
2017-04-03 |
2025-04-08 |
16 |
True |
True |
False |
False |
|
|
|
0 |
|
3032844 |
7823024 |
3.650000 |
0 |
|
Development in Galaxy |
Tool Dependencies and Conda |
https://training.galaxyproject.org//topics/dev/tutorials/conda/slides.html |
|
|
2017-06-20 |
2023-04-14 |
33 |
False |
True |
False |
False |
|
|
|
0 |
|
3032649 |
7822765 |
2.350000 |
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 |
|
3032652 |
7822769 |
2.350000 |
0 |
|
Development in Galaxy |
Galaxy Interactive Tours |
https://training.galaxyproject.org//topics/dev/tutorials/interactive-tours/slides.html |
|
|
2017-01-12 |
2021-07-27 |
14 |
False |
True |
False |
False |
|
|
|
0 |
|
3032649 |
7822765 |
2.350000 |
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 |
|
420 |
504 |
1.500000 |
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 |
|
232 |
341 |
2.866667 |
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 |
|
1216 |
1616 |
2.766667 |
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 |
|
237 |
327 |
2.966667 |
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 |
|
2747 |
4435 |
2.550000 |
0 |
|
Development in Galaxy |
Debugging Galaxy |
https://training.galaxyproject.org//topics/dev/tutorials/debugging/tutorial.html |
|
|
2021-06-15 |
2025-11-05 |
15 |
True |
False |
False |
False |
|
|
|
0 |
|
595 |
1199 |
2.833333 |
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 |
|
271 |
324 |
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 |
2025-11-05 |
10 |
True |
False |
False |
False |
|
|
|
0 |
|
728 |
1089 |
2.633333 |
0 |
|
Development in Galaxy |
Writing Automated Tests for Galaxy |
https://training.galaxyproject.org//topics/dev/tutorials/writing_tests/tutorial.html |
|
|
2022-07-15 |
2025-11-05 |
6 |
True |
False |
False |
False |
|
|
|
0 |
|
273 |
701 |
2.100000 |
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 |
|
26 |
29 |
2.483333 |
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 |
diff, Remove beginning1, tp_replace_in_line, wordcloud, tp_grep_tool, tp_find_and_replace, wc_gnu |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
59 |
74 |
1.316667 |
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 |
diff, Filter1, Cut1, tp_replace_in_line, wordcloud, datamash_ops, Add_a_column1, sort1 |
|
UseGalaxy.cz |
0 |
|
154 |
181 |
1.566667 |
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 |
2025-10-21 |
2 |
True |
False |
False |
True |
param_value_from_file, compose_text_param, Cut1, Remove beginning1, wordcloud, barchart_gnuplot, datamash_ops, regexColumn1, interactive_tool_openrefine, tp_grep_tool, tp_head_tool, tp_sort_header_tool, filter_tabular |
UseGalaxy.eu |
|
0 |
|
21 |
25 |
0.000000 |
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 |
|
194 |
237 |
1.950000 |
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 |
phylo_index, phylogenetic_occupancy_matcher, crsconverter, estimate_endem |
UseGalaxy.eu |
|
0 |
|
79 |
104 |
0.983333 |
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_spectral_indices, srs_diversity_maps, srs_global_indices, srs_process_data, srs_preprocess_s2 |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr |
|
0 |
|
614 |
788 |
1.616667 |
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_cat, regex1, Filter1, mergeCols1, pampa_communitymetrics, datamash_transpose, pampa_presabs, pampa_glmsp, Count1, pampa_glmcomm, regexColumn1, pampa_plotglm, tp_easyjoin_tool, tp_cut_tool, tp_sort_header_tool |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au |
0 |
|
1098 |
1446 |
1.850000 |
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 |
|
890 |
1249 |
1.333333 |
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_ivr, cb_dissim, cb_eco, cb_qecb |
|
|
0 |
|
178 |
327 |
1.816667 |
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 |
Filter1, spocc_occ, tp_find_and_replace, tp_cut_tool, interactive_tool_wallace, tabular_to_csv |
UseGalaxy.eu, UseGalaxy.fr |
|
0 |
|
3192 |
4818 |
1.150000 |
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, xarray_mapplot, graphicsmagick_image_montage, xarray_coords_info, cdo_operations |
UseGalaxy.eu |
UseGalaxy.cz |
0 |
|
2381 |
2754 |
0.466667 |
0 |
|
Ecology |
RAD-Seq de-novo data analysis |
https://training.galaxyproject.org//topics/ecology/tutorials/de-novo-rad-seq/tutorial.html |
|
Data handling, Sequence composition calculation, Sequencing quality control, Statistical calculation |
2017-02-14 |
2025-06-03 |
14 |
True |
False |
False |
True |
stacks_populations, stacks_denovomap, stacks_procrad, fastqc |
UseGalaxy.be, UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
2689 |
4280 |
2.083333 |
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 |
tab2csv_R, mergeCols1, Filter1, Paste1, Remove beginning1, regionalgam_ab_index, regionalgam_plot_trend, Count1, tp_awk_tool, regexColumn1, regionalgam_gls, regionalgam_flight_curve, csv2tab_R, ggplot2_point, regionalgam_autocor_acf, flight-curve, regionalgam_glmmpql |
|
|
0 |
|
345 |
460 |
3.333333 |
0 |
|
Ecology |
Metabarcoding/eDNA through Obitools |
https://training.galaxyproject.org//topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html |
|
Sequence analysis, Sequence composition calculation, Sequencing quality control, Statistical calculation |
2022-02-28 |
2025-06-03 |
12 |
True |
False |
True |
True |
obi_tab, obi_annotate, Filter1, Cut1, unzip, obi_uniq, join1, obi_clean, obi_stat, ncbi_blastn_wrapper, obi_grep, seq_filter_by_id, obi_illumina_pairend, obi_ngsfilter, fastq_groomer, wc_gnu, fastqc |
UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr |
0 |
|
4518 |
6270 |
1.933333 |
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 |
obis_data, tp_cut_tool, obisindicators |
UseGalaxy.eu |
|
0 |
|
316 |
396 |
2.033333 |
0 |
|
Ecology |
Preparing genomic data for phylogeny reconstruction |
https://training.galaxyproject.org//topics/ecology/tutorials/phylogeny-data-prep/tutorial.html |
|
Sequence analysis, Genetic variation analysis, Genome annotation, Sequence clustering, Sequence assembly validation, Multiple sequence alignment |
2022-10-21 |
2025-06-03 |
5 |
True |
False |
False |
True |
regex1, phykit_alignment_based, Filter1, clipkit, tp_replace_in_line, repeatmasker_wrapper, glimmer_gbk_to_orf, collapse_dataset, proteinortho, busco, proteinortho_grab_proteins, clustalw, funannotate_predict |
|
|
0 |
|
2220 |
3060 |
2.750000 |
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 |
ecoregion_eco_map, mergeCols1, unzip, ecoregion_GeoNearestNeighbor, regexColumn1, interactive_tool_jupyter_notebook, ecoregion_taxa_seeker, ecoregion_brt_analysis, tp_cut_tool, ecoregion_cluster_estimate, ecoregion_clara_cluster, filter_tabular |
UseGalaxy.eu |
|
0 |
|
257 |
344 |
3.016667 |
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 |
ecoregion_eco_map, Filter1, unzip, column_remove_by_header, ecoregion_GeoNearestNeighbor, regexColumn1, ecoregion_taxa_seeker, ecoregion_brt_analysis, tp_cut_tool, WormsMeasurements, ClaraGuess |
UseGalaxy.eu |
|
0 |
|
41 |
44 |
2.183333 |
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 |
Cross-assembly, Taxonomic classification, Expression analysis, Statistical calculation |
2024-03-04 |
2024-06-27 |
4 |
True |
False |
False |
True |
est_abundance, recentrifuge, upload1, kraken2 |
UseGalaxy.eu, UseGalaxy.fr |
Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main) |
0 |
|
854 |
1140 |
3.266667 |
0 |
|
Ecology |
RAD-Seq Reference-based data analysis |
https://training.galaxyproject.org//topics/ecology/tutorials/ref-based-rad-seq/tutorial.html |
|
Read mapping, Generation, Genome indexing, Sequence composition calculation, Data handling, Sequencing quality control, Sequence alignment, Validation, Statistical calculation |
2017-02-14 |
2025-11-06 |
15 |
True |
False |
False |
True |
Filter1, Cut1, cat1, tp_replace_in_line, multiqc, bwa, regex_replace, Summary_Statistics1, bwa_wrapper, stacks_procrad, Count1, stacks_refmap, Convert characters1, stacks_populations, Grep1, tp_sort_header_tool, fastqc, addValue |
|
|
0 |
|
3144 |
4896 |
1.816667 |
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 |
|
108 |
116 |
1.616667 |
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 |
fastp, ncbi_blastn_wrapper, Count1, cshl_fastq_to_fasta |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.no |
0 |
|
453 |
568 |
0.716667 |
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 |
gdal_ogr2ogr, Filter1, spocc_occ, Summary_Statistics1, Count1 |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no |
|
0 |
|
650 |
805 |
0.916667 |
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 |
|
202 |
240 |
1.066667 |
0 |
|
Ecology |
Marine Omics identifying biosynthetic gene clusters |
https://training.galaxyproject.org//topics/ecology/tutorials/marine_omics_bgc/tutorial.html |
|
Sequence motif recognition, Protein feature detection, Genome annotation |
2024-08-19 |
2025-06-03 |
3 |
True |
False |
False |
True |
sanntis_marine, regex1, SanntiS_marine, interproscan, prodigal |
|
|
0 |
|
181 |
214 |
2.500000 |
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 |
ecology_link_between_var, Remove beginning1, tool_anonymization, ecology_presence_abs_abund, ecology_homogeneity_normality, regexColumn1, ecology_beta_diversity, tp_cut_tool, ecology_stat_presence_abs |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr |
0 |
|
1624 |
2265 |
2.683333 |
0 |
|
Ecology |
Data submission using ENA upload Tool |
https://training.galaxyproject.org//topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html |
|
Primer removal, Sequencing quality control, Read pre-processing, Visualisation, Validation, Read mapping, Sequence trimming |
2024-12-13 |
2025-03-20 |
2 |
True |
False |
False |
False |
regex1, __FILTER_EMPTY_DATASETS__, Paste1, cutadapt, multiqc, __RELABEL_FROM_FILE__, collection_element_identifiers, ab1_fastq_converter, ncbi_blastn_wrapper, fastq_to_fasta_python, falco, fastq_groomer, bg_uniq, fastq_filter |
UseGalaxy.eu |
UseGalaxy.cz |
0 |
|
239 |
249 |
0.566667 |
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 |
|
238 |
301 |
1.250000 |
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 |
2025-11-06 |
3 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
9 |
12 |
0.000000 |
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 |
|
156 |
188 |
0.816667 |
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 |
|
276 |
317 |
1.583333 |
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 |
|
584 |
740 |
1.483333 |
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 |
|
900 |
1089 |
1.666667 |
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 |
|
1924 |
2281 |
0.666667 |
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 |
|
96 |
111 |
1.233333 |
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 |
|
1611 |
1896 |
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 |
|
1266 |
1462 |
0.766667 |
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 |
|
539 |
629 |
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 |
|
648856 |
1305888 |
1.633333 |
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 |
|
150 |
174 |
2.400000 |
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 |
|
648857 |
1305891 |
2.266667 |
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 |
|
138 |
156 |
0.766667 |
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 |
|
30 |
32 |
0.016667 |
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 |
|
648889 |
1305936 |
3.033333 |
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 |
|
Pathway visualisation, Genome visualisation, Structure visualisation, Read mapping, Sequence composition calculation, Gene regulatory network analysis, Enrichment analysis, Primer removal, Sequencing quality control, Read pre-processing, Peak calling, Mapping, Sequence trimming, Statistical calculation |
2018-09-17 |
2025-04-08 |
14 |
True |
True |
False |
True |
deeptools_plot_correlation, trim_galore, Filter1, cat1, macs2_callpeak, deeptools_compute_matrix, deeptools_bam_compare, deeptools_bam_coverage, bbgtobigwig, jbrowse2, samtools_idxstats, bedtools_sortbed, deeptools_plot_fingerprint, deeptools_multi_bam_summary, bedtools_mergebed, deeptools_plot_heatmap, bowtie2, fastqc |
UseGalaxy.eu, UseGalaxy.org (Main) |
|
0 |
|
3038711 |
7834543 |
5.983333 |
0 |
|
Epigenetics |
CUT&RUN data analysis |
https://training.galaxyproject.org//topics/epigenetics/tutorials/cut_and_run/tutorial.html |
|
Peak calling, Read mapping, Sequence alignment analysis, Sequence trimming, Gene regulatory network analysis, Data handling, Primer removal, Enrichment analysis, Formatting, Sequencing quality control, Read pre-processing, Visualisation, Mapping, Validation |
2024-03-06 |
2025-03-19 |
5 |
True |
False |
False |
True |
bedtools_intersectbed, deeptools_compute_matrix, __FLATTEN__, trim_galore, multiqc, bamFilter, macs2_callpeak, datamash_transpose, pe_histogram, wig_to_bigWig, Grep1, falco, idr, bowtie2, __EXTRACT_DATASET__, Extract genomic DNA 1, bedtools_bamtobed, picard_MarkDuplicates, deeptools_plot_fingerprint, meme_chip, deeptools_plot_heatmap |
|
|
0 |
|
6120 |
7752 |
1.333333 |
0 |
|
Epigenetics |
ATAC-Seq data analysis |
https://training.galaxyproject.org//topics/epigenetics/tutorials/atac-seq/tutorial.html |
|
Peak calling, Read mapping, Sequence alignment analysis, Sequence composition calculation, Gene regulatory network analysis, Enrichment analysis, Primer removal, Formatting, Data handling, Sequencing quality control, Read pre-processing, Visualisation, Mapping, Sequence trimming, Statistical calculation |
2019-09-02 |
2024-08-08 |
23 |
True |
True |
True |
True |
Filter1, Cut1, pe_histogram, bedtools_intersectbed, cutadapt, wig_to_bigWig, pygenomeTracks, macs2_callpeak, deeptools_compute_matrix, Grep1, samtools_idxstats, bamFilter, picard_MarkDuplicates, bedtools_bamtobed, tp_sort_header_tool, deeptools_plot_heatmap, bowtie2, fastqc |
|
|
0 |
|
3096755 |
7937784 |
4.133333 |
0 |
|
Epigenetics |
Hi-C analysis of Drosophila melanogaster cells using HiCExplorer |
https://training.galaxyproject.org//topics/epigenetics/tutorials/hicexplorer/tutorial.html |
|
Formatting, Read mapping, Visualisation |
2018-02-23 |
2025-08-11 |
30 |
True |
False |
False |
True |
hicexplorer_hicinfo, hicexplorer_hicfindtads, hicexplorer_hicfindrestrictionsites, hicexplorer_hicpca, pygenomeTracks, hicexplorer_hicmergematrixbins, hicexplorer_hicbuildmatrix, hicexplorer_hicdetectloops, hicexplorer_hiccorrectmatrix, hicexplorer_hicplotmatrix, bowtie2 |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.no, UseGalaxy.org (Main) |
0 |
|
7478 |
12552 |
1.500000 |
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 |
|
Read mapping, Sequence composition calculation, Gene regulatory network analysis, Enrichment analysis, Primer removal, Sequencing quality control, Read pre-processing, Peak calling, Sequence trimming, Statistical calculation |
2017-09-18 |
2025-04-08 |
10 |
True |
False |
False |
True |
deeptools_plot_correlation, trim_galore, deeptools_compute_gc_bias, deeptools_compute_matrix, deeptools_bam_compare, bam_to_sam, deeptools_bam_coverage, macs2_callpeak, samtools_idxstats, deeptools_plot_fingerprint, deeptools_multi_bam_summary, deeptools_plot_heatmap, bowtie2, fastqc |
UseGalaxy.be |
Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
1928 |
2842 |
2.783333 |
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 |
Read mapping, Generation, Genome indexing, Gene regulatory network analysis, Sequence composition calculation, Enrichment analysis, Sequencing quality control, Peak calling, Mapping, Sequence alignment, Statistical calculation |
2016-12-20 |
2025-04-08 |
11 |
True |
False |
False |
True |
deeptools_plot_correlation, trimmomatic, bedtools_intersectbed, bwa, deeptools_compute_gc_bias, deeptools_compute_matrix, deeptools_bam_compare, samtools_idxstats, deeptools_correct_gc_bias, deeptools_plot_fingerprint, deeptools_multi_bam_summary, deeptools_plot_heatmap, macs2_callpeak, fastqc |
UseGalaxy.be, UseGalaxy.fr, UseGalaxy.org (Main) |
Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
7227 |
13223 |
3.300000 |
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 |
Cut1, Remove beginning1, minfi_analysis, chipeakanno_annopeaks, clusterprofiler_bitr, clusterprofiler_go |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no |
|
0 |
|
3034811 |
7826010 |
4.233333 |
0 |
|
Epigenetics |
DNA Methylation data analysis |
https://training.galaxyproject.org//topics/epigenetics/tutorials/methylation-seq/tutorial.html |
Epigenomics |
Sequencing quality control, Visualisation, Read mapping, Sequence composition calculation, Statistical calculation |
2017-02-16 |
2025-04-03 |
24 |
True |
False |
False |
True |
pileometh, metilene, wig_to_bigWig, replace_column_with_key_value_file, deeptools_compute_matrix, bwameth, tp_awk_tool, tp_tail_tool, deeptools_plot_profile, falco, fastqc |
|
|
0 |
|
14959 |
24893 |
2.033333 |
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 |
|
3032746 |
7822770 |
2.350000 |
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 |
|
3032746 |
7822770 |
2.350000 |
0 |
|
Evolution |
Phylogenetics - Back to basics |
https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo/tutorial.html |
|
Sequence analysis, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree generation (from molecular sequences), Phylogenetic tree reconstruction, Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic analysis, Multiple sequence alignment |
2024-05-10 |
2024-05-10 |
1 |
True |
False |
False |
True |
rbc_mafft, newick_display, iqtree, fasttree |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
4945 |
6385 |
1.900000 |
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 |
Phylogenetic tree generation, Antimicrobial resistance prediction, Variant calling, Phylogenetic tree visualisation |
2022-03-16 |
2025-05-26 |
13 |
True |
False |
False |
True |
clustering_from_distmat, snp_sites, tp_easyjoin_tool, samtools_view, snippy, bcftools_consensus, tb_variant_filter, upload1, addName, tp_cat, __MERGE_COLLECTION__, tp_replace_in_line, tp_grep_tool, Grep1, tp_sed_tool, trimmomatic, collapse_dataset, snp_dists, tb_profiler_profile |
UseGalaxy.eu |
|
0 |
|
2847 |
4068 |
2.750000 |
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 |
Phylogenetic tree analysis, Sequence analysis |
2022-03-16 |
2025-06-04 |
12 |
True |
False |
False |
True |
upload1, raxml, interactive_tool_rstudio |
UseGalaxy.eu |
|
0 |
|
2235 |
3211 |
2.283333 |
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 |
|
1111425 |
2444073 |
2.050000 |
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 (maximum likelihood and Bayesian methods), Phylogenetic tree generation (from molecular sequences) |
2025-03-14 |
2025-03-14 |
1 |
True |
False |
False |
False |
upload1, fasttree |
Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) |
GalaxyTrakr |
0 |
|
93 |
115 |
2.950000 |
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 |
|
1111425 |
2444073 |
2.050000 |
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 |
|
1111425 |
2444073 |
2.050000 |
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 |
|
1111425 |
2444073 |
2.050000 |
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 |
|
1111425 |
2444073 |
2.050000 |
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 |
|
1111425 |
2444073 |
2.050000 |
0 |
|
FAIR Data, Workflows, and Research |
Data management in Medicinal Chemistry |
https://training.galaxyproject.org//topics/fair/tutorials/med-chem-data/tutorial.html |
|
|
2025-11-23 |
2025-11-23 |
0 |
True |
False |
True |
True |
ctb_silicos_qed, chembl, ctb_im_rxn_maker, get_pdb, md_converter, openbabel_compound_convert, 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 |
|
798301 |
1674376 |
1.800000 |
0 |
|
FAIR Data, Workflows, and Research |
Uploading Data to Zenodo from Galaxy |
https://training.galaxyproject.org//topics/fair/tutorials/zenodo-in-galaxy/tutorial.html |
|
|
2025-11-06 |
2025-11-06 |
1 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
8 |
8 |
1.400000 |
0 |
|
FAIR Data, Workflows, and Research |
Integrating InvenioRDM-compatible Repositories with Galaxy |
https://training.galaxyproject.org//topics/fair/tutorials/inveniordm-integration/tutorial.html |
|
|
2025-11-06 |
2025-11-06 |
1 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
6 |
7 |
4.766667 |
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 |
|
596 |
784 |
1.666667 |
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 |
|
864 |
1109 |
1.700000 |
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 |
|
582 |
682 |
1.000000 |
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 |
|
98 |
129 |
2.150000 |
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 |
|
340 |
432 |
1.383333 |
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 |
|
146 |
162 |
0.533333 |
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 |
|
330 |
432 |
1.666667 |
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 |
|
859009 |
1818749 |
3.400000 |
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 |
|
372 |
461 |
2.633333 |
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 |
|
241 |
267 |
1.350000 |
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 |
|
273 |
332 |
2.333333 |
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 |
|
176 |
212 |
1.450000 |
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 |
|
152 |
186 |
2.366667 |
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 |
|
85 |
89 |
1.883333 |
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 |
|
365 |
421 |
1.183333 |
0 |
|
FAIR Data, Workflows, and Research |
FAIR Bioimage Metadata |
https://training.galaxyproject.org//topics/fair/tutorials/bioimage-metadata/tutorial.html |
|
|
2023-09-13 |
2025-11-21 |
5 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
287 |
345 |
2.450000 |
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 |
|
59 |
68 |
2.416667 |
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 |
|
48 |
56 |
3.916667 |
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 |
2025-11-21 |
7 |
True |
False |
True |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
279 |
316 |
2.133333 |
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 |
|
223 |
267 |
1.583333 |
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 |
|
255 |
312 |
1.300000 |
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 |
Cut1, Remove beginning1, tp_sorted_uniq, Grouping1, datamash_ops, ggplot2_point, csv_to_tabular, upload1 |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) |
Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz |
0 |
|
872 |
1206 |
2.800000 |
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, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
MISSISSIPPI |
0 |
|
5968 |
7429 |
2.983333 |
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 |
|
185 |
242 |
2.900000 |
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 |
|
1973 |
2514 |
2.283333 |
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 |
|
3032746 |
7822773 |
2.350000 |
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 |
|
2484911 |
5986793 |
2.283333 |
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 |
|
4686 |
6194 |
3.050000 |
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 |
|
2739 |
3696 |
3.266667 |
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 |
|
5132 |
7965 |
2.216667 |
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 |
|
187 |
215 |
1.666667 |
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 |
|
3028 |
3916 |
3.533333 |
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 |
|
2426 |
3208 |
2.383333 |
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 |
|
7415 |
9830 |
1.616667 |
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 |
|
795 |
1055 |
4.650000 |
0 |
|
Using Galaxy and Managing your Data |
Using dataset collections |
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/collections/tutorial.html |
|
Generation, Read mapping, Genome indexing, Sequence alignment |
2016-09-30 |
2024-12-05 |
20 |
True |
False |
True |
False |
lofreq_call, collapse_dataset, bwa_mem, snpSift_extractFields |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
15964 |
21829 |
3.000000 |
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 |
|
408 |
614 |
2.200000 |
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 |
|
Sequencing quality control, Visualisation, Read mapping, Validation |
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 |
GalaxyTrakr |
0 |
|
206 |
243 |
1.583333 |
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 |
|
2128 |
3407 |
2.816667 |
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 |
|
84 |
99 |
3.433333 |
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 |
|
130 |
171 |
3.550000 |
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 |
|
35 |
37 |
0.100000 |
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 |
|
1656 |
2211 |
2.750000 |
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 |
|
5496 |
7077 |
2.833333 |
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 |
|
267 |
321 |
2.400000 |
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 visualisation, Gene prediction, Genome annotation, Coding region prediction |
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 |
|
3051496 |
7854463 |
4.283333 |
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 |
chromeister, gecko, clustalw, tp_awk_tool |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz |
0 |
|
2988081 |
7662396 |
4.550000 |
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 |
Read mapping, Genome annotation, Antimicrobial resistance prediction, Genome visualisation |
2024-01-23 |
2025-06-10 |
9 |
True |
False |
True |
True |
bakta, tbl2gff3, staramr_search, Grep1, upload1, bowtie2, jbrowse |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr |
Galaxy@AuBi, UseGalaxy.org (Main) |
0 |
|
3448 |
4780 |
3.066667 |
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, Differential protein expression profiling, Genome annotation, Genome visualisation, Sequence assembly validation, Gene prediction, Sequence alignment |
2025-06-20 |
2025-06-25 |
2 |
True |
False |
False |
True |
omark, busco, rna_star, gffread, braker3, helixer, jbrowse |
|
|
0 |
|
341 |
411 |
1.750000 |
0 |
|
Genome Annotation |
Masking repeats with RepeatMasker |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/repeatmasker/tutorial.html |
Sequence composition, complexity and repeats, Genomics |
Repeat sequence detection, Genome annotation, Mapping, RNA-Seq analysis, Editing |
2021-11-29 |
2025-06-03 |
22 |
True |
False |
True |
True |
repeatmodeler, red, repeatmasker_wrapper, bedtools_maskfastabed |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
10046 |
12802 |
1.383333 |
0 |
|
Genome Annotation |
Secondary metabolite discovery |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html |
|
Data handling, Differential gene expression analysis, Sequence clustering, Gene prediction, Service invocation |
2024-02-21 |
2024-09-27 |
2 |
True |
False |
False |
True |
Remove beginning1, ctb_silicos_qed, ctb_simsearch, bp_genbank2gff3, collapse_dataset, ncbi_acc_download, tp_awk_tool, ctb_chemfp_mol2fps, interactive_tool_jupyter_notebook, edu.tamu.cpt.gff3.customGbkToGff, ctb_np-likeness-calculator, antismash, openbabel_remDuplicates |
UseGalaxy.eu |
|
0 |
|
658 |
831 |
1.283333 |
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 |
iframe, list_organism, create_or_update, create_account, jbrowse |
|
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no |
0 |
|
2807688 |
7046245 |
5.133333 |
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 |
Sequence annotation, Differential protein expression profiling, Genome annotation, Genome visualisation, Sequence assembly validation, Gene prediction, Sequence alignment |
2025-03-17 |
2025-06-20 |
4 |
True |
False |
False |
True |
omark, busco, rna_star, gffread, braker3, fasta-stats, jbrowse |
|
|
0 |
|
1338 |
1660 |
1.883333 |
0 |
|
Genome Annotation |
Genome annotation with Helixer |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/helixer/tutorial.html |
Biodiversity, Genomics, Zoology, Plant biology |
Sequence annotation, Differential protein expression profiling, Genome annotation, Genome visualisation, Sequence assembly validation, Gene prediction |
2024-08-21 |
2025-06-04 |
8 |
True |
False |
False |
True |
omark, busco, gffread, jcvi_gff_stats, helixer, jbrowse |
|
|
0 |
|
1208 |
1444 |
1.733333 |
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 |
Protein feature detection, Structural variation detection, Genome visualisation, Nucleic acid feature detection, Scaffolding, Sequence motif recognition, Genome assembly, Multilocus sequence typing, Genome annotation |
2024-02-01 |
2024-10-15 |
6 |
True |
False |
True |
True |
bakta, integron_finder, Grouping1, plasmidfinder, tp_tail_tool, tbl2gff3, tp_replace_in_column, upload1, jbrowse, isescan |
UseGalaxy.eu, UseGalaxy.fr |
Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main) |
0 |
|
6331 |
8580 |
2.633333 |
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 |
|
3032746 |
7822777 |
2.350000 |
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 |
|
35068 |
63897 |
1.450000 |
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 |
|
43 |
49 |
1.500000 |
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 |
Data handling, Data retrieval, Sequence database search |
2025-03-14 |
2025-03-14 |
1 |
True |
False |
False |
False |
Cut1, cat1, Remove beginning1, sort1, datasets_download_genome, bg_uniq, upload1 |
UseGalaxy.fr |
UseGalaxy.cz |
0 |
|
76 |
92 |
3.566667 |
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, Genome comparison, Sequencing quality control, Sequence composition calculation, Validation, Sequence assembly validation |
2025-03-14 |
2025-03-14 |
1 |
True |
False |
False |
False |
checkm2, drep_dereplicate, upload1 |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
GalaxyTrakr |
0 |
|
85 |
95 |
2.383333 |
0 |
|
Genome Annotation |
Bacterial pangenomics |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-pangenomics/tutorial.html |
Genomics, Microbiology |
Sequence assembly, Rarefaction, Genome annotation, Essential dynamics |
2025-03-14 |
2025-03-14 |
1 |
True |
False |
False |
False |
ppanggolin_all, upload1, ppanggolin_msa |
UseGalaxy.eu, UseGalaxy.fr |
|
0 |
|
87 |
100 |
0.966667 |
0 |
|
Genome Annotation |
Genome annotation with Funannotate |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/funannotate/tutorial.html |
Gene and protein families |
Sequence annotation, Protein feature detection, Information extraction, Genome visualisation, Fold recognition, Sequence motif recognition, Formatting, Query and retrieval, Genome annotation, Sequence assembly validation, Sequence alignment, Homology-based gene prediction |
2021-11-29 |
2025-06-10 |
26 |
True |
False |
True |
True |
interproscan, picard_MergeSamFiles, funannotate_predict, aegean_parseval, funannotate_annotate, busco, rna_star, eggnog_mapper, funannotate_compare, jbrowse |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
10675 |
15120 |
1.950000 |
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 |
Phylogenetic tree generation, Database search, De-novo assembly, Transcriptome assembly, Coding region prediction, Sequence alignment analysis, Multiple sequence alignment |
2022-09-08 |
2025-06-03 |
10 |
True |
False |
False |
True |
Filter1, Cut1, cat1, orfipy, bg_diamond_view, collapse_dataset, rbc_mafft, rapidnj, join1, bg_diamond, bg_diamond_makedb, gops_intersect_1, tab2fasta, regexColumn1, Add_a_column1, tp_split_on_column |
UseGalaxy.eu, UseGalaxy.org (Main) |
UseGalaxy.cz |
0 |
|
1844 |
2595 |
3.066667 |
0 |
|
Genome Annotation |
Genome annotation with Maker (short) |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html |
|
Sequence annotation, Sequence assembly validation, Genome annotation, Genome visualisation |
2021-01-12 |
2024-02-29 |
3 |
True |
False |
False |
True |
maker_map_ids, maker, busco, gffread, jcvi_gff_stats, fasta-stats, jbrowse |
|
UseGalaxy.be |
0 |
|
3962 |
5567 |
2.933333 |
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 |
Primer removal, Read pre-processing, Transposon prediction, Sequence trimming |
2019-07-02 |
2024-03-18 |
12 |
True |
True |
False |
True |
bg_find_subsequences, Filter1, Cut1, __EXTRACT_DATASET__, cutadapt, deeptools_bam_coverage, tp_easyjoin_tool, Add_a_column1, gff_to_prot, bowtie_wrapper, transit_gumbel, tp_sort_header_tool |
UseGalaxy.no, UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.eu |
0 |
|
3040998 |
7837718 |
4.100000 |
0 |
|
Genome Annotation |
Genome annotation with Maker |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html |
|
Sequence annotation, Genome annotation, Operation, Genome visualisation, Ab-initio gene prediction, Sequence assembly validation, Gene prediction, Homology-based gene prediction |
2018-09-24 |
2024-02-29 |
14 |
True |
False |
False |
True |
maker_map_ids, maker, busco, snap_training, augustus_training, gffread, jcvi_gff_stats, fasta-stats, jbrowse |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
13785 |
24388 |
1.850000 |
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 |
Protein feature detection, Information extraction, Fold recognition, Sequence alignment analysis, Sequence motif recognition, Query and retrieval, Genome annotation, Homology-based gene prediction |
2022-07-20 |
2025-06-03 |
12 |
True |
False |
False |
True |
interproscan, bg_diamond, ncbi_blastp_wrapper, eggnog_mapper |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.no |
0 |
|
4221 |
5668 |
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 |
create_or_update, iframe, jbrowse |
UseGalaxy.no |
UseGalaxy.cz, UseGalaxy.eu |
0 |
|
1445 |
2204 |
2.433333 |
0 |
|
Genome Annotation |
Long non-coding RNAs (lncRNAs) annotation with FEELnc |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/lncrna/tutorial.html |
|
Sequence annotation, Annotation, RNA-Seq analysis, Transcriptome assembly, Classification |
2022-09-23 |
2024-09-18 |
11 |
True |
False |
True |
True |
tp_cat, Extract_features1, stringtie, feelnc, gffread |
|
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
1895 |
2530 |
2.150000 |
0 |
|
Genome Annotation |
CRISPR screen analysis |
https://training.galaxyproject.org//topics/genome-annotation/tutorials/crispr-screen/tutorial.html |
|
Sequence composition calculation, Sequence trimming, Primer removal, Sequencing quality control, Read pre-processing, Genetic variation analysis, Validation, Statistical calculation |
2021-10-15 |
2024-08-08 |
12 |
True |
True |
True |
True |
cutadapt, multiqc, tp_awk_tool, mageck_mle, mageck_test, volcanoplot, mageck_count, fastqc |
UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no |
0 |
|
2640525 |
6458390 |
4.200000 |
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 |
Phylogenetic tree generation, Genome visualisation, Variant calling, Phylogenetic tree visualisation |
2018-02-26 |
2025-03-19 |
24 |
True |
False |
False |
True |
jbrowse, snippy |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) |
GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
15133 |
24176 |
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 |
|
3037865 |
7829664 |
4.666667 |
0 |
|
Imaging |
Using BioImage.IO models for image analysis in Galaxy |
https://training.galaxyproject.org//topics/imaging/tutorials/process-image-bioimageio/tutorial.html |
|
Data handling, Visualisation, Image annotation, Image analysis |
2025-04-09 |
2025-11-21 |
7 |
True |
False |
False |
True |
__EXTRACT_DATASET__, bioimage_inference, ip_threshold, image_math, ip_overlay_images, ip_split_image, ip_binary_to_labelimage |
UseGalaxy.eu |
|
0 |
|
177 |
214 |
3.300000 |
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 |
2025-11-21 |
5 |
True |
False |
False |
False |
omero_get_value, omero_get_id, omero_metadata_import, omero_roi_import, omero_filter, omero_import |
|
|
0 |
|
188 |
239 |
2.900000 |
0 |
|
Imaging |
Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy |
https://training.galaxyproject.org//topics/imaging/tutorials/parameter-tuning/tutorial.html |
|
Data handling, Visualisation, Image annotation, Image analysis |
2025-04-28 |
2025-11-21 |
2 |
True |
False |
False |
True |
param_value_from_file, collapse_dataset, ip_threshold, ip_filter_standard, ip_segmetrics, ip_histogram_equalization, tp_split_on_column |
UseGalaxy.eu |
UseGalaxy.cz |
0 |
|
87 |
100 |
1.966667 |
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 |
|
Data handling, Visualisation, Image annotation, Image analysis |
2025-03-20 |
2025-11-21 |
4 |
True |
False |
False |
True |
idr_download_by_ids, __EXTRACT_DATASET__, unzip, ip_histogram_equalization, ip_overlay_images, ip_points_to_label, ip_spot_detection_2d, ip_binary_to_labelimage |
UseGalaxy.cz, UseGalaxy.eu |
|
0 |
|
176 |
219 |
1.266667 |
0 |
|
Imaging |
Object tracking using CellProfiler |
https://training.galaxyproject.org//topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html |
|
Quantification, Parsing, Image analysis |
2021-03-17 |
2025-11-21 |
10 |
True |
False |
False |
True |
cp_color_to_gray, cp_export_to_spreadsheet, cp_measure_object_size_shape, unzip, cp_save_images, cp_track_objects, cp_overlay_outlines, cp_measure_object_intensity, cp_common, cp_cellprofiler, cp_tile, cp_identify_primary_objects |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
2177 |
2716 |
1.066667 |
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 |
|
Data handling, Visualisation, Image annotation, Image analysis |
2025-08-11 |
2025-11-21 |
2 |
True |
False |
False |
True |
__EXTRACT_DATASET__, graphicsmagick_image_convert, ip_points_to_label, ip_2d_feature_extraction, interactive_tool_qupath, ip_split_image, ip_imageinfo |
UseGalaxy.eu |
|
0 |
|
214 |
260 |
1.250000 |
0 |
|
Imaging |
Nucleoli segmentation and feature extraction using CellProfiler |
https://training.galaxyproject.org//topics/imaging/tutorials/tutorial-CP/tutorial.html |
|
Quantification, Parsing, Image analysis |
2020-07-01 |
2025-11-21 |
11 |
True |
True |
False |
True |
cp_display_data_on_image, cp_image_math, cp_gray_to_color, cp_measure_image_quality, cp_measure_granularity, cp_relate_objects, idr_download_by_ids, cp_export_to_spreadsheet, cp_cellprofiler, cp_enhance_or_suppress_features, cp_save_images, cp_measure_image_intensity, cp_measure_object_intensity, cp_measure_texture, cp_identify_primary_objects, cp_measure_image_area_occupied, cp_measure_object_size_shape, cp_mask_image, cp_convert_objects_to_image, cp_common |
UseGalaxy.be, UseGalaxy.eu |
Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
3036663 |
7828597 |
3.583333 |
0 |
|
Imaging |
Voronoi segmentation |
https://training.galaxyproject.org//topics/imaging/tutorials/voronoi-segmentation/tutorial.html |
|
Data handling, Visualisation, Image annotation, Image analysis |
2025-05-13 |
2025-11-21 |
6 |
True |
False |
False |
True |
colorize_labels, unzip, repeat_channels, ip_convertimage, ip_threshold, image_math, ip_overlay_images, ip_filter_standard, ip_count_objects, voronoi_tessellation, ip_2d_feature_extraction, ip_imageinfo, ip_binary_to_labelimage |
UseGalaxy.eu |
|
0 |
|
264 |
403 |
3.783333 |
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 |
2025-11-21 |
4 |
True |
False |
False |
True |
ip_spot_detection_2d, ip_curve_fitting, ip_points_association_nn |
UseGalaxy.cz, UseGalaxy.eu |
|
0 |
|
160 |
186 |
1.183333 |
0 |
|
Imaging |
Introduction to Image Analysis using Galaxy |
https://training.galaxyproject.org//topics/imaging/tutorials/imaging-introduction/tutorial.html |
|
Image analysis, Data handling, Visualisation, Image annotation |
2019-08-13 |
2025-11-21 |
16 |
True |
False |
False |
True |
unzip, ip_histogram_equalization, ip_threshold, ip_overlay_images, ip_filter_standard, ip_count_objects, ip_imageinfo, ip_binary_to_labelimage |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au |
|
0 |
|
2659 |
3716 |
1.733333 |
0 |
|
Imaging |
Training Custom YOLO Models for Segmentation of Bioimages |
https://training.galaxyproject.org//topics/imaging/tutorials/yolo-segmentation-training/tutorial.html |
|
Data handling, Image analysis, Visualisation, Image annotation |
2025-07-25 |
2025-11-21 |
6 |
True |
False |
False |
True |
unzip, interactive_tool_anylabeling, graphicsmagick_image_convert, json2yolosegment, yolo_training, ip_histogram_equalization |
UseGalaxy.eu |
|
0 |
|
214 |
272 |
1.266667 |
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 |
2025-11-21 |
8 |
True |
False |
False |
True |
unet_coreograph, celesta, palom, gate_finder, ashlar, basic_illumination, ip_convertimage, vitessce_spatial, scanpy_compute_graph, scimap_mcmicro_to_anndata, quantification, mesmer, rename_tiff_channels, squidpy_spatial, scimap_phenotyping |
|
|
0 |
|
1421 |
1913 |
1.816667 |
0 |
|
Imaging |
Analyse HeLa fluorescence siRNA screen |
https://training.galaxyproject.org//topics/imaging/tutorials/hela-screen-analysis/tutorial.html |
|
Image analysis, Data handling, Visualisation, Image annotation |
2019-08-13 |
2025-11-21 |
14 |
True |
False |
False |
True |
unzip, collapse_dataset, ip_threshold, ip_filter_standard, ip_2d_feature_extraction, ip_2d_filter_segmentation_by_features, ip_binary_to_labelimage |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.no |
0 |
|
776 |
999 |
2.050000 |
0 |
|
Imaging |
FAIR Bioimage Metadata |
https://training.galaxyproject.org//topics/imaging/tutorials/bioimage-metadata/tutorial.html |
|
|
2025-11-23 |
2025-11-23 |
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 |
|
|
2025-11-23 |
2025-11-23 |
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 |
2025-11-05 |
66 |
True |
False |
True |
True |
Cut1, Grouping1, gops_intersect_1, tp_tail_tool, tp_replace_in_column, Add_a_column1, get_flanks1, CONVERTER_interval_to_bed_0, tp_sort_header_tool, upload1 |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.no |
0 |
|
20401 |
33564 |
3.300000 |
0 |
|
Introduction to Galaxy Analyses |
NGS data logistics |
https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html |
|
SNP detection, Read mapping, Generation, Genome indexing, Data handling, Formatting, Sequencing quality control, Sequence contamination filtering, Sequence alignment, Validation |
2017-02-22 |
2025-07-24 |
38 |
True |
False |
True |
True |
snpSift_extractFields, bwa_mem, Filter1, lofreq_call, samtools_stats, multiqc, bwa, collapse_dataset, lofreq_viterbi, snpEff, lofreq_indelqual, snpeff_sars_cov_2, bwa_mem2, samtools_view, picard_MarkDuplicates, snpEff_build_gb, fasterq_dump, fastp |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
MISSISSIPPI, UseGalaxy.cz |
0 |
|
20201 |
34454 |
3.416667 |
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 |
Cut1, Remove beginning1, tp_sorted_uniq, Grouping1, datamash_ops, ggplot2_point, csv_to_tabular, upload1 |
Galaxy@AuBi, UseGalaxy.eu, UseGalaxy.org (Main) |
MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
2185 |
2914 |
4.050000 |
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 |
cat1, {{version_paste}}, {{version_replace_text_line}}, {{version_filter}}, {{version_unique}}, tp_sort_header_tool, {{version_replace_text_column}}, tabular_to_csv, tp_split_on_column, Remove beginning1, {{version_split}}, Count1, {{version_cut_advanced}}, {{version_cut_columns}}, upload1, {{version_sort}}, tp_cat, Filter1, Cut1, {{version_join}}, tp_sorted_uniq, datamash_ops, {{version_datamash}}, join1, {{version_count}}, Add_a_column1, wc_gnu, {{version_wc}}, {{version_select_first}}, {{version_cat}}, {{version_remove_beginning}}, Grouping1, Show beginning1, {{version_compute}}, regexColumn1, {{version_remove_columns_by_header}} |
|
|
0 |
|
5944 |
8649 |
3.416667 |
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 |
tp_cat, Filter1, cat1, gops_intersect_1, gene2exon1 |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
MISSISSIPPI |
0 |
|
20185 |
31866 |
3.566667 |
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 |
|
3032865 |
7823034 |
2.350000 |
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 |
|
3032865 |
7823034 |
2.350000 |
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 |
|
8084 |
11398 |
1.466667 |
0 |
|
Introduction to Galaxy Analyses |
Best Practices for Citing Galaxy |
https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-cite/tutorial.html |
|
|
2025-11-06 |
2025-11-06 |
1 |
True |
False |
False |
False |
|
|
UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr |
0 |
|
21 |
23 |
0.033333 |
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 |
|
441 |
502 |
2.716667 |
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, Sequencing quality control, Statistical calculation |
2018-08-27 |
2025-11-17 |
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 |
|
3086947 |
7907222 |
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 |
2025-11-06 |
35 |
True |
False |
True |
True |
Cut1, Remove beginning1, tp_sorted_uniq, Grouping1, datamash_ops, ggplot2_point, csv_to_tabular, upload1 |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) |
Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz |
0 |
|
23056 |
36538 |
3.933333 |
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, datamash_ops, tp_head_tool, upload1, tp_sort_header_tool, comp1 |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
Galaxy@AuBi, MISSISSIPPI, UseGalaxy.no |
0 |
|
48236 |
77811 |
3.433333 |
0 |
|
Introduction to Galaxy Analyses |
Very Short Introductions: QC |
https://training.galaxyproject.org//topics/introduction/tutorials/vsi_qc/tutorial.html |
|
Sequence contamination filtering, Sequencing quality control, Validation |
2024-03-26 |
2024-06-25 |
4 |
True |
False |
False |
False |
multiqc, fastp |
Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
GalaxyTrakr, MISSISSIPPI, UseGalaxy.no |
0 |
|
316 |
382 |
2.966667 |
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 |
|
269 |
350 |
1.916667 |
0 |
|
Metabolomics |
Mass spectrometry: LC-MS analysis |
https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms/tutorial.html |
|
Label-free quantification, Chromatographic alignment, Peak detection, Mass spectrum visualisation, Chromatogram visualisation, Data filtering, Validation |
2019-07-02 |
2025-09-21 |
13 |
True |
False |
False |
True |
xcms_export_samplemetadata, abims_xcms_retcor, xcms_plot_chromatogram, abims_CAMERA_annotateDiffreport, abims_xcms_fillPeaks, Batch_correction, abims_xcms_xcmsSet, generic_filter, msnbase_readmsdata, abims_xcms_group, wsdl_hmdb, quality_metrics, Univariate, xcms_merge |
|
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
12743 |
20782 |
1.583333 |
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 |
|
Label-free quantification, Filtering, Peak detection, Correlation, Format validation, Chromatogram visualisation, Standardisation and normalisation, Data filtering, Validation, Chromatographic alignment, Imputation, Spectral library search, Clustering, Mass spectrum visualisation, Formatting |
2023-05-08 |
2023-11-09 |
5 |
True |
False |
False |
True |
matchms_similarity, matchms_filtering, ramclustr_define_experiment, riassigner, abims_xcms_retcor, ramclustr, msconvert, abims_xcms_fillPeaks, abims_xcms_xcmsSet, msnbase_readmsdata, matchms_formatter, abims_xcms_group, waveica, xcms_merge |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au |
0 |
|
2696 |
3466 |
1.483333 |
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_filtering, Filter1, cardinal_mz_images, cardinal_spectra_plots, cardinal_data_exporter, cardinal_quality_report |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
3006 |
4268 |
1.750000 |
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 |
param_value_from_file, tp_cat, qcxms_production_run, qcxms_getres, openbabel_compound_convert, qcxms_neutral_run, split_file_to_collection, xtb_molecular_optimization, tp_cut_tool, __FILTER_FAILED_DATASETS__, ctb_im_conformers |
UseGalaxy.eu |
UseGalaxy.org.au |
0 |
|
896844 |
1934119 |
2.850000 |
0 |
|
Metabolomics |
Molecular formula assignment and mass recalibration with MFAssignR package |
https://training.galaxyproject.org//topics/metabolomics/tutorials/mfassignr/tutorial.html |
|
Annotation, Mass spectra calibration, Visualisation, Deisotoping |
2025-05-19 |
2025-05-19 |
1 |
True |
False |
False |
True |
mfassignr_histnoise, mfassignr_snplot, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_isofiltr, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_findRecalSeries |
|
|
0 |
|
112 |
133 |
2.050000 |
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 |
join_files_on_column_fuzzy, cardinal_classification, Filter1, cardinal_preprocessing, Summary_Statistics1, maldi_quant_preprocessing, cardinal_mz_images, maldi_quant_peak_detection, Grep1, cardinal_combine, cardinal_segmentations, cardinal_quality_report |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
1974 |
2827 |
1.833333 |
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 |
|
3032865 |
7823035 |
2.350000 |
0 |
|
Metabolomics |
Mass spectrometry: LC-MS preprocessing with XCMS |
https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html |
|
Label-free quantification, Chromatographic alignment, Peak detection, Mass spectrum visualisation, Chromatogram visualisation, Data filtering, Validation |
2020-02-04 |
2024-10-15 |
14 |
True |
True |
False |
False |
xcms_export_samplemetadata, abims_xcms_retcor, abims_CAMERA_annotateDiffreport, abims_xcms_fillPeaks, abims_xcms_xcmsSet, msnbase_readmsdata, abims_xcms_summary, abims_xcms_group, intens_check, idchoice, xcms_plot_chromatogram, xcms_merge |
UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no |
0 |
|
3038964 |
7832620 |
4.633333 |
0 |
|
Metabolomics |
Mass spectrometry: GC-MS analysis with the metaMS package |
https://training.galaxyproject.org//topics/metabolomics/tutorials/gcms/tutorial.html |
|
Label-free quantification, Chromatographic alignment, Peak detection, Mass spectrum visualisation, Chromatogram visualisation, Data filtering, Validation |
2021-09-22 |
2025-10-01 |
8 |
True |
False |
False |
False |
xcms_export_samplemetadata, metams_runGC, abims_xcms_fillPeaks, abims_xcms_xcmsSet, msnbase_readmsdata, abims_xcms_group, xcms_plot_chromatogram, xcms_merge |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.no |
0 |
|
1565 |
2494 |
1.683333 |
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 |
Batch_correction, generic_filter, Multivariate, intens_check, quality_metrics, normalization |
UseGalaxy.fr |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no |
0 |
|
2838 |
3824 |
1.916667 |
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 |
|
3032865 |
7823038 |
2.350000 |
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 |
DNA barcoding, Sequence clustering, Sequencing quality control, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequence read processing |
2017-06-22 |
2024-08-09 |
4 |
True |
False |
False |
True |
mothur_screen_seqs, metaphlan2, humann2, mothur_unique_seqs, mothur_align_seqs, mothur_count_seqs, mothur_filter_seqs, mothur_pre_cluster, krona-text, metaphlan2krona, humann2_renorm_table, mothur_classify_otu, mothur_summary_seqs, humann2_regroup_table, mothur_make_biom, mothur_classify_seqs, mothur_make_shared, mothur_make_group, taxonomy_krona_chart, mothur_merge_files, mothur_cluster_split |
|
UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
8546 |
11657 |
2.716667 |
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 |
Sequence assembly visualisation, Aggregation, Antimicrobial resistance prediction, Mapping assembly, Scatter plot plotting, Box-Whisker plot plotting, Pairwise sequence alignment, Sequence analysis, Genome assembly, De-novo assembly |
2019-06-25 |
2024-06-14 |
4 |
True |
False |
True |
True |
minimap2, nanoplot, gfa_to_fa, PlasFlow, staramr_search, unicycler, racon, miniasm, bandage_image |
UseGalaxy.eu |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
3210 |
4491 |
3.016667 |
0 |
|
Microbiome |
MGnify v5.0 Amplicon Pipeline |
https://training.galaxyproject.org//topics/microbiome/tutorials/mgnify-amplicon/tutorial.html |
Metagenomics, Taxonomy, Sequence analysis |
DNA barcoding, Sequence composition calculation, Nucleic acid design, Sequencing quality control, Analysis, Read pre-processing, Mapping, Sequence contamination filtering, Validation, Alignment, Sequence trimming, Sequence feature detection, Nucleic acid feature detection, Comparison, Formatting, Visualisation, k-mer counting, Statistical calculation |
2025-07-30 |
2025-11-18 |
3 |
True |
False |
False |
True |
collection_column_join, ampvis2_heatmap, lotus2, mgnify_seqprep, CONVERTER_gz_to_uncompressed, cshl_fasta_formatter, gops_concat_1, mapseq, __UNZIP_COLLECTION__, param_value_from_file, fastq_dl, multiqc, fastq_to_fasta_python, filter_tabular, fastq_filter, fastqc, __MERGE_COLLECTION__, infernal_cmsearch, query_tabular, CONVERTER_uncompressed_to_gz, bedtools_getfastabed, bedtools_maskfastabed, collection_element_identifiers, biom_convert, Add_a_column1, ampvis2_load, wc_gnu, fastp, __FILTER_FROM_FILE__, __FILTER_EMPTY_DATASETS__, trimmomatic, Grouping1, collapse_dataset, taxonomy_krona_chart, tp_awk_tool, seqprep, cmsearch_deoverlap, prinseq, tp_find_and_replace |
|
|
0 |
|
152 |
187 |
3.033333 |
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 |
Aggregation, Mapping assembly, Cross-assembly, Phylogenetic tree reconstruction, Antimicrobial resistance prediction, Phylogenetic tree analysis, Scatter plot plotting, Sequence alignment analysis, Sequence composition calculation, Phylogenetic tree generation (from molecular sequences), Pairwise sequence alignment, Multiple sequence alignment, Data handling, Genome assembly, Sequencing quality control, Mapping, De-novo assembly, Phylogenetic tree generation, Sequence contamination filtering, Validation, Sequence assembly visualisation, Sequence assembly, Box-Whisker plot plotting, Variant calling, Multilocus sequence typing, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Base-calling, Visualisation, Taxonomic classification, Statistical calculation |
2023-01-26 |
2025-11-18 |
12 |
True |
False |
True |
True |
compose_text_param, collection_column_join, krakentools_extract_kraken_reads, barchart_gnuplot, flye, fasta_merge_files_and_filter_unique_sequences, krakentools_kreport2krona, bamtools_split_mapped, CONVERTER_gz_to_uncompressed, mlst, tp_replace_in_column, fasta2tab, kraken2, table_compute, clair3, tp_split_on_column, param_value_from_file, minimap2, Remove beginning1, nanoplot, samtools_fastx, multiqc, bcftools_consensus, tp_multijoin_tool, Count1, snpSift_filter, split_file_to_collection, tp_head_tool, __FILTER_FAILED_DATASETS__, __BUILD_LIST__, add_line_to_file, porechop, snpSift_extractFields, fastqc, bandage_image, samtools_depth, Cut1, Paste1, fasttree, tp_sorted_uniq, newick_display, tab2fasta, bedtools_getfastabed, collection_element_identifiers, Grep1, Add_a_column1, tp_cut_tool, clustalw, ggplot2_heatmap, fastp, regex1, __FILTER_EMPTY_DATASETS__, medaka_consensus_pipeline, abricate, samtools_coverage, Grouping1, bcftools_norm, collapse_dataset, taxonomy_krona_chart, regexColumn1, tp_find_and_replace |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
4763 |
7158 |
3.383333 |
0 |
|
Microbiome |
Clinical Metaproteomics 2: Discovery |
https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html |
|
Protein quantification, Filtering, Imputation, Clustering, Principal component plotting, Formatting, Visualisation, Standardisation and normalisation, Heat map generation, Statistical calculation |
2025-11-23 |
2025-11-23 |
0 |
True |
False |
True |
True |
tp_cat, maxquant, Filter1, Cut1, Remove beginning1, fasta_cli, fasta_merge_files_and_filter_unique_sequences, ident_params, Grouping1, peptide_shaker, msconvert, dbbuilder, query_tabular, Grep1, fasta2tab, filter_tabular, search_gui |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
0 |
0 |
0.000000 |
0 |
|
Microbiome |
Clinical Metaproteomics 4: Quantitation |
https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-4-quantitation/tutorial.html |
|
Protein quantification, Imputation, Clustering, Principal component plotting, Visualisation, Standardisation and normalisation, Heat map generation, Statistical calculation |
2025-11-23 |
2025-11-23 |
0 |
True |
False |
True |
True |
Grouping1, maxquant, Cut1, Grep1 |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
0 |
0 |
0.000000 |
0 |
|
Microbiome |
Calculating α and β diversity from microbiome taxonomic data |
https://training.galaxyproject.org//topics/microbiome/tutorials/diversity/tutorial.html |
|
Aggregation, Visualisation |
2024-08-01 |
2025-06-17 |
7 |
True |
False |
True |
True |
krakentools_beta_diversity, krakentools_alpha_diversity |
Galaxy@Pasteur, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, GalaxyTrakr |
0 |
|
6518 |
7848 |
1.250000 |
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 |
Aggregation, Genome annotation, Visualisation, Taxonomic classification, Statistical calculation |
2023-05-03 |
2025-04-24 |
6 |
True |
False |
True |
True |
est_abundance, __UNZIP_COLLECTION__, kraken_biom, krakentools_kreport2krona, interactive_tool_pavian, taxonomy_krona_chart, kraken2, metaphlan, interactive_tool_phinch |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
11988 |
15994 |
2.000000 |
0 |
|
Microbiome |
Assembly of metagenomic sequencing data |
https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html |
Metagenomics, Sequence assembly |
Read mapping, Sequence alignment analysis, Sequence file editing, Sequence composition calculation, Data handling, Genome assembly, Sequencing quality control, Read pre-processing, Sequence contamination filtering, Sequence trimming, Sequence assembly visualisation, Variant calling, Primer removal, Formatting, Visualisation, Local alignment, Sequence assembly validation, Statistical calculation |
2022-12-05 |
2025-06-16 |
6 |
True |
False |
True |
True |
tp_cat, filter_tabular, collection_column_join, cutadapt, megahit, coverm_contig, seqtk_subseq, metaspades, megahit_contig2fastg, random_lines1, ngsutils_bam_filter, quast, bandage_image, bandage_info, bg_uniq, bowtie2, bamtools, fastqc |
|
UseGalaxy.cz, UseGalaxy.eu |
0 |
|
4316 |
6024 |
3.050000 |
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 |
Variant calling, DNA barcoding, Analysis, Visualisation, Deposition |
2024-06-05 |
2025-07-03 |
11 |
True |
False |
True |
True |
cat1, __SORTLIST__, dada2_plotQualityProfile, dada2_mergePairs, dada2_makeSequenceTable, tp_replace_in_column, __UNZIP_COLLECTION__, tp_head_tool, dada2_assignTaxonomyAddspecies, tp_replace_in_line, dada2_removeBimeraDenovo, collection_element_identifiers, dada2_filterAndTrim, dada2_seqCounts, Add_a_column1, interactive_tool_phyloseq, dada2_dada, Grouping1, phyloseq_from_dada2, dada2_learnErrors |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
6768 |
9536 |
2.333333 |
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 |
|
690 |
872 |
1.650000 |
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 |
2025-11-23 |
2025-11-23 |
0 |
True |
False |
True |
True |
unipept, msstatstmt, Grep1 |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
0 |
0 |
0.000000 |
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 |
Sequencing quality control, Visualisation, Taxonomic classification, Sequence contamination filtering, Sequence composition calculation, Validation, Statistical calculation |
2020-11-24 |
2024-07-31 |
5 |
True |
False |
False |
True |
Remove beginning1, tp_replace_in_line, multiqc, taxonomy_krona_chart, fastp, datamash_reverse, kraken2, porechop, fastqc |
UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr |
0 |
|
8024 |
11082 |
2.600000 |
0 |
|
Microbiome |
Clinical Metaproteomics 3: Verification |
https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html |
|
|
2025-11-23 |
2025-11-23 |
0 |
True |
False |
True |
True |
tp_cat, Filter1, Cut1, Remove beginning1, pepquery2, fasta_merge_files_and_filter_unique_sequences, uniprotxml_downloader, Grouping1, collapse_dataset, dbbuilder, query_tabular |
UseGalaxy.cz, UseGalaxy.eu |
UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
0 |
0 |
0.000000 |
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 |
Sequencing quality control, Aggregation, Visualisation, Taxonomic classification, Sequence contamination filtering, Sequence composition calculation, Statistical calculation |
2022-09-29 |
2024-11-29 |
5 |
True |
False |
True |
True |
Filter1, fastqc, krakentools_kreport2krona, taxonomy_krona_chart, kraken2, porechop, fastp |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
2607 |
3759 |
2.783333 |
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 |
minimap2, Cut1, cat1, Filter1, tp_sorted_uniq, Grouping1, CONVERTER_fasta_to_tabular, join1, count_gff_features, tp_tail_tool, tab2fasta, histogram_rpy, tp_replace_in_column, add_column_headers, Add_a_column1, sort1, ggplot2_histogram, MQoutputfilter |
UseGalaxy.fr |
|
0 |
|
288 |
332 |
0.883333 |
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 |
Phylogenetic inference, Phylogenetic tree editing, Phylogenetic tree visualisation, Sequence composition calculation, Sequence alignment analysis, Sequence comparison, Species frequency estimation, Sequencing quality control, Read pre-processing, Sequence similarity search, Validation, Sequence trimming, Primer removal, Conversion, Taxonomic classification, Visualisation, Phylogenetic analysis, Statistical calculation |
2020-02-13 |
2025-06-16 |
6 |
True |
False |
True |
True |
humann_unpack_pathways, combine_metaphlan2_humann2, cutadapt, tp_sort_header_tool, humann_split_stratified_table, humann_regroup_table, multiqc, humann, humann_renorm_table, fastq_paired_end_interlacer, fastqc, Cut1, humann_rename_table, Grep1, metaphlan, export2graphlan, graphlan_annotate, taxonomy_krona_chart, graphlan, bg_sortmerna, tp_find_and_replace |
UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.no |
0 |
|
757 |
980 |
2.500000 |
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 |
Aggregation, Phylogenetic inference, Phylogenetic tree editing, Phylogenetic tree visualisation, Sequence composition calculation, Sequence alignment analysis, Sequence comparison, Species frequency estimation, Sequencing quality control, Read pre-processing, Sequence similarity search, Validation, Sequence trimming, Primer removal, Conversion, Taxonomic classification, Visualisation, Phylogenetic analysis, Statistical calculation |
2019-11-21 |
2025-06-16 |
6 |
True |
True |
True |
True |
humann_unpack_pathways, cutadapt, tp_sort_header_tool, humann_split_stratified_table, humann_regroup_table, multiqc, humann, humann_renorm_table, fastq_paired_end_interlacer, fastqc, Cut1, humann_rename_table, combine_metaphlan_humann, Grep1, metaphlan, export2graphlan, graphlan_annotate, Grouping1, taxonomy_krona_chart, graphlan, bg_sortmerna, tp_find_and_replace |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.eu |
0 |
|
3039422 |
7831559 |
4.266667 |
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, Target-Decoy, Protein identification, Expression analysis, de Novo sequencing |
2025-11-23 |
2025-11-23 |
0 |
True |
False |
True |
True |
uniprotxml_downloader, dbbuilder, metanovo, fasta_merge_files_and_filter_unique_sequences |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.org (Main) |
0 |
|
0 |
0 |
0.000000 |
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 |
|
45 |
53 |
2.950000 |
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 |
|
409 |
660 |
3.150000 |
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, Sequencing quality control, Sequence composition calculation, Validation, Sequence assembly validation |
2023-12-05 |
2025-05-15 |
6 |
True |
False |
True |
False |
megahit, checkm_lineage_wf |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr |
UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
5465 |
6685 |
1.500000 |
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 |
|
572 |
880 |
2.783333 |
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 |
DNA barcoding, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree analysis, Sequencing quality control, Visualisation, Taxonomic classification, Phylogenetic tree generation, Phylogenetic analysis, Sequence read processing |
2019-05-13 |
2024-06-14 |
5 |
True |
False |
True |
True |
mothur_screen_seqs, XY_Plot_1, mothur_unique_seqs, mothur_heatmap_sim, mothur_sub_sample, mothur_count_seqs, mothur_filter_seqs, mothur_count_groups, mothur_remove_groups, mothur_pre_cluster, mothur_dist_seqs, mothur_venn, mothur_chimera_vsearch, mothur_classify_otu, mothur_remove_lineage, mothur_remove_seqs, mothur_summary_seqs, mothur_tree_shared, newick_display, mothur_summary_single, mothur_classify_seqs, mothur_dist_shared, mothur_make_shared, collapse_dataset, mothur_rarefaction_single, mothur_cluster, mothur_cluster_split |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr |
0 |
|
5346 |
9019 |
4.633333 |
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 |
DNA barcoding, Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic tree analysis, Sequencing quality control, Visualisation, Taxonomic classification, Phylogenetic tree generation, Phylogenetic analysis, Sequence read processing |
2017-02-12 |
2024-03-14 |
4 |
True |
False |
False |
True |
mothur_screen_seqs, XY_Plot_1, mothur_unique_seqs, mothur_align_seqs, mothur_heatmap_sim, mothur_sub_sample, mothur_count_seqs, mothur_filter_seqs, mothur_count_groups, mothur_pre_cluster, mothur_remove_groups, mothur_dist_seqs, mothur_venn, mothur_chimera_vsearch, mothur_classify_otu, mothur_remove_lineage, mothur_remove_seqs, mothur_summary_seqs, mothur_make_biom, mothur_tree_shared, mothur_seq_error, mothur_taxonomy_to_krona, mothur_summary_single, newick_display, mothur_classify_seqs, mothur_get_groups, mothur_dist_shared, mothur_make_shared, mothur_cluster_split, taxonomy_krona_chart, mothur_rarefaction_single, mothur_cluster, mothur_make_contigs |
UseGalaxy.be, UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
11988 |
17623 |
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 |
|
Read mapping, Generation, Genome indexing, Sequence alignment analysis, Multiple sequence alignment, Primer removal, Sequence analysis, Sequence contamination filtering, Sequencing quality control, Local alignment, Global alignment, Sequence alignment |
2023-05-15 |
2024-03-20 |
4 |
True |
False |
False |
True |
compose_text_param, rbc_mafft, samtools_view, param_value_from_file, fatovcf, __APPLY_RULES__, upload1, fasta_regex_finder, bwa_mem, Cut1, ivar_trim, datamash_ops, qualimap_bamqc, Grep1, Add_a_column1, EMBOSS: maskseq51, fastp, ivar_consensus, mimodd_info, samtools_merge, fasta_compute_length, __ZIP_COLLECTION__ |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.org (Main) |
0 |
|
1038 |
1229 |
2.316667 |
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 |
Antimicrobial resistance prediction, Genome visualisation, Phylogenetic tree visualisation, Local alignment, Sequence composition calculation, Sequence alignment analysis, Global alignment, Variant calling, Sequence analysis, Sequence contamination filtering, Sequencing quality control, Taxonomic classification, Phylogenetic tree generation, Sequence alignment, Validation, Statistical calculation |
2020-07-25 |
2025-11-18 |
31 |
True |
False |
True |
True |
samtools_stats, tbvcfreport, kraken2, EMBOSS:%20seqret84, __FLATTEN__, snippy, multiqc, bcftools_consensus, tb_variant_filter, jvarkit_wgscoverageplotter, upload1, fastqc, EMBOSS: seqret84, qualimap_bamqc, tp_sed_tool, fastp, mosdepth, tp_awk_tool, tb_profiler_profile, jbrowse |
|
|
0 |
|
7478 |
11563 |
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 |
|
Data retrieval, Read mapping, Generation, Genome indexing, Sequence file editing, Sequence alignment analysis, Multiple sequence alignment, Data handling, Primer removal, Sequence analysis, Sequence contamination filtering, Sequencing quality control, De-novo assembly, Phylogenetic analysis, Sequence alignment |
2022-11-21 |
2024-10-04 |
10 |
True |
False |
False |
False |
bwa_mem, __RELABEL_FROM_FILE__, ivar_consensus, collapse_dataset, seqtk_subseq, iqtree, Show beginning1, bamtools_split_ref, rbc_mafft, qualimap_bamqc, vapor, Grep1, tp_find_and_replace, samtools_view, upload1, fastp |
UseGalaxy.eu, UseGalaxy.org (Main) |
UseGalaxy.cz |
0 |
|
2049 |
2981 |
3.016667 |
0 |
|
Transcriptomics |
Whole transcriptome analysis of Arabidopsis thaliana |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html |
|
Differential gene expression analysis, RNA-Seq analysis, Read mapping, Sequence composition calculation, Sequence trimming, Primer removal, Gene expression analysis, Sequencing quality control, Read pre-processing, Visualisation, RNA-Seq quantification, Validation |
2021-04-08 |
2025-08-10 |
18 |
True |
True |
True |
True |
trim_galore, Filter1, Cut1, cat1, __MERGE_COLLECTION__, multiqc, salmon, sample_seqs, rbc_mirdeep2_mapper, targetfinder, deseq2, sort1, rbc_mirdeep2_quantifier, falco, filter_by_fasta_ids |
UseGalaxy.cz |
|
0 |
|
2893446 |
7319880 |
4.916667 |
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 |
|
Sequence analysis, Phylogenetic tree editing, Phylogenetic analysis, Phylogenetic inference (from molecular sequences), Multiple sequence alignment |
2025-03-26 |
2025-04-27 |
2 |
True |
False |
True |
True |
Filter1, Cut1, Remove beginning1, trimal, rbc_mafft, tapscan_classify, iqtree, ete_treeviewer, quicktree, filter_by_fasta_ids |
UseGalaxy.eu |
|
0 |
|
226 |
276 |
1.083333 |
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, bg_diamond, ncbi_blastp_wrapper |
Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.no |
0 |
|
1623 |
2049 |
3.000000 |
0 |
|
Single Cell |
Analysis of plant scRNA-Seq Data with Scanpy |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-plant/tutorial.html |
|
Differential gene expression analysis, Principal component visualisation, Expression profile clustering |
2021-04-08 |
2025-02-13 |
7 |
True |
False |
True |
True |
scanpy_inspect, anndata_manipulate, scanpy_plot, anndata_import, scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_normalize, scanpy_remove_confounders |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
2728 |
3415 |
1.616667 |
0 |
|
Proteomics |
Statistical analysis of DIA data |
https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.html |
|
Tag-based peptide identification, Differential protein expression profiling, Spectrum calculation |
2020-12-02 |
2023-11-09 |
9 |
True |
False |
False |
True |
histogram_rpy, msstats, Filter1, Grep1 |
UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
1342 |
1877 |
2.583333 |
0 |
|
Proteomics |
Neoantigen 5b: IEDB binding Validated Neopeptides |
https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-hla-binding-novel-peptides/tutorial.html |
|
|
2025-01-14 |
2025-11-14 |
3 |
True |
False |
False |
True |
Filter1, Cut1, Remove beginning1, pepquery2, query_tabular, iedb_api, table_compute |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
55 |
58 |
0.600000 |
0 |
|
Proteomics |
Proteogenomics 2: Database Search |
https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html |
|
Peptide database search, Conversion |
2018-11-20 |
2025-05-08 |
24 |
True |
False |
True |
True |
ident_params, search_gui, peptide_shaker, mz_to_sqlite, query_tabular, tab2fasta |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
1533 |
2279 |
4.750000 |
0 |
|
Proteomics |
Library Generation for DIA Analysis |
https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html |
|
Protein quantification, Imputation, Clustering, Principal component plotting, Visualisation, Standardisation and normalisation, Heat map generation, Statistical calculation |
2020-12-02 |
2025-06-02 |
12 |
True |
False |
False |
True |
maxquant, Filter1, OpenSwathAssayGenerator, OpenSwathDecoyGenerator, TargetedFileConverter, diapysef |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
4573 |
5979 |
1.366667 |
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 |
peptide_genomic_coordinate, query_tabular, ncbi_blastp_wrapper, pep_pointer |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.no |
0 |
|
1665 |
2396 |
2.616667 |
0 |
|
Proteomics |
metaQuantome 3: Taxonomy |
https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html |
Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy |
Filtering, Indexing, Statistical inference, Query and retrieval, Quantification, Heat map generation, Principal component visualisation, Differential protein expression analysis, Functional clustering, Visualisation |
2020-10-29 |
2024-03-15 |
14 |
True |
False |
False |
True |
metaquantome_viz, metaquantome_sample, metaquantome_stat, metaquantome_db, metaquantome_expand, metaquantome_filter |
UseGalaxy.be, UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
447 |
585 |
2.266667 |
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 |
2025-11-06 |
2 |
True |
False |
False |
True |
regex1, arriba_get_filters, query_tabular, tab2fasta, tp_awk_tool, CONVERTER_gz_to_uncompressed, rna_star, arriba |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
141 |
169 |
0.800000 |
0 |
|
Proteomics |
Neoantigen 2: Database merge and FragPipe discovery |
https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.html |
|
|
2025-01-14 |
2025-11-06 |
2 |
True |
False |
False |
True |
Remove beginning1, fasta_merge_files_and_filter_unique_sequences, collapse_dataset, fragpipe, fragpipe_manifest_generator, query_tabular, Grep1, validate_fasta_database |
UseGalaxy.eu, UseGalaxy.org (Main) |
UseGalaxy.org.au |
0 |
|
167 |
195 |
1.283333 |
0 |
|
Proteomics |
Clinical Metaproteomics 2: Discovery |
https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html |
|
Protein quantification, Filtering, Imputation, Clustering, Principal component plotting, Formatting, Visualisation, Standardisation and normalisation, Heat map generation, Statistical calculation |
2024-02-06 |
2025-08-10 |
5 |
True |
False |
True |
True |
tp_cat, maxquant, Filter1, Cut1, Remove beginning1, fasta_cli, fasta_merge_files_and_filter_unique_sequences, ident_params, Grouping1, peptide_shaker, msconvert, dbbuilder, query_tabular, Grep1, fasta2tab, filter_tabular, search_gui |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
342 |
456 |
6.650000 |
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 |
FeatureFinderMultiplex, IDFilter, IDMapper, IDMerger, FileFilter, MzTabExporter, FileMerger, PeptideIndexer, ConsensusID, FalseDiscoveryRate, MSGFPlusAdapter, HighResPrecursorMassCorrector, IDConflictResolver |
|
|
0 |
|
856 |
1179 |
1.416667 |
0 |
|
Proteomics |
Proteogenomics 1: Database Creation |
https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html |
|
Variant calling, Sequence annotation, RNA-Seq analysis, Transcriptome assembly, Sequence alignment, Statistical calculation |
2018-11-20 |
2025-05-08 |
29 |
True |
False |
True |
True |
gffcompare_to_bed, fasta_merge_files_and_filter_unique_sequences, cat_multi_datasets, stringtie, custom_pro_db, bed_to_protein_map, tab2fasta, freebayes, regexColumn1, hisat2, tp_replace_in_column, translate_bed, query_tabular, fasta2tab, sqlite_to_tabular, filter_tabular, gffcompare |
UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
5849 |
9570 |
2.600000 |
0 |
|
Proteomics |
Neoantigen 5a: Predicting HLA Binding |
https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-predicting-hla-binding/tutorial.html |
|
Read mapping, Genetic variation analysis |
2025-01-14 |
2025-11-06 |
2 |
True |
False |
False |
True |
seq2hla, optitype, query_tabular, tp_awk_tool |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
62 |
67 |
0.033333 |
0 |
|
Proteomics |
Clinical Metaproteomics 4: Quantitation |
https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.html |
|
Protein quantification, Imputation, Clustering, Principal component plotting, Visualisation, Standardisation and normalisation, Heat map generation, Statistical calculation |
2024-02-06 |
2025-08-10 |
5 |
True |
False |
True |
True |
Grouping1, maxquant, Cut1, Grep1 |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
178 |
244 |
3.100000 |
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 |
tp_sort_header_tool, Grep1, cardinal_quality_report, cardinal_data_exporter |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
2734 |
4228 |
1.683333 |
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 |
fasta_merge_files_and_filter_unique_sequences, dbbuilder, tab2fasta, DecoyDatabase, fasta2tab, addValue |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) |
0 |
|
4782 |
7604 |
2.166667 |
0 |
|
Proteomics |
Label-free data analysis using MaxQuant |
https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-label-free/tutorial.html |
|
Protein quantification, Tag-based peptide identification, Imputation, Spectrum calculation, Clustering, Principal component plotting, Differential protein expression profiling, Visualisation, Standardisation and normalisation, Heat map generation, Statistical calculation |
2020-04-29 |
2025-05-21 |
14 |
True |
False |
False |
True |
maxquant, Filter1, Cut1, msstats, histogram_rpy, Grep1, Add_a_column1, tp_sort_header_tool |
UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
19940 |
29143 |
1.766667 |
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_basic_plots, pdaug_ml_models, pdaug_sequence_property_based_descriptors, pdaug_addclasslabel, pdaug_merge_dataframes |
UseGalaxy.be |
|
0 |
|
1026 |
1528 |
2.200000 |
0 |
|
Proteomics |
Neoantigen 4: Variant Annotation |
https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-variant-annotation/tutorial.html |
|
|
2025-01-14 |
2025-11-14 |
3 |
True |
False |
False |
True |
column_regex_find_and_replace, query_tabular, tab2fasta, Convert characters1, regexColumn1, concatenate, select, cut, pep_pointer |
|
|
0 |
|
76 |
91 |
1.250000 |
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 |
Jvenn, retrieve_from_hpa, prot_features, rna_abbased_data, retr_pepatlas1, MQoutputfilter, IDconverter, tp_cut_tool |
|
UseGalaxy.be, UseGalaxy.fr |
0 |
|
1675 |
2275 |
2.500000 |
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 |
|
Protein quantification, Tag-based peptide identification, Imputation, Spectrum calculation, Clustering, Principal component plotting, Differential protein expression profiling, Visualisation, Standardisation and normalisation, Heat map generation, Statistical calculation |
2021-02-17 |
2025-09-22 |
19 |
True |
False |
True |
True |
maxquant, Filter1, Cut1, Summary_Statistics1, datamash_ops, msstats, tp_easyjoin_tool, tp_replace_in_column, Grep1, fasta2tab, uniprot, ggplot2_heatmap2 |
|
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
8482 |
13658 |
2.666667 |
0 |
|
Proteomics |
Neoantigen 3: PepQuery2 Verification |
https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-peptide-verification/tutorial.html |
|
Formatting, Filtering |
2025-01-14 |
2025-11-06 |
2 |
True |
False |
False |
True |
pepquery2, ncbi_blastp_wrapper, msconvert, query_tabular, tab2fasta |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
56 |
64 |
2.016667 |
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 |
Jvenn, cluter_profiler, retrieve_from_hpa, rna_abbased_data, MQoutputfilter, IDconverter, reactome_analysis |
|
UseGalaxy.be, UseGalaxy.fr |
0 |
|
3068 |
4458 |
2.766667 |
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 |
OpenSwathWorkflow, pyprophet_score, msconvert, pyprophet_peptide, pyprophet_protein, pyprophet_export, Grep1, pyprophet_merge |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
3202 |
4560 |
2.516667 |
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 |
encyclopedia_quantify, msconvert, encyclopedia_searchtolib |
|
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
1996 |
2717 |
1.766667 |
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 |
search_gui, PeakPickerHiRes, peptide_shaker, Grep1, FileConverter |
|
|
0 |
|
3126 |
5001 |
1.883333 |
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 |
FileInfo, PeakPickerHiRes, IDFilter, XTandemAdapter, msconvert, IDMerger, TextExporter, FidoAdapter, Grep1, PeptideIndexer, ConsensusID, FalseDiscoveryRate, IDPosteriorErrorProbability, MSGFPlusAdapter, IDScoreSwitcher |
|
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
3529 |
5934 |
2.883333 |
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 |
unipept, msstatstmt, Grep1 |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
275 |
365 |
2.750000 |
0 |
|
Proteomics |
Neoantigen 1b: Non-Reference-Database-Generation |
https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html |
|
Sequence annotation, Variant calling, RNA-Seq analysis, Transcriptome assembly, Sequence alignment, Statistical calculation |
2025-01-14 |
2025-11-14 |
4 |
True |
False |
False |
True |
fasta_merge_files_and_filter_unique_sequences, custom_pro_db, CONVERTER_gz_to_uncompressed, fasta2tab, sqlite_to_tabular, gffcompare, filter_tabular, column_regex_find_and_replace, tp_cat, stringtie, bed_to_protein_map, tab2fasta, query_tabular, gffcompare_to_bed, freebayes, regexColumn1, hisat2, translate_bed, concatenate |
|
|
0 |
|
77 |
85 |
0.416667 |
0 |
|
Proteomics |
Multiomics data analysis using MultiGSEA |
https://training.galaxyproject.org//topics/proteomics/tutorials/multiGSEA-tutorial/tutorial.html |
|
Pathway analysis, Aggregation, Gene-set enrichment analysis |
2025-03-10 |
2025-03-11 |
2 |
True |
False |
False |
True |
Filter1, multigsea, tp_grep_tool |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
271 |
295 |
1.550000 |
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 |
search_gui, peptide_shaker, unipept, query_tabular, sqlite_to_tabular |
UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz |
0 |
|
2903 |
4617 |
2.716667 |
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 |
tp_cat, Filter1, Cut1, Remove beginning1, pepquery2, fasta_merge_files_and_filter_unique_sequences, uniprotxml_downloader, Grouping1, collapse_dataset, dbbuilder, query_tabular |
UseGalaxy.cz, UseGalaxy.eu |
UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
198 |
264 |
4.366667 |
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 |
FileInfo, FeatureFinderMultiplex, XTandemAdapter, IDMapper, Summary_Statistics1, tp_tail_tool, histogram_rpy, TextExporter, Grep1, FidoAdapter, PeptideIndexer, MultiplexResolver, FalseDiscoveryRate, IDPosteriorErrorProbability, ProteinQuantifier, IDScoreSwitcher, IDConflictResolver |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
1351 |
1890 |
1.566667 |
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_basic_plots, pdaug_sequence_property_based_descriptors, pdaug_peptide_data_access, pdaug_addclasslabel, pdaug_tsvtofasta, pdaug_merge_dataframes, pdaug_peptide_sequence_analysis |
UseGalaxy.be |
|
0 |
|
736 |
1000 |
2.366667 |
0 |
|
Proteomics |
MaxQuant and MSstats for the analysis of TMT data |
https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.html |
|
Protein quantification, Imputation, Clustering, Principal component plotting, Visualisation, Standardisation and normalisation, Heat map generation, Statistical calculation |
2021-08-13 |
2025-01-08 |
11 |
True |
False |
False |
True |
maxquant, msstatstmt |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.org (Main) |
0 |
|
4265 |
5699 |
1.633333 |
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 |
wolf_psort, Filter1, tp_sorted_uniq, get_subontology_from, Convert characters1, tp_easyjoin_tool, Grep1, term_id_vs_term_name, tp_cut_tool, uniprot, bg_uniq, comp1 |
|
|
0 |
|
649 |
968 |
1.483333 |
0 |
|
Proteomics |
metaQuantome 2: Function |
https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html |
Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics |
Filtering, Indexing, Statistical inference, Query and retrieval, Quantification, Heat map generation, Principal component visualisation, Differential protein expression analysis, Functional clustering, Visualisation |
2020-10-29 |
2024-03-15 |
14 |
True |
False |
False |
True |
metaquantome_viz, metaquantome_sample, metaquantome_stat, metaquantome_db, metaquantome_expand, metaquantome_filter |
UseGalaxy.be, UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
416 |
587 |
4.233333 |
0 |
|
Proteomics |
metaQuantome 1: Data creation |
https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html |
Proteomics, Proteogenomics, Biodiversity, Taxonomy |
Label-free quantification, Formatting, Filtering, Visualisation, Prediction and recognition |
2020-10-16 |
2024-03-14 |
20 |
True |
False |
False |
True |
regex1, flashlfq, Filter1, Cut1, Remove beginning1, tp_replace_in_line, peptide_shaker, search_gui, unipept, msconvert, query_tabular, tp_replace_in_column, Grep1 |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
887 |
1501 |
3.750000 |
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 |
|
207 |
261 |
1.116667 |
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, Target-Decoy, Protein identification, Expression analysis, de Novo sequencing |
2024-02-06 |
2025-07-30 |
7 |
True |
False |
True |
True |
uniprotxml_downloader, dbbuilder, metanovo, fasta_merge_files_and_filter_unique_sequences |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.org (Main) |
0 |
|
586 |
885 |
3.950000 |
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 |
|
3032865 |
7823043 |
2.350000 |
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 |
|
7656 |
12371 |
0.900000 |
0 |
|
Sequence analysis |
Mapping |
https://training.galaxyproject.org//topics/sequence-analysis/tutorials/mapping/tutorial.html |
Mapping |
Genome visualisation, Read mapping, Sequence alignment analysis, Sequence composition calculation, Sequence trimming, Data handling, Primer removal, Sequencing quality control, Read pre-processing, Validation, Statistical calculation |
2016-10-04 |
2025-03-31 |
43 |
True |
True |
True |
True |
trim_galore, samtools_stats, multiqc, bamFilter, bowtie2, jbrowse, fastqc |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
3098106 |
7932617 |
5.083333 |
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 |
|
DNA barcoding, Sequence clustering, Sequence file editing, Demultiplexing, Data handling, Sequencing quality control, Visualisation, Taxonomic classification, Sequence read processing, Phylogenetic analysis |
2024-01-08 |
2024-03-05 |
2 |
True |
False |
False |
True |
cshl_fastq_to_fasta, unzip, __SORTLIST__, cshl_fastx_reverse_complement, fastq_masker_by_quality, qiime_align_seqs, ncbi_blastn_wrapper, seqtk_trimfq, mothur_degap_seqs, tab2fasta, collection_element_identifiers, fastq_to_tabular, fastq_groomer, __FILTER_FROM_FILE__, regex1, ab1_fastq_converter, aligned_to_consensus, mothur_merge_files, filter_by_fasta_ids, seqtk_mergepe |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr |
|
0 |
|
3292 |
4127 |
1.700000 |
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 |
|
Sequence analysis, Local alignment, Global alignment, PCR primer design, Sequence alignment analysis, Sequence alignment, Multiple sequence alignment |
2025-03-20 |
2025-11-20 |
3 |
True |
False |
False |
True |
ncbi_makeblastdb, rbc_mafft, split_file_to_collection, varvamp, fasta_compute_length, EMBOSS: degapseq20 |
UseGalaxy.eu |
|
0 |
|
571 |
665 |
1.033333 |
0 |
|
Sequence analysis |
Quality Control |
https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-control/tutorial.html |
|
Scatter plot plotting, Sequence composition calculation, Box-Whisker plot plotting, Sequence trimming, Primer removal, Sequencing quality control, Read pre-processing, Validation, Statistical calculation |
2016-10-04 |
2025-03-29 |
48 |
True |
True |
True |
True |
nanoplot, cutadapt, multiqc, fastqe, pycoqc, fastqc |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr |
0 |
|
3139619 |
8017245 |
5.366667 |
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 assembly validation, Sequence trimming |
2024-04-16 |
2024-04-16 |
2 |
True |
False |
False |
True |
ncbi_fcs_adaptor, ncbi_fcs_gx |
UseGalaxy.eu, UseGalaxy.org (Main) |
|
0 |
|
1818 |
2465 |
2.300000 |
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 |
Cross-assembly, Read mapping, Sequencing quality control, Visualisation, Taxonomic classification, Sequence contamination filtering, Expression analysis, Statistical calculation |
2024-07-15 |
2025-03-20 |
4 |
True |
False |
True |
True |
est_abundance, recentrifuge, kraken2, falco, upload1, fastp |
UseGalaxy.eu, UseGalaxy.fr |
GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main) |
0 |
|
1598 |
2092 |
2.766667 |
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 |
|
3938 |
4973 |
1.600000 |
0 |
|
Single Cell |
Generating a single cell matrix using Alevin |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin/tutorial.html |
|
RNA-Seq quantification, Sequence composition calculation, Gene expression analysis |
2021-03-03 |
2025-11-18 |
25 |
True |
False |
True |
True |
anndata_manipulate, Cut1, anndata_inspect, sceasy_convert, join1, _salmon_kallisto_mtx_to_10x, alevin, _ensembl_gtf2gene_list, _dropletBarcodePlot, dropletutils_read_10x, dropletutils_empty_drops |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
3447 |
5240 |
3.483333 |
0 |
|
Single Cell |
Converting between common single cell data formats |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-data-ingest/tutorial.html |
|
Loading, Community profiling |
2024-02-13 |
2025-03-11 |
4 |
True |
False |
False |
True |
Filter1, Cut1, anndata_inspect, datamash_transpose, sceasy_convert, monocle3_create, join1, tabular_to_fastq, tp_tail_tool, regexColumn1, scanpy_filter_cells, dropletutils, tp_cut_tool, seurat_read10x, dropletutils_read_10x, anndata_ops, fastq_to_tabular |
|
UseGalaxy.org (Main) |
0 |
|
2523 |
3004 |
1.316667 |
0 |
|
Single Cell |
Pre-processing of 10X Single-Cell RNA Datasets |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html |
|
Sequencing quality control, Loading, Sequence alignment, Validation, Community profiling |
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 |
|
12460 |
16111 |
1.866667 |
0 |
|
Single Cell |
Pre-processing of Single-Cell RNA Data |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing/tutorial.html |
|
Data handling, Read summarisation, Sequencing quality control, RNA-Seq quantification, Sequence alignment analysis, Sequence alignment, Validation |
2019-02-22 |
2025-04-08 |
5 |
True |
True |
False |
True |
collection_column_join, samtools_stats, multiqc, featurecounts, rna_star, tp_sed_tool, bamFilter, umi_tools_count, umi_tools_extract, __FLATTEN__ |
UseGalaxy.eu |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
3039214 |
7831310 |
4.633333 |
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 |
anndata_manipulate, edger, __EXTRACT_DATASET__, tp_replace_in_line, anndata_inspect, column_remove_by_header, tp_awk_tool, tp_replace_in_column, scanpy_filter, volcanoplot, decoupler_pseudobulk |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
1522 |
1754 |
0.633333 |
0 |
|
Single Cell |
Single-cell quality control with scater |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scater-qc/tutorial.html |
|
Sequence visualisation, Sequencing quality control, Read pre-processing |
2019-10-23 |
2025-02-14 |
6 |
True |
False |
False |
True |
scater_plot_dist_scatter, scater_filter, scater_create_qcmetric_ready_sce, scater_plot_pca |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
703 |
794 |
0.716667 |
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, Cut1, gprofiler_gost, tp_split_on_column |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) |
|
0 |
|
922195 |
1996962 |
2.783333 |
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 |
|
Differential gene expression analysis, Imputation, Peak calling, Read mapping, Generation, Genome indexing, Gene regulatory network analysis, Sequence composition calculation, Enrichment analysis, Principal component visualisation, Sequencing quality control, Visualisation, Expression profile clustering, Mapping, Sequence alignment, Statistical calculation |
2023-04-24 |
2025-10-16 |
10 |
True |
False |
False |
True |
bwa_mem, anndata_inspect, episcanpy_preprocess, tp_sorted_uniq, scanpy_plot, macs2_callpeak, sinto_fragments, bedtools_sortbed, sinto_barcode, falco, episcanpy_build_matrix, fastqc |
UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
5979 |
7036 |
1.083333 |
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 |
|
3000408 |
7709004 |
2.350000 |
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 |
|
614 |
850 |
3.650000 |
0 |
|
Single Cell |
Removing the effects of the cell cycle |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html |
|
Differential gene expression analysis, Principal component visualisation, Expression profile clustering |
2023-01-25 |
2025-03-11 |
14 |
True |
False |
False |
True |
scanpy_inspect, anndata_manipulate, cat1, anndata_inspect, scanpy_plot, scanpy_regress_variable, scanpy_cluster_reduce_dimension, tp_easyjoin_tool, sort1, table_compute, addValue |
|
|
0 |
|
2103 |
2476 |
0.766667 |
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 |
retrieve_scxa, sceasy_convert, scanpy_read_10x, regexColumn1, tp_grep_tool, tp_find_and_replace, hca_matrix_downloader, seurat_read10x, anndata_ops |
|
|
0 |
|
576 |
761 |
3.650000 |
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 |
|
Differential gene expression analysis, Essential dynamics, Read mapping, Generation, Genome indexing, Gene expression profiling, Principal component visualisation, Expression profile clustering, Dimensionality reduction, Sequence alignment |
2024-07-11 |
2025-07-02 |
5 |
True |
False |
False |
True |
scanpy_inspect, bwa_mem, Cut1, anndata_manipulate, anndata_inspect, snapatac2_plotting, scanpy_plot, replace_column_with_key_value_file, snapatac2_peaks_and_motif, snapatac2_preprocessing, snapatac2_clustering, scanpy_filter, scanpy_normalize, fasta_compute_length, anndata_ops |
|
|
0 |
|
1533 |
1857 |
1.100000 |
0 |
|
Single Cell |
Clustering 3K PBMCs with Scanpy |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html |
|
Differential gene expression analysis, Principal component visualisation, Expression profile clustering |
2019-12-19 |
2025-04-29 |
16 |
True |
True |
True |
True |
scanpy_inspect, anndata_manipulate, anndata_inspect, scanpy_plot, anndata_import, datamash_ops, scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_normalize, scanpy_remove_confounders |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no |
0 |
|
3040880 |
7834465 |
4.366667 |
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 |
2025-11-18 |
23 |
True |
False |
True |
True |
anndata_manipulate, Cut1, Paste1, anndata_inspect, tp_replace_in_column, anndata_ops |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.org (Main) |
0 |
|
2512 |
3529 |
2.550000 |
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 |
|
3240 |
3701 |
0.966667 |
0 |
|
Single Cell |
Understanding Barcodes |
https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-umis/tutorial.html |
|
Sequence composition calculation, Sequencing quality control, Statistical calculation |
2019-02-20 |
2025-02-14 |
11 |
True |
False |
True |
True |
seq_filter_by_id, fastqc, umi_tools_extract |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
Galaxy@AuBi, UseGalaxy.no |
0 |
|
6325 |
7871 |
1.250000 |
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 profile clustering, Expression analysis |
2019-03-25 |
2025-02-14 |
7 |
True |
False |
False |
True |
raceid_filtnormconf, raceid_trajectory, datamash_transpose, datamash_ops, raceid_inspecttrajectory, tp_sed_tool, tp_head_tool, raceid_inspectclusters, raceid_clustering |
UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
1075 |
1269 |
1.283333 |
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 |
|
282 |
425 |
1.416667 |
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 |
|
3292 |
3913 |
1.516667 |
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 |
|
Differential gene expression analysis, Principal component visualisation, Expression profile clustering |
2021-03-24 |
2025-04-23 |
24 |
True |
False |
True |
True |
anndata_manipulate, scanpy_find_markers, scanpy_plot, scanpy_scale_data, scanpy_run_umap, scanpy_filter, anndata_ops, scanpy_inspect, anndata_inspect, scanpy_compute_graph, Cut1, scanpy_normalise_data, join1, scanpy_plot_embed, scanpy_cluster_reduce_dimension, scanpy_filter_genes, retrieve_scxa, scanpy_find_cluster, scanpy_run_tsne, scanpy_find_variable_genes, scanpy_filter_cells, scanpy_run_pca, scanpy_normalize, interactive_tool_cellxgene_vip |
|
|
0 |
|
5375 |
8468 |
2.666667 |
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 |
seurat_create, Filter1, Cut1, seurat_clustering, seurat_plot, seurat_data, seurat_preprocessing, seurat_reduce_dimension, csv_to_tabular |
MISSISSIPPI, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
1274 |
1536 |
1.200000 |
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_find_clusters, retrieve_scxa, seurat_run_umap, seurat_find_markers, seurat_plot, seurat_scale_data, seurat_find_variable_genes, seurat_find_neighbours, seurat_read10x, seurat_run_pca, seurat_normalise_data, seurat_filter_cells |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
1947 |
2381 |
1.400000 |
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_find_cluster, scanpy_run_tsne, scanpy_parameter_iterator, scanpy_compute_graph, scanpy_plot_embed, scanpy_run_umap |
UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
283 |
317 |
1.083333 |
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_manipulate, Cut1, Paste1, unzip, anndata_inspect, anndata_import, tp_replace_in_column, scanpy_filter_cells, anndata_ops |
UseGalaxy.org.au |
|
0 |
|
448 |
530 |
1.633333 |
0 |
|
Single Cell |
Evaluating Reference Data for Bulk RNA Deconvolution |
https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html |
|
Annotation, Visualisation |
2025-02-02 |
2025-03-11 |
3 |
True |
False |
False |
True |
collection_column_join, bg_column_arrange_by_header, music_construct_eset, tp_easyjoin_tool, table_compute, Remove beginning1, tp_multijoin_tool, Count1, music_deconvolution, Cut1, Paste1, datamash_transpose, join1, __DUPLICATE_FILE_TO_COLLECTION__, tp_sed_tool, Add_a_column1, annotatemyids, tp_cut_tool, ggplot2_point, collapse_dataset, ggplot2_violin, tp_awk_tool |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
109 |
129 |
0.883333 |
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 |
|
Dimensionality reduction, Gene expression profiling, Essential dynamics |
2025-02-28 |
2025-07-02 |
2 |
True |
False |
False |
True |
anndata_manipulate, __EXTRACT_DATASET__, anndata_inspect, snapatac2_plotting, Show beginning1, snapatac2_peaks_and_motif, collection_element_identifiers, snapatac2_preprocessing, snapatac2_clustering, fasta_compute_length, __FILTER_FROM_FILE__ |
UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
460 |
517 |
0.866667 |
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 |
|
3032865 |
7823047 |
2.350000 |
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 |
|
4541 |
5362 |
1.283333 |
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_plot_trajectory, anndata_manipulate, scanpy_run_diffmap, scanpy_find_cluster, scanpy_run_dpt, scanpy_compute_graph, scanpy_plot_embed, scanpy_run_paga, scanpy_run_fdg |
|
UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
1289 |
1624 |
2.133333 |
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 |
regex1, Cut1, datamash_transpose, retrieve_scxa, anndata_inspect, music_construct_eset, scanpy_read_10x, join1, tp_awk_tool, tp_easyjoin_tool, tp_sed_tool, annotatemyids, sort1, tp_cut_tool, music_manipulate_eset, table_compute, add_line_to_file |
|
UseGalaxy.cz |
0 |
|
739 |
1237 |
2.166667 |
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 |
|
991324 |
2167818 |
1.983333 |
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 |
|
6391 |
7258 |
0.800000 |
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 |
monocle3_diffExp, Filter1, Cut1, monocle3_plotCells, anndata_inspect, datamash_transpose, monocle3_create, monocle3_learnGraph, join1, monocle3_partition, monocle3_topmarkers, regexColumn1, monocle3_preprocess, tp_cut_tool, monocle3_orderCells, monocle3_reduceDim |
UseGalaxy.eu, UseGalaxy.org (Main) |
|
0 |
|
3918 |
4858 |
1.500000 |
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 |
regex1, column_remove_by_header, music_construct_eset, tp_awk_tool, tp_easyjoin_tool, tp_sed_tool, annotatemyids, sort1, tp_cut_tool, music_manipulate_eset, table_compute |
|
UseGalaxy.cz |
0 |
|
726 |
1136 |
1.716667 |
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 |
|
2076933 |
4736732 |
2.183333 |
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 |
|
1474699 |
3288724 |
2.133333 |
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 |
plotly_ml_performance_plots, sklearn_ensemble, plotly_regression_performance_plots, sklearn_svm_classifier |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
5695 |
10233 |
0.783333 |
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 |
csv_to_tabular, ggplot2_point, sklearn_numeric_clustering |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr |
0 |
|
8498 |
14070 |
0.933333 |
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, sklearn_to_categorical, model_prediction, keras_train_and_eval, ml_visualization_ex |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
2890958 |
7291394 |
3.233333 |
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.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.fr, UseGalaxy.no |
0 |
|
3035650 |
7826803 |
5.350000 |
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 |
__EXTRACT_DATASET__, flexynesis_utils, tp_cut_tool, table_compute, tp_sort_header_tool, flexynesis_cbioportal_import |
UseGalaxy.eu |
|
0 |
|
42 |
42 |
0.700000 |
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 |
|
222 |
284 |
2.233333 |
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_alternative_genes_pathwaymapper, pancancer_targene_cell_line_predictions, pancancer_apply_weights, pancancer_within_disease_analysis, pancancer_compare_within_models, pancancer_classifier, pancancer_pathway_count_heatmaps, pancancer_visualize_decisions, pancancer_external_sample_status_prediction, pancancer_map_mutation_class, pancancer_targene_summary_figures, pancancer_targene_pharmacology |
|
|
0 |
|
793 |
1233 |
3.083333 |
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 |
pmids_to_pubtator_matrix, pubmed_by_queries, interactive_tool_simtext_app |
UseGalaxy.eu |
|
0 |
|
490 |
667 |
2.650000 |
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_build_pipeline, plotly_regression_performance_plots, plotly_parallel_coordinates_plot, sklearn_ensemble, sklearn_searchcv |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.no |
0 |
|
13225 |
21324 |
0.683333 |
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 |
datamash_transpose, __EXTRACT_DATASET__, flexynesis_plot, flexynesis, join1, Show beginning1, tp_easyjoin_tool, pick_value, tp_cut_tool, table_compute, tp_sort_header_tool, tabpfn |
UseGalaxy.eu |
|
0 |
|
73 |
104 |
1.933333 |
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 |
Remove beginning1, sklearn_build_pipeline, plotly_regression_performance_plots, sklearn_generalized_linear, sklearn_ensemble, sklearn_searchcv |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.no |
0 |
|
3036104 |
7827135 |
3.633333 |
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 |
|
779897 |
1627356 |
3.900000 |
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, plotly_regression_performance_plots, model_prediction, keras_train_and_eval |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.no |
0 |
|
2895541 |
7280478 |
3.083333 |
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 |
keras_model_config, keras_model_builder, sklearn_to_categorical, model_prediction, keras_train_and_eval, ml_visualization_ex, tp_cut_tool |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
2551625 |
6194204 |
2.983333 |
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, keras_train_and_eval, ml_visualization_ex |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
2479 |
3166 |
1.633333 |
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 |
__EXTRACT_DATASET__, flexynesis_plot, flexynesis, datamash_ops, tp_replace_in_column, Add_a_column1 |
UseGalaxy.eu |
|
0 |
|
57 |
65 |
0.816667 |
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 |
Remove beginning1, sklearn_build_pipeline, sklearn_svm_classifier, sklearn_generalized_linear, sklearn_nn_classifier, plotly_ml_performance_plots, sklearn_ensemble, sklearn_searchcv |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.no |
0 |
|
3035666 |
7827139 |
4.533333 |
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, keras_train_and_eval, ml_visualization_ex |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.be, UseGalaxy.no |
0 |
|
2965970 |
7572759 |
3.133333 |
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, __EXTRACT_DATASET__, flexynesis_plot, flexynesis_utils |
UseGalaxy.eu |
|
0 |
|
32 |
36 |
4.166667 |
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, Cut1, interactive_tool_ml_jupyter_notebook |
UseGalaxy.eu |
|
0 |
|
1208 |
1530 |
1.466667 |
0 |
|
Statistics and machine learning |
Interval-Wise Testing for omics data |
https://training.galaxyproject.org//topics/statistics/tutorials/iwtomics/tutorial.html |
|
Differential gene expression analysis, Differentially-methylated region identification, Comparison, Genome annotation, Peak calling |
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 |
|
373 |
495 |
2.866667 |
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 |
|
1049612 |
2309661 |
3.083333 |
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 |
|
438 |
545 |
0.750000 |
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 |
|
4136 |
6155 |
1.083333 |
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 |
rpranker, rpscore, rpfba, rpthermo |
|
|
0 |
|
650 |
962 |
2.966667 |
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 |
|
1034 |
1598 |
2.633333 |
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 |
rrparser, get_sbml_model, rp2paths, rpextractsink, retropath2, rpcompletion |
|
|
0 |
|
589 |
857 |
2.483333 |
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 |
|
2086391 |
4763772 |
2.183333 |
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 |
|
3032865 |
7823056 |
2.350000 |
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 |
|
290 |
512 |
2.500000 |
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 |
|
25 |
25 |
0.083333 |
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 |
|
157 |
170 |
2.500000 |
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 |
|
28 |
30 |
0.016667 |
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 |
|
266 |
288 |
0.983333 |
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 |
|
11 |
11 |
0.000000 |
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 |
|
229 |
421 |
5.933333 |
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 |
|
166 |
295 |
1.150000 |
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 |
|
318 |
365 |
4.000000 |
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 |
|
139 |
162 |
1.483333 |
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 |
|
87 |
91 |
0.283333 |
0 |
|
Transcriptomics |
RNA-RNA interactome data analysis |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-interactome/tutorial.html |
|
Primer removal, Sequencing quality control, Read pre-processing, Sequence composition calculation, Sequence trimming, Statistical calculation |
2020-03-23 |
2023-11-09 |
12 |
True |
False |
False |
True |
cutadapt, chira_extract, chira_map, query_tabular, chira_merge, chira_collapse, fastqc, chira_quantify |
UseGalaxy.be, UseGalaxy.no, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au |
0 |
|
1486 |
2242 |
2.783333 |
0 |
|
Transcriptomics |
CLIP-Seq data analysis from pre-processing to motif detection |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/clipseq/tutorial.html |
|
Primer removal, Sequencing quality control, Read pre-processing, Mapping, Sequence composition calculation, Sequence alignment, Sequence trimming, Statistical calculation |
2018-08-17 |
2023-11-09 |
23 |
True |
False |
False |
True |
cutadapt, __SORTLIST__, umi_tools_extract, deeptools_multi_bam_summary, peakachu, umi_tools_dedup, sort1, fastqc, __MERGE_COLLECTION__, wig_to_bigWig, bedtools_slopbed, rcas, bctools_extract_alignment_ends, rna_star, deeptools_plot_correlation, Extract genomic DNA 1, tp_awk_tool, deeptools_plot_fingerprint, meme_chip, bedtools_genomecoveragebed_bedgraph |
|
UseGalaxy.no |
0 |
|
8314 |
16337 |
1.866667 |
0 |
|
Transcriptomics |
Genome-wide alternative splicing analysis |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html |
|
Sequence annotation, RNA-Seq analysis, Transcriptome assembly, Sequence composition calculation, Sequence comparison, Protein sequence analysis, Data handling, Formatting, Sequence analysis, Sequence contamination filtering, Sequencing quality control, Visualisation, De-novo assembly, Sequence assembly validation, Sequence alignment, Validation, Statistical calculation |
2023-05-17 |
2025-03-28 |
11 |
True |
True |
False |
True |
cat1, isoformswitchanalyzer, gene2exon1, __FLATTEN__, gffcompare, pfamscan, addValue, Remove beginning1, multiqc, tp_uniq_tool, rseqc_junction_saturation, cpat, stringtie_merge, sort1, fastqc, rseqc_read_distribution, tp_cat, Filter1, Cut1, rna_quast, rseqc_inner_distance, stringtie, rseqc_infer_experiment, rna_star, collection_element_identifiers, tp_grep_tool, Add_a_column1, gffread, gtftobed12, fastp, __FILTER_FROM_FILE__, rseqc_geneBody_coverage, pygenomeTracks, tp_awk_tool, rseqc_junction_annotation |
|
UseGalaxy.cz, UseGalaxy.fr |
0 |
|
1678742 |
3729113 |
4.016667 |
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 enrichment analysis, Gene set testing |
2018-12-31 |
2023-11-09 |
13 |
True |
False |
False |
True |
Cut1, goseq, join1, egsea, Add_a_column1, tp_cut_tool, tp_sort_header_tool, fgsea |
UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
26272 |
42112 |
1.933333 |
0 |
|
Transcriptomics |
De novo transcriptome assembly, annotation, and differential expression analysis |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/full-de-novo/tutorial.html |
|
Transcriptome assembly, Sequence composition calculation, de Novo sequencing, Sequencing quality control, De-novo assembly, Gene functional annotation, Coding region prediction, Validation, Statistical calculation |
2020-02-13 |
2023-11-09 |
8 |
True |
False |
False |
True |
trinity_run_de_analysis, trinity_contig_exn50_statistic, trinity_filter_low_expr_transcripts, trinity, trimmomatic, multiqc, trinity_samples_qccheck, trinity_analyze_diff_expr, describe_samples, trinotate, trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, transdecoder, trinity_define_clusters_by_cutting_tree, fastqc |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no |
0 |
|
14651 |
26477 |
2.433333 |
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 |
datamash_transpose, Cut1, join1, ggplot2_heatmap2 |
UseGalaxy.eu, UseGalaxy.org (Main) |
GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
77795 |
127970 |
1.350000 |
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 |
Filter1, Cut1, cat1, goseq, Grouping1, length_and_gc_content, Show beginning1, deg_annotate, Multivariate, deseq2, tp_easyjoin_tool, Add_a_column1, table_compute, volcanoplot, tp_sort_header_tool, ggplot2_heatmap2 |
UseGalaxy.eu, UseGalaxy.fr |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) |
0 |
|
994 |
1293 |
1.666667 |
0 |
|
Transcriptomics |
1: RNA-Seq reads to counts |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html |
|
Sequence composition calculation, Sequence trimming, Data handling, Primer removal, Read summarisation, Formatting, Sequencing quality control, Read pre-processing, RNA-Seq quantification, Sequence alignment, Validation, Statistical calculation |
2018-09-23 |
2024-08-09 |
33 |
True |
False |
False |
True |
rseqc_geneBody_coverage, collection_column_join, cutadapt, multiqc, rseqc_infer_experiment, featurecounts, hisat2, samtools_idxstats, picard_MarkDuplicates, rseqc_read_distribution, fastqc |
UseGalaxy.eu |
MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
78874 |
143104 |
2.600000 |
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 |
samtools_sort, tp_sort_header_tool, blockclust, blockbuster |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
1040 |
1413 |
2.916667 |
0 |
|
Transcriptomics |
Differential abundance testing of small RNAs |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/srna/tutorial.html |
|
Differential gene expression analysis, RNA-Seq analysis, Sequence composition calculation, Primer removal, Gene expression analysis, Sequencing quality control, Read pre-processing, RNA-Seq quantification, Sequence alignment, Sequence trimming, Statistical calculation |
2017-06-29 |
2023-11-09 |
26 |
True |
False |
False |
True |
trim_galore, Filter1, salmon, fastq_manipulation, bedtools_bamtofastq, hisat2, deseq2, samtool_filter2, fastqc |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
6950 |
12177 |
2.083333 |
0 |
|
Transcriptomics |
Network analysis with Heinz |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html |
|
Differential gene expression analysis, RNA-Seq analysis, Pathway or network analysis |
2018-10-11 |
2024-01-15 |
16 |
True |
True |
False |
True |
heinz_visualization, heinz, Cut1, heinz_scoring, deseq2, heinz_bum |
UseGalaxy.be, UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
3034912 |
7826238 |
5.583333 |
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 |
mergeCols1, tp_replace_in_line, annotatemyids, tp_cut_tool, limma_voom |
UseGalaxy.be, UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au |
0 |
|
44039 |
74378 |
2.283333 |
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 |
goenrichment, Filter1, goslimmer |
Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
|
0 |
|
23168 |
37603 |
1.333333 |
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 |
|
153828 |
251942 |
1.316667 |
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 |
|
3032865 |
7823058 |
2.350000 |
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 |
|
3035445 |
7826939 |
4.083333 |
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 |
|
3033884 |
7824356 |
5.883333 |
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 |
|
4264 |
5459 |
1.950000 |
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 |
|
22085 |
34576 |
2.183333 |
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 |
|
10796 |
13231 |
1.450000 |
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 |
volcanoplot, interactive_tool_rstudio |
UseGalaxy.eu, UseGalaxy.org.au |
|
0 |
|
30969 |
42280 |
1.683333 |
0 |
|
Transcriptomics |
Reference-based RNA-Seq data analysis |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/ref-based/tutorial.html |
|
Differential gene expression analysis, Read mapping, Pathway or network analysis, Enrichment analysis, Data handling, Sequencing quality control, Read pre-processing, RNA-Seq quantification, Validation, Sequence trimming, Exonic splicing enhancer prediction, RNA-Seq analysis, Primer removal, Formatting, Read summarisation, Visualisation, Gene functional annotation, Sequence alignment, Pathway or network visualisation |
2016-10-05 |
2025-11-14 |
105 |
True |
False |
True |
True |
cat1, goseq, cutadapt, samtools_view, table_compute, tp_sort_header_tool, __FLATTEN__, pathview, dexseq_count, multiqc, ChangeCase, deseq2, __TAG_FROM_FILE__, dexseq, ggplot2_heatmap2, rseqc_read_distribution, tp_cat, Filter1, Cut1, __MERGE_COLLECTION__, tp_replace_in_line, rseqc_infer_experiment, join1, rna_star, tp_tail_tool, collection_element_identifiers, tp_grep_tool, Add_a_column1, falco, gtftobed12, __FILTER_FROM_FILE__, rseqc_geneBody_coverage, __EXTRACT_DATASET__, Grouping1, pygenomeTracks, featurecounts, deg_annotate, samtools_idxstats, picard_MarkDuplicates, length_and_gc_content |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
187678 |
351132 |
2.783333 |
0 |
|
Transcriptomics |
Pathway analysis with the MINERVA Platform |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/minerva-pathways/tutorial.html |
|
Annotation, RNA-Seq analysis, Sequence composition calculation, Sequence trimming, Data handling, Primer removal, Read summarisation, Sequencing quality control, Read pre-processing, RNA-Seq quantification, Gene functional annotation, Sequence alignment, Validation, Statistical calculation |
2024-03-28 |
2024-07-26 |
3 |
True |
False |
False |
True |
collection_column_join, goseq, cutadapt, tp_sort_header_tool, multiqc, limma_voom, fastqc, rseqc_read_distribution, Cut1, tp_replace_in_line, tp_sorted_uniq, join1, Grep1, Add_a_column1, annotatemyids, rseqc_geneBody_coverage, __EXTRACT_DATASET__, featurecounts, hisat2, fasterq_dump |
UseGalaxy.eu, UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) |
0 |
|
627 |
744 |
1.533333 |
0 |
|
Transcriptomics |
De novo transcriptome reconstruction with RNA-Seq |
https://training.galaxyproject.org//topics/transcriptomics/tutorials/de-novo/tutorial.html |
|
Differential gene expression analysis, Sequence annotation, RNA-Seq analysis, Transcriptome assembly, Sequence composition calculation, Read summarisation, Sequencing quality control, RNA-Seq quantification, Sequence alignment, Statistical calculation |
2017-02-19 |
2024-06-14 |
36 |
True |
False |
True |
True |
Filter1, trimmomatic, stringtie, featurecounts, deeptools_bam_coverage, stringtie_merge, hisat2, deseq2, gffcompare, fastqc |
Galaxy@AuBi, UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
16800 |
28892 |
2.650000 |
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 |
|
3032865 |
7823060 |
2.350000 |
0 |
|
Variant Analysis |
Calling very rare variants |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/dunovo/tutorial.html |
|
Read mapping, Generation, Genome indexing, Sequence composition calculation, Variant calling, Sequencing quality control, Sequence alignment, Statistical calculation |
2017-02-22 |
2024-12-09 |
21 |
True |
False |
False |
True |
bwa_mem, Filter1, correct_barcodes, dunovo, make_families, allele_counts_1, sequence_content_trimmer, naive_variant_caller, bamleftalign, align_families, fastqc |
UseGalaxy.org (Main) |
|
0 |
|
2011 |
3125 |
1.766667 |
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, mimodd_varreport, mimodd_varcall, mimodd_map, snpEff, tp_find_and_replace, mimodd_varextract, mimodd_vcf_filter |
UseGalaxy.be, UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
4399 |
6455 |
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 |
|
Sequence analysis, Genetic variation analysis |
2022-05-19 |
2024-09-17 |
13 |
True |
False |
True |
True |
gene_iobio_display_generation_iframe, Filter1, gemini_load, bcftools_norm, CONVERTER_uncompressed_to_gz, regexColumn1, CONVERTER_gz_to_uncompressed, snpEff, tp_grep_tool, pyega3, bcftools_merge, gemini_inheritance |
UseGalaxy.eu |
UseGalaxy.cz, UseGalaxy.org.au |
0 |
|
1951 |
3440 |
3.600000 |
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 |
|
Read mapping, Generation, Sequence alignment analysis, Genome indexing, Sequence composition calculation, Data handling, Variant calling, Sequencing quality control, Visualisation, Sequence alignment, Validation, Statistical calculation |
2019-03-13 |
2025-03-20 |
16 |
True |
False |
False |
True |
bwa_mem, gemini_load, gemini_annotate, gemini_query, multiqc, trimmomatic, bg_column_arrange_by_header, varscan_somatic, snpEff, tp_easyjoin_tool, bamFilter, samtools_calmd, falco, bamleftalign, samtools_rmdup, fastqc |
UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz, UseGalaxy.fr |
0 |
|
14475 |
25988 |
2.500000 |
0 |
|
Variant Analysis |
Calling variants in diploid systems |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/dip/tutorial.html |
|
Variant calling, Sequence analysis, Genetic variation analysis, Statistical calculation |
2017-02-20 |
2025-04-28 |
17 |
True |
False |
False |
True |
gemini_load, gemini_query, gemini_db_info, vcfallelicprimitives, freebayes, snpEff |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr |
UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
15407 |
26460 |
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 |
|
Sequence visualisation, Read mapping, Generation, Genome indexing, Sequence composition calculation, Variant calling, Sequencing quality control, Copy number estimation, Visualisation, Genome alignment, Sequence alignment, Validation, Statistical calculation |
2022-10-05 |
2025-03-20 |
14 |
True |
False |
False |
True |
bwa_mem, __EXTRACT_DATASET__, tp_replace_in_line, multiqc, trimmomatic, __RELABEL_FROM_FILE__, bamleftalign, circos, samtools_calmd, Grep1, control_freec, samtools_view, tp_text_file_with_recurring_lines, falco, __BUILD_LIST__, samtools_rmdup, fastqc |
|
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au |
0 |
|
1877 |
2403 |
2.000000 |
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 |
Read mapping, Generation, Genome indexing, Sequence alignment analysis, Sequence composition calculation, Variant calling, Formatting, Data handling, Sequencing quality control, Sequence alignment, Statistical calculation |
2017-02-16 |
2024-03-15 |
23 |
True |
False |
False |
True |
bwa_mem, Cut1, picard_MergeSamFiles, vcf2tsv, freebayes, bamFilter, picard_MarkDuplicates, bamleftalign, vcffilter2, fastqc |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
8636 |
15511 |
2.133333 |
0 |
|
Variant Analysis |
Exome sequencing data analysis for diagnosing a genetic disease |
https://training.galaxyproject.org//topics/variant-analysis/tutorials/exome-seq/tutorial.html |
|
Read mapping, Generation, Genome indexing, Sequence composition calculation, Variant calling, Sequence analysis, Sequencing quality control, Genetic variation analysis, Sequence alignment, Validation, Statistical calculation |
2016-08-19 |
2025-05-11 |
29 |
True |
False |
True |
True |
bwa_mem, gemini_load, snpEff_download, trimmomatic, multiqc, bcftools_norm, freebayes, snpEff, samtools_view, samtools_rmdup, fastqc, gemini_inheritance |
UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au |
0 |
|
35492 |
64304 |
2.733333 |
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, Read mapping, Genome indexing, Data handling, Primer removal, Read pre-processing, Visualisation, Sequence alignment, Sequence trimming |
2025-02-24 |
2025-02-24 |
1 |
True |
False |
False |
True |
fastq_dump, trim_galore, Filter1, bwa_mem, tp_replace_in_line, vcf2tsv, collapse_dataset, bcftools_call, ncbi_acc_download, tp_awk_tool, tp_replace_in_column, bcftools_mpileup, ggplot2_point |
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au |
UseGalaxy.cz |
0 |
|
264 |
362 |
1.050000 |
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 |
|
Service discovery, Database search, Genetic variation analysis |
2024-08-06 |
2024-09-27 |
3 |
True |
False |
False |
False |
beacon2_cnv |
|
UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au |
0 |
|
183 |
220 |
2.366667 |
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, cnv_vcf2json, cnv_phenopacket, beacon2_cnv |
|
UseGalaxy.eu |
0 |
|
322 |
362 |
0.516667 |
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 |
Cut1, Remove beginning1, circos, random_lines1, Grep1, upload1 |
Galaxy@AuBi, Galaxy@Pasteur, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) |
GalaxyTrakr, UseGalaxy.no |
0 |
|
3063284 |
7871564 |
4.000000 |
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 |
Cut1, gff2bed1, circos_wiggle_to_scatter, circos_gc_skew, deeptools_bam_coverage, circos, circos_interval_to_text, circos_interval_to_tile |
UseGalaxy.cz, UseGalaxy.fr |
Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au |
0 |
|
1442 |
1822 |
1.883333 |
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 |
|
1390510 |
3104764 |
2.133333 |
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 |
|
3032865 |
7823066 |
2.350000 |
0 |