Expand Topic Title Link EDAM topic EDAM operation Creation Last modification Version Tutorial Slides Video Workflows Tools Servers with precise tool versions Servers with tool but different versions Feedback number Feedback mean note Visitors Page views Visit duration Video views
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 4175411 9683493 2.066667 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 4175411 9683493 2.066667 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 1741 2806 5.383333 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 0 778 1094 10.733333 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 0 179 202 9.416667 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 0 156 166 4.700000 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 2572 3267 1.200000 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 1236 1393 3.283333 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 4191651 9713875 3.400000 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 4175411 9683493 2.066667 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 4175411 9683493 2.066667 0
Galaxy Server administration Running Jobs on Remote Resources with Pulsar https://training.galaxyproject.org//topics/admin/tutorials/pulsar/tutorial.html 2019-01-28 2026-01-23 59 True True True False 0 4178241 9688009 9.700000 0
Galaxy Server administration Reference Data with CVMFS https://training.galaxyproject.org//topics/admin/tutorials/cvmfs/tutorial.html 2019-01-27 2026-07-12 56 True True True False 0 4177855 9687011 11.333333 0
Galaxy Server administration Setting up Celery Workers for Galaxy https://training.galaxyproject.org//topics/admin/tutorials/celery/tutorial.html 2022-07-16 2025-11-24 19 True True False False 0 3320588 6863175 11.266667 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 2025-11-24 10 True True True False 0 4176111 9684397 20.466667 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 2026-01-23 109 True True True False 0 4201828 9732013 5.650000 0
Galaxy Server administration Data Libraries https://training.galaxyproject.org//topics/admin/tutorials/data-library/tutorial.html 2021-01-14 2025-11-24 35 True True True False 0 4159826 9621010 8.900000 0
Galaxy Server administration Advanced customisation of a Galaxy instance https://training.galaxyproject.org//topics/admin/tutorials/advanced-galaxy-customisation/slides.html 2017-06-27 2023-04-17 18 False True False False 0 4175411 9683493 2.066667 0
Galaxy Server administration Galaxy Interactive Tools https://training.galaxyproject.org//topics/admin/tutorials/interactive-tools/tutorial.html 2020-02-27 2026-01-23 30 True True True False 0 4177947 9687215 9.416667 0
Galaxy Server administration Reference Data with Data Managers https://training.galaxyproject.org//topics/admin/tutorials/reference-genomes/tutorial.html Generation, Read mapping, Sequence alignment, Genome indexing 2019-01-28 2026-01-23 7 True True False False bwa, data_manager_fetch_genome_all_fasta_dbkey, bwa_mem_index_builder_data_manager 0 4176191 9684462 20.600000 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 4175411 9683493 2.066667 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 4176208 9684693 9.416667 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 4182170 9695376 7.700000 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 4176889 9685746 9.866667 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 2025-11-24 65 True True True False 0 4179771 9690828 10.866667 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 4175411 9683493 2.066667 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 4175411 9683493 2.066667 0
Galaxy Server administration Galaxy Monitoring with Telegraf and Grafana https://training.galaxyproject.org//topics/admin/tutorials/monitoring/tutorial.html 2019-01-31 2026-04-29 56 True True True False 0 4178496 9689051 7.000000 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 4175411 9683493 2.066667 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 4175411 9683493 2.066667 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 4175411 9683493 2.066667 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 2164859 4087578 1.633333 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 4175411 9683493 2.066667 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 4177737 9686672 12.466667 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 4176426 9685023 16.916667 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 4175411 9683493 2.066667 0
Galaxy Server administration Enable upload via FTP https://training.galaxyproject.org//topics/admin/tutorials/ftp/tutorial.html 2021-06-18 2025-12-18 29 True False False False 0 1391 1857 11.016667 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 0 769 872 7.433333 0
Galaxy Server administration Monitoring Galaxy and Pulsar with Sentry https://training.galaxyproject.org//topics/admin/tutorials/sentry/tutorial.html 2023-04-19 2025-12-18 13 True False False False 0 298 348 15.800000 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 0 107 119 39.366667 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 3190 5126 3.550000 0
Galaxy Server administration Training Infrastructure as a Service (TIaaS) https://training.galaxyproject.org//topics/admin/tutorials/tiaas/tutorial.html 2020-02-12 2025-11-24 45 True False True False 0 680 882 15.183333 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 1001 1422 16.483333 0
Galaxy Server administration Galaxy Monitoring with Reports https://training.galaxyproject.org//topics/admin/tutorials/reports/tutorial.html 2019-01-31 2026-01-23 49 True False False False 0 592 765 15.866667 0
Galaxy Server administration Reference Data with CVMFS without Ansible https://training.galaxyproject.org//topics/admin/tutorials/cvmfs-manual/tutorial.html 2020-06-17 2026-07-12 11 True False False False 0 524 680 14.416667 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 0 725 872 17.250000 0
Galaxy Server administration Upgrading Galaxy https://training.galaxyproject.org//topics/admin/tutorials/upgrading/tutorial.html 2021-06-08 2026-01-23 11 True False True False 0 845 1243 9.016667 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 8435 16600 1.683333 0
Galaxy Server administration Mapping Jobs to Destinations using TPV https://training.galaxyproject.org//topics/admin/tutorials/job-destinations/tutorial.html 2021-01-17 2026-01-23 44 True False True False 0 1919 2913 10.950000 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 0 281 328 11.916667 0
Galaxy Server administration Use Apptainer containers for running Galaxy jobs https://training.galaxyproject.org//topics/admin/tutorials/apptainer/tutorial.html 2021-01-08 2026-07-12 20 True False True False 0 1286 1606 11.550000 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 0 225 243 22.583333 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 0 143 154 20.150000 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 0 157 182 29.933333 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 0 121 144 31.083333 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, UseGalaxy.ca 0 2809791 5575344 1.800000 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, UseGalaxy.ca 0 2871903 5711116 1.816667 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, UseGalaxy.ca 0 2824678 5607720 1.800000 0
Assembly An Introduction to Genome Assembly https://training.galaxyproject.org//topics/assembly/tutorials/general-introduction/tutorial.html Visualisation, Formatting, Sequence composition calculation, Sequence assembly validation, Validation, Statistical calculation, De-novo assembly, Sequencing quality control 2017-05-23 2026-01-23 30 True True True True fastqc, fastq_paired_end_interlacer, quast, velveth, velvetg, multiqc Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 4215630 9748333 8.900000 0
Assembly Hybrid genome assembly - Nanopore and Illumina https://training.galaxyproject.org//topics/assembly/tutorials/hybrid_denovo_assembly/tutorial.html Visualisation, Generation, Sequence assembly, Sequence assembly validation, Validation, Genome indexing, Read mapping, Read alignment, Aggregation, Cross-assembly, Genome assembly, De-novo assembly, Analysis, Sequencing quality control, Sequence alignment, Mapping assembly 2025-11-03 2026-07-24 3 True False False True bwa_mem, quast, multiqc, pilon, busco, unicycler, flye UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.no 0 1900 2279 4.400000 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, Visualisation, Sequence contamination filtering, Read mapping, Genome assembly, Sequence assembly validation, Sequencing quality control 2021-03-24 2026-01-05 18 True False True True bandage_info, quast, fastp, bandage_image, falco, upload1, shovill UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr 0 12234 18498 9.500000 0
Assembly Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Sequence file editing, Visualisation, Read pre-processing, Sequence assembly validation, Sequence trimming, Statistical calculation, Sequence contamination filtering, Primer removal, Sequence assembly visualisation, Sequencing quality control, Formatting, Variant calling, Sequence composition calculation, Read mapping, Local alignment, Genome assembly, Data handling, Sequence alignment analysis 2026-08-16 2026-08-16 0 True False True True fastqc, bandage_info, filter_tabular, quast, metaspades, bandage_image, random_lines1, bg_uniq, coverm_contig, bowtie2, collection_column_join, megahit, megahit_contig2fastg, bamtools, seqtk_subseq, cutadapt, tp_cat, ngsutils_bam_filter UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 6 6 0.000000 0
Assembly Chloroplast genome assembly https://training.galaxyproject.org//topics/assembly/tutorials/chloroplast-assembly/tutorial.html Generation, Genome visualisation, Sequence assembly, Coding region prediction, Read mapping, Read alignment, Genome indexing, Cross-assembly, Genome annotation, Box-Whisker plot plotting, Sequence alignment, Gene prediction, De-novo assembly, Genome assembly, Analysis, Sequence assembly visualisation, Scatter plot plotting, Mapping assembly 2020-12-04 2026-01-23 22 True False True True bandage_info, bwa_mem, nanoplot, bandage_image, jbrowse, upload1, fasta-stats, pilon, flye, prokka UseGalaxy.eu GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 8989 13810 8.066667 0
Assembly Decontamination of a genome assembly https://training.galaxyproject.org//topics/assembly/tutorials/assembly-decontamination/tutorial.html Genomics, Sequence assembly, Biodiversity Taxonomic classification, Data handling 2024-09-04 2025-06-04 5 True False True True ncbi_dustmasker_wrapper, ncbi_blastn_wrapper, tp_sed_tool, Filter1, Cut1, parse_mito_blast, kraken2, gfastats, tp_cat UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz 0 2432 2935 8.966667 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 file editing, Pairwise sequence alignment, Read mapping, Validation, Aggregation, Sequence contamination filtering, Box-Whisker plot plotting, Data handling, Genome assembly, Sequence assembly visualisation, Sequencing quality control, Scatter plot plotting 2020-04-21 2025-05-15 14 True True True True bandage_info, fasta_filter_by_length, samtools_stats, nanoplot, fastp, minimap2, bandage_image, seqtk_sample, collapse_dataset, bowtie2, samtools_view, __ZIP_COLLECTION__, fasterq_dump, unicycler, multiqc, samtools_fastx UseGalaxy.org.au, UseGalaxy.eu Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 4182233 9694632 10.833333 0
Assembly Genome Assembly Quality Control https://training.galaxyproject.org//topics/assembly/tutorials/assembly-quality-control/tutorial.html Biodiversity, Sequence assembly, Data quality management Visualisation, Phasing, De-novo assembly, Genome assembly, Sequence assembly validation, Scaffolding, k-mer counting 2022-08-26 2025-06-04 6 True True False True quast, meryl, busco, merqury, chromeister UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.cz 0 3276011 6731079 10.200000 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 Visualisation, Sequence assembly validation, Statistical calculation, Sequence contamination filtering, Box-Whisker plot plotting, De-novo assembly, Sequence assembly visualisation, Sequencing quality control, Sequence alignment, Scatter plot plotting, Mapping assembly, Sequence composition calculation, Read mapping, Cross-assembly, Sequencing error detection, Genome assembly, Filtering 2021-03-24 2026-01-05 16 True False False True __EXTRACT_DATASET__, fastqc, bwa_mem2, nanoplot, polypolish, fastp, porechop, bandage_image, quast, upload1, filtlong, __FLATTEN__, CONVERTER_bz2_to_uncompressed, flye UseGalaxy.be, UseGalaxy.eu GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr 0 11943 17715 7.750000 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 Visualisation, Pairwise sequence alignment, Read pre-processing, Sequence assembly validation, Mapping, Sequence trimming, Read binning, Primer removal, Sequence alignment, Phasing, De-novo assembly, Genome assembly, Data handling, k-mer counting, Scaffolding 2021-06-04 2026-04-13 59 True False True True bionano_scaffold, Convert characters1, quast, tp_cut_tool, collapse_dataset, merqury, salsa, meryl, cat1, genomescope, sort1, Add_a_column1, gfa_to_fa, bwa_mem2, pretext_map, minimap2, pretext_snapshot, collection_column_join, gfastats, bellerophon, tp_grep_tool, yahs, hifiasm, bedtools_bamtobed, busco, cutadapt, purge_dups, tp_find_and_replace UseGalaxy.cz 0 20291 29133 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 Visualisation, Pairwise sequence alignment, Data deposition, Sequence trimming, Sequence assembly validation, Data parsing, Genotyping, Sequence alignment, Phasing, De-novo assembly, Genome assembly, Data handling, Sequence assembly visualisation, Sequence alignment analysis, Scaffolding, k-mer counting 2023-06-23 2025-06-04 8 True False True True bandage_image, collapse_dataset, merqury, meryl, bg_diamond, genomescope, blobtoolkit, smudgeplot, CONVERTER_gz_to_uncompressed, bwa_mem2, pretext_map, __EXTRACT_DATASET__, minimap2, interactive_tool_blobtoolkit, pretext_snapshot, gfastats, bellerophon, samtools_stats, busco, tp_find_and_replace UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.org (Main) 0 2750 3475 9.100000 0
Assembly Genome assembly using PacBio data https://training.galaxyproject.org//topics/assembly/tutorials/hifi-assembly/tutorial.html Genomics, Sequence assembly, Biodiversity Visualisation, De-novo assembly, Genome assembly, Sequence assembly validation, Cross-assembly, Mapping assembly 2021-11-29 2025-06-04 2 True False False True quast, hifiasm, fasta-stats, busco, gfa_to_fa, flye UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no 0 2080 2495 6.916667 0
Assembly De Bruijn Graph Assembly https://training.galaxyproject.org//topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html Formatting, Genome assembly, De-novo assembly, Optimisation and refinement, Sequence assembly visualisation, Sequence assembly 2017-05-24 2026-01-07 26 True True False True velveth, spades, bandage_image, velvetg, fasta-stats, velvetoptimiser UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz 0 4182551 9694668 10.850000 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 2026-04-22 5 True False True True mitohifi, compress_file UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 1473 1751 12.400000 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, Read mapping, Genome visualisation, Mapping, Sequence alignment 2018-06-14 2026-04-13 30 True False False True Cut1, addValue, collapse_dataset, bedtools_intersectbed, tp_cat, circos_interval_to_tiles, join1, Filter1, tp_sed_tool, cat1, lastz_wrapper_2, datamash_ops, circos_aln_to_links, fasta_compute_length, circos, upload1, tp_sort_header_tool, bedtools_complementbed, tp_grep_tool, fasta_filter_by_length, tp_replace_in_column, random_lines1, jbrowse, tp_replace_in_line, bedtools_sortbed, mergeCols1, Grep1 0 7106 13418 8.200000 0
Assembly Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data https://training.galaxyproject.org//topics/assembly/tutorials/vgp_workflow_training/tutorial.html Sequence assembly, Chromosome conformation capture Visualisation, Sequence assembly validation 2022-04-06 2026-05-18 27 True False True False quast Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 5016 6567 7.200000 0
Assembly Unicycler Assembly https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html Sequence assembly, Genomics, Microbiology Visualisation, Sequence composition calculation, Coding region prediction, Sequence assembly validation, Validation, Statistical calculation, Genome annotation, Aggregation, Gene prediction, Genome assembly, Sequencing quality control 2017-10-11 2026-01-23 25 True True False True fastqc, quast, unicycler, multiqc, prokka UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 4189132 9706589 7.116667 0
Assembly Large genome assembly and polishing https://training.galaxyproject.org//topics/assembly/tutorials/largegenome/tutorial.html Genomics, Sequence assembly, Biodiversity Visualisation, Pairwise sequence alignment, Sequence assembly validation, Statistical calculation, Sequence contamination filtering, Box-Whisker plot plotting, De-novo assembly, Base-calling, Sequence assembly visualisation, Sequencing quality control, Scatter plot plotting, Mapping assembly, Variant calling, Sequence composition calculation, Sequence assembly, Validation, Cross-assembly, Genome assembly 2023-03-06 2026-01-23 15 True False True True fastqc, quast, nanoplot, meryl, fastp, minimap2, bandage_image, multiqc, barchart_gnuplot, fasta-stats, busco, genomescope, medaka_consensus_pipeline, racon, flye UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz 0 8734 11199 5.533333 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 2026-02-12 4 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 1720793 2974513 1.366667 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, UseGalaxy.ca 0 4154712 9614957 2.066667 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, UseGalaxy.ca 0 3693964 8058439 1.983333 0
Earth Data science Introduction to climate data https://training.galaxyproject.org//topics/climate/tutorials/introduction/slides.html 2020-10-11 2026-07-13 3 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 4175411 9683493 2.066667 0
Earth Data science Getting your hands-on climate data https://training.galaxyproject.org//topics/climate/tutorials/climate-101/tutorial.html Visualisation 2020-04-30 2026-07-13 16 True False False True tp_awk_tool, ggplot2_point, psy_maps, datamash_ops, interactive_tool_panoply, Grep1, cds_essential_variability, climate_stripes UseGalaxy.eu 0 1288 1732 8.133333 0
Earth Data science Ocean's variables study https://training.galaxyproject.org//topics/climate/tutorials/ocean-variables/tutorial.html 2023-11-29 2025-05-10 5 True False False True interactive_tool_divand, interactive_tool_odv, divand_full_analysis UseGalaxy.eu 0 321 370 13.450000 0
Earth Data science Functionally Assembled Terrestrial Ecosystem Simulator (FATES) https://training.galaxyproject.org//topics/climate/tutorials/fates/tutorial.html Visualisation 2020-10-25 2026-07-13 19 True True True True __EXTRACT_DATASET__, xarray_select, ggplot2_point, interactive_tool_panoply, xarray_metadata_info, tp_find_and_replace, ctsm_fates UseGalaxy.eu, UseGalaxy.org (Main) 0 4177057 9685999 8.383333 0
Earth Data science Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools https://training.galaxyproject.org//topics/climate/tutorials/pangeo/tutorial.html Visualisation 2022-02-18 2026-07-13 7 True True True True __EXTRACT_DATASET__, regexColumn1, xarray_select, ggplot2_point, xarray_mapplot, xarray_coords_info, xarray_netcdf2netcdf, xarray_metadata_info, __MERGE_COLLECTION__, graphicsmagick_image_montage, climate_stripes UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 3568869 7658657 14.266667 0
Earth Data science 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_odv_history, interactive_tool_odv, harmonize_insitu_to_netcdf, tool_biogeochemical_calibration, tool_odv UseGalaxy.eu 0 150 165 12.050000 0
Earth Data science Pangeo Notebook in Galaxy - Introduction to Xarray https://training.galaxyproject.org//topics/climate/tutorials/pangeo-notebook/tutorial.html 2022-02-18 2026-07-13 12 True True True True interactive_tool_pangeo_notebook UseGalaxy.eu 0 3569182 7659282 15.516667 0
Earth Data science Sentinel 5P data visualisation https://training.galaxyproject.org//topics/climate/tutorials/sentinel5_data/tutorial.html 2024-01-26 2026-08-14 4 True False False True interactive_tool_copernicus_notebook, interactive_tool_panoply UseGalaxy.eu 0 442 496 7.183333 0
Earth Data science Analyse Argo data https://training.galaxyproject.org//topics/climate/tutorials/argo_pangeo/tutorial.html 2024-03-24 2025-05-10 2 True False False True interactive_tool_odv, argo_getdata, timeseries_extraction, xarray_metadata_info, xarray_coords_info UseGalaxy.eu 0 442 506 11.783333 0
Earth Data science Ocean Data View (ODV) https://training.galaxyproject.org//topics/climate/tutorials/ocean-data-view/tutorial.html 2023-11-27 2026-08-14 3 True False False False interactive_tool_odv UseGalaxy.eu, UseGalaxy.fr 0 599 706 9.583333 0
Earth Data science Collaboration with JupyterGIS https://training.galaxyproject.org//topics/climate/tutorials/jupytergis_collaboration/tutorial.html 2025-04-03 2026-08-14 6 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 286 338 9.966667 0
Earth Data science Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab https://training.galaxyproject.org//topics/climate/tutorials/fates-jupyterlab/tutorial.html 2020-10-25 2026-07-13 17 True False False False interactive_tool_jupyter_notebook UseGalaxy.eu, UseGalaxy.org (Main) 0 639 1051 9.983333 0
Earth Data science 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, c3s, spocc_occ, argo_getdata UseGalaxy.eu UseGalaxy.be 0 223 267 19.533333 0
Earth Data science Visualize Climate data with Panoply netCDF viewer https://training.galaxyproject.org//topics/climate/tutorials/panoply/tutorial.html 2020-03-05 2026-07-13 19 True False False False interactive_tool_panoply UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 6929 10981 1.950000 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 0 191 208 14.083333 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 0 222 263 16.383333 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 0 284 300 13.183333 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 2026-08-12 3 True False False False 0 81 85 14.750000 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 2025-11-27 3 True False False False 0 69 72 52.533333 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 2026-04-30 6 True False False False 0 199 224 21.966667 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 2026-08-05 8 True False False False 0 130 155 32.600000 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 99 116 36.266667 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 split_file_to_collection, ctb_alignit, sort1, openbabel_addh, tp_cat, rdconf UseGalaxy.cz 0 1509 2095 10.250000 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 tp_grep_tool, gmx_solvate, gmx_sim, gmx_em, get_pdb, gmx_setup, gmx_editconf UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 29531 51118 2.450000 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 xchem_transfs_scoring, rxdock_rbcavity, sucos_max_score, ctb_frankenstein_ligand, split_file_to_collection, enumerate_charges, rdock_rbdock, collapse_dataset, rdock_rbcavity, openbabel_compound_convert, xchem_pose_scoring, rxdock_rbdock 0 3429 5499 9.100000 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, minimizer, namd_nvt, namd_npt 0 4502 7377 4.633333 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 openbabel_svg_depiction, ctb_silicos_qed, ctb_im_rxn_maker, chembl, openbabel_compound_convert, get_pdb, md_converter UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.no 0 673 789 13.283333 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 tp_grep_tool, gmx_solvate, gmx_sim, bio3d_rmsf, ambertools_acpype, bio3d_rmsd, bio3d_pca_visualize, gmx_em, mdanalysis_cosine_analysis, bio3d_pca, openbabel_compound_convert, get_pdb, gmx_energy, md_converter, vmd_hbonds, gmx_setup, gmx_editconf, gmx_merge_topology_files UseGalaxy.org.au, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 12348 21091 4.883333 0
Computational chemistry Protein-ligand docking https://training.galaxyproject.org//topics/computational-chemistry/tutorials/cheminformatics/tutorial.html 2019-10-19 2026-07-23 18 True False False True ctb_chemfp_butina_clustering, fpocket, collapse_dataset, ctb_chemfp_mol2fps, ctb_obgrep, tp_cat, sdf_to_tab, get_pdb, openbabel_compound_convert, ctb_remIons, ctb_filter, openbabel_svg_depiction, ctb_compound_convert, docking, ctb_np-likeness-calculator, tp_grep_tool, ctb_change_title, ctb_remDuplicates, ctb_online_data_fetch, chembl, prepare_receptor, prepare_box, ctb_chemfp_nxn_clustering, tp_find_and_replace UseGalaxy.org (Main) 0 21511 35936 3.250000 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_rmsf, bio3d_rmsd, mdanalysis_rdf, mdanalysis_cosine_analysis, bio3d_pca, mdanalysis_ramachandran_plot, mdanalysis_dihedral, mdanalysis_distance UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no 0 33881 59204 2.450000 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, UseGalaxy.ca 0 2032 2691 11.550000 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 4175411 9683494 2.066667 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 2026-02-04 4 True False True False 0 723 939 14.816667 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 0 109 118 10.750000 0
Contributing to the Galaxy Training Material Creating a new tutorial https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial/tutorial.html Sequence file editing, Primer removal, Data handling, Read pre-processing, Read mapping, Sequence trimming 2018-06-20 2025-11-20 33 True False True True fastq_to_tabular, Filter1, random_lines1, Cut1, tp_sed_tool, bam_to_sam, tp_cut_tool, bowtie2, seqtk_subseq, cutadapt, c3s, tp_cat, tp_sorted_uniq 0 2081 2970 13.533333 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 0 144 148 26.266667 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 0 104 104 12.316667 0
Contributing to the Galaxy Training Material FAIR Galaxy Training Material https://training.galaxyproject.org//topics/contributing/tutorials/fair-gtn/tutorial.html 2026-08-16 2026-08-16 0 True False False False 0 2 2 0.000000 0
Contributing to the Galaxy Training Material Creating content in Markdown https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-content/tutorial.html Validation, Sequencing quality control 2017-06-25 2025-04-08 85 True False False False multiqc, upload1 0 4042 10107 7.533333 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 4175411 9683495 2.066667 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 0 194 216 27.650000 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 4175660 9683766 14.000000 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 0 742 1095 13.483333 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 0 433 749 14.633333 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 0 368 526 13.216667 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 0 329 417 20.700000 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 0 122 140 22.666667 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 5954 7110 2.016667 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 2025-12-01 33 True False False False 0 1358 1822 4.750000 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 0 642 836 17.700000 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 0 761 983 9.933333 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 0 124 166 23.550000 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 0 340 423 20.666667 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 0 169 186 12.050000 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 Sequence file editing, Generation, Data handling, Genome indexing, Read mapping, Sequence alignment 2021-08-04 2023-11-09 5 True False False True bwa_mem, trimmomatic, tp_replace_in_line, __ZIP_COLLECTION__, seqtk_subseq, __UNZIP_COLLECTION__, Grep1, samtools_fastx UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 4325 6062 9.400000 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 Sequence contamination filtering, Visualisation, Validation, Tree-based sequence alignment, Read mapping, Sequencing quality control, Variant classification 2021-06-08 2025-12-18 11 True False True True fastp, pangolin, falco, bcftools_consensus, collapse_dataset, compose_text_param, snpSift_filter, multiqc UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr 0 3303 4099 9.150000 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_upload, ena_consensus_submit 0 3854807 8593210 8.783333 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 SNP detection, Formatting, Generation, Read mapping, Validation, Genome indexing, Sequence contamination filtering, Data handling, Sequencing quality control, Sequence alignment 2020-06-24 2024-06-14 16 True False True True picard_MarkDuplicates, bwa_mem, samtools_stats, fastp, lofreq_call, Filter1, snpSift_extractFields, tp_cut_tool, lofreq_indelqual, lofreq_viterbi, fasterq_dump, Grep1, snpeff_sars_cov_2, multiqc UseGalaxy.eu, UseGalaxy.org (Main) MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 14362 21389 6.483333 0
Variant Analysis Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html Tree-based sequence alignment, Methylation analysis, Variant calling, Variant classification 2021-06-30 2025-03-28 18 True False True False nextclade, pangolin, Filter1, fasta_regex_finder, upload1, datamash_ops UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 7868 13824 7.600000 0
Using Galaxy and Managing your Data SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis https://training.galaxyproject.org//topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.html SNP detection, Data handling 2021-05-31 2024-06-14 12 True True True False jq, fastq_to_fasta_python, fasterq_dump, fastq_dump, snpeff_sars_cov_2, tp_cat, query_tabular UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3956371 8929356 11.633333 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 Generation, Genome visualisation, Sequence composition calculation, Read mapping, Statistical calculation, Genome indexing, Sequencing quality control, Sequence alignment 2023-07-10 2024-02-29 2 True False False False fastqc, jbrowse, bwa_mem UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@AuBi, Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz 0 1800 2281 11.666667 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, UseGalaxy.ca 0 2449347 4782505 42.216667 0
Foundations of Data Science R basics in Galaxy https://training.galaxyproject.org//topics/data-science/tutorials/r-basics/tutorial.html 2019-10-08 2024-06-14 11 True False True False interactive_tool_rstudio UseGalaxy.eu 0 3117 4167 9.533333 0
Foundations of Data Science Introduction to Python https://training.galaxyproject.org//topics/data-science/tutorials/python-basics/tutorial.html 2021-11-08 2024-10-15 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 1831 2339 9.983333 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, UseGalaxy.ca 0 279 326 8.833333 0
Foundations of Data Science Python - Math https://training.galaxyproject.org//topics/data-science/tutorials/python-math/tutorial.html 2022-04-25 2023-02-13 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 1173 1431 9.500000 0
Foundations of Data Science Python - Functions https://training.galaxyproject.org//topics/data-science/tutorials/python-functions/tutorial.html 2022-04-25 2023-02-13 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 1091 1269 7.616667 0
Foundations of Data Science Advanced Python https://training.galaxyproject.org//topics/data-science/tutorials/python-advanced-np-pd/tutorial.html 2021-11-08 2024-10-15 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 677 864 13.850000 0
Foundations of Data Science Advanced R in Galaxy https://training.galaxyproject.org//topics/data-science/tutorials/r-advanced/tutorial.html 2019-12-09 2024-10-15 11 True False True False interactive_tool_rstudio UseGalaxy.eu 0 1771 2704 11.650000 0
Foundations of Data Science Introduction to sequencing with Python (part one) https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture2/tutorial.html 2024-01-23 2024-02-20 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 404 475 14.233333 0
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 2023-06-16 2024-05-07 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 794 900 10.783333 0
Foundations of Data Science Python - Basic Types & Type Conversion https://training.galaxyproject.org//topics/data-science/tutorials/python-types/tutorial.html 2022-04-25 2023-02-13 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 483 762 12.833333 0
Foundations of Data Science Plotting in Python https://training.galaxyproject.org//topics/data-science/tutorials/python-plotting/tutorial.html 2021-11-08 2024-10-15 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 692 816 12.983333 0
Foundations of Data Science Data Manipulation Olympics - SQL https://training.galaxyproject.org//topics/data-science/tutorials/data-manipulation-olympics-sql/tutorial.html 2023-06-16 2024-05-07 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 995 1097 2.700000 0
Foundations of Data Science dplyr & tidyverse for data processing https://training.galaxyproject.org//topics/data-science/tutorials/r-dplyr/tutorial.html 2021-10-20 2024-10-15 6 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 746 937 8.466667 0
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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 2026-03-30 4 True True True False ncbi_blastp_wrapper Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@Pasteur, GalaxyTrakr, IPK Galaxy Blast Suite, MISSISSIPPI, PepSimili, PhagePromotor, UseGalaxy.no 0 2606640 5132915 25.200000 0
Foundations of Data Science CLI basics https://training.galaxyproject.org//topics/data-science/tutorials/cli-basics/tutorial.html 2021-09-30 2024-10-15 10 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 1343 1839 11.016667 0
Foundations of Data Science SQL Educational Game - Murder Mystery https://training.galaxyproject.org//topics/data-science/tutorials/sql-game/tutorial.html 2021-10-11 2023-11-23 6 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 809 875 6.466667 0
Foundations of Data Science One protein along the UniProt page https://training.galaxyproject.org//topics/data-science/tutorials/online-resources-protein/tutorial.html 2023-09-07 2026-03-30 6 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 729 774 7.133333 0
Foundations of Data Science CLI Educational Game - Bashcrawl https://training.galaxyproject.org//topics/data-science/tutorials/cli-bashcrawl/tutorial.html 2021-09-30 2024-10-15 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 2433 2745 2.733333 0
Foundations of Data Science Advanced CLI in Galaxy https://training.galaxyproject.org//topics/data-science/tutorials/cli-advanced/tutorial.html 2021-09-30 2024-10-15 11 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 1106 1372 10.650000 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 0 435 673 8.500000 0
Foundations of Data Science Advanced SQL https://training.galaxyproject.org//topics/data-science/tutorials/sql-advanced/tutorial.html 2021-10-11 2024-12-13 9 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 1582 1955 4.033333 0
Foundations of Data Science Variant Calling Workflow https://training.galaxyproject.org//topics/data-science/tutorials/bash-variant-calling/tutorial.html 2022-07-07 2023-10-23 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 10389 13499 4.116667 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 UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 578 762 9.700000 0
Foundations of Data Science Make & Snakemake https://training.galaxyproject.org//topics/data-science/tutorials/snakemake/tutorial.html 2021-11-18 2025-07-09 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 3736 4742 2.833333 0
Foundations of Data Science Basics of using Git from the Command Line https://training.galaxyproject.org//topics/data-science/tutorials/git-cli/tutorial.html 2022-06-16 2023-11-16 6 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 233 479 12.600000 0
Foundations of Data Science Introduction to SQL https://training.galaxyproject.org//topics/data-science/tutorials/sql-basic/tutorial.html 2021-10-11 2024-12-13 8 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 779 949 9.766667 0
Foundations of Data Science SQL with R https://training.galaxyproject.org//topics/data-science/tutorials/sql-r/tutorial.html 2021-10-11 2023-11-16 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 687 848 7.666667 0
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Development in Galaxy JavaScript plugins https://training.galaxyproject.org//topics/dev/tutorials/visualization-charts/tutorial.html 2017-06-22 2025-04-08 20 True True False False 0 4176206 9684437 10.083333 0
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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 2017-01-17 2023-11-16 22 True True True False 0 4176294 9684623 15.366667 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 4175656 9683814 18.683333 0
Development in Galaxy ToolFactory: Generating Tools From Simple Scripts https://training.galaxyproject.org//topics/dev/tutorials/tool-generators/tutorial.html 2021-05-26 2024-06-14 10 True True True False 0 3963998 8954441 10.316667 0
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Development in Galaxy Generic plugins https://training.galaxyproject.org//topics/dev/tutorials/visualization-generic/tutorial.html 2016-09-30 2023-11-09 21 True True False False 0 4175851 9684099 12.033333 0
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Development in Galaxy Prerequisites for building software/conda packages https://training.galaxyproject.org//topics/dev/tutorials/conda_sys/slides.html 2018-02-15 2021-05-28 6 False True False False 0 4175411 9683506 2.066667 0
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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 3055 4820 6.133333 0
Development in Galaxy nb2workflow: Generating Galaxy Tools From Jupyter Notebooks https://training.galaxyproject.org//topics/dev/tutorials/tool-from-notebook/tutorial.html 2025-12-04 2025-12-04 1 True False False False 0 112 119 11.183333 0
Development in Galaxy Debugging Galaxy https://training.galaxyproject.org//topics/dev/tutorials/debugging/tutorial.html 2021-06-15 2026-02-19 16 True False False False 0 707 1313 12.033333 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 0 327 418 20.083333 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 91 95 34.683333 0
Development in Galaxy Writing Automated Tests for Galaxy https://training.galaxyproject.org//topics/dev/tutorials/writing_tests/tutorial.html 2022-07-15 2026-02-19 7 True False False False 0 356 784 18.433333 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 1470 1918 9.216667 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 0 285 395 13.200000 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 0 367 426 14.816667 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 0 531 617 14.500000 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 2026-08-12 7 True False False True tp_grep_tool, Remove beginning1, tp_replace_in_line, diff, tp_find_and_replace, wordcloud UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu 0 344 401 10.600000 0
Digital Humanities Transcribing Audio and Video files with Automated Speech Recognition https://training.galaxyproject.org//topics/digital-humanities/tutorials/Whisper_speech_recognition/tutorial.html 2026-04-08 2026-04-08 1 True False False True tp_grep_tool, whisperx, tp_find_and_replace UseGalaxy.eu 0 177 195 9.850000 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 2026-04-29 3 True False False True tp_grep_tool, filter_tabular, regexColumn1, Remove beginning1, Cut1, barchart_gnuplot, interactive_tool_openrefine, datamash_ops, param_value_from_file, compose_text_param, tp_sort_header_tool, tp_head_tool, wordcloud UseGalaxy.eu 0 309 344 14.333333 0
Digital Humanities Montreal Forced Aligner https://training.galaxyproject.org//topics/digital-humanities/tutorials/mfa_tutorial/tutorial.html 2026-07-22 2026-07-22 1 True False False True mfa_g2p, mfa_find_oovs, mfa_align, mfa_merge, unzip UseGalaxy.eu 0 50 52 17.783333 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 2026-05-06 7 True False False True Cut1, datamash_ops, tp_replace_in_line, Add_a_column1, tp_sort_header_tool, diff, Grep1, wordcloud UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu 0 321 358 10.900000 0
Digital Humanities Text-Mining articles with GROBID https://training.galaxyproject.org//topics/digital-humanities/tutorials/grobid/tutorial.html 2026-08-13 2026-08-13 1 True False False False grobid_grobid, grobid_dataset_annotate, Grep1, tesseract UseGalaxy.eu 0 6 6 0.916667 0
Ecology Object detection with YOLO https://training.galaxyproject.org//topics/ecology/tutorials/yolo_predict_deepsea/tutorial.html 2026-05-06 2026-05-08 3 True False False True yolo_predict, unzip, yolo_training UseGalaxy.eu 0 130 152 41.766667 0
Ecology RAD-Seq Reference-based data analysis https://training.galaxyproject.org//topics/ecology/tutorials/ref-based-rad-seq/tutorial.html Generation, Sequence composition calculation, Validation, Read mapping, Statistical calculation, Genome indexing, Data handling, Sequencing quality control, Sequence alignment 2017-02-14 2026-05-07 16 True False False True fastqc, Convert characters1, regex_replace, stacks_procrad, multiqc, Filter1, Cut1, cat1, stacks_populations, addValue, tp_replace_in_line, bwa, bwa_wrapper, tp_sort_header_tool, Grep1, Summary_Statistics1, Count1, stacks_refmap 0 3677 5528 5.600000 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_holoviz, interactive_tool_copernicus_notebook UseGalaxy.eu 0 304 347 14.833333 0
Ecology Data submission using ENA upload Tool https://training.galaxyproject.org//topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html Visualisation, Primer removal, Validation, Read pre-processing, Read mapping, Sequencing quality control, Sequence trimming 2024-12-13 2026-07-24 4 True False False False fastq_to_fasta_python, ncbi_blastn_wrapper, regex1, bg_uniq, falco, collection_element_identifiers, fastq_filter, __FILTER_EMPTY_DATASETS__, ab1_fastq_converter, Paste1, cutadapt, fastq_groomer, multiqc, __RELABEL_FROM_FILE__ UseGalaxy.eu UseGalaxy.cz 0 452 476 5.750000 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 2026-05-07 14 True False False True stacks_denovomap, stacks_genotypes UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 1010 1372 9.700000 0
Ecology Champs blocs indicators https://training.galaxyproject.org//topics/ecology/tutorials/champs-blocs/tutorial.html 2023-01-04 2026-05-07 13 True False False True cb_dissim, cb_qecb, cb_div, cb_ivr, cb_eco 0 241 398 28.200000 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 2026-05-07 24 True False True True datamash_transpose, pampa_communitymetrics, pampa_presabs, regexColumn1, regex1, Filter1, pampa_glmcomm, pampa_glmsp, tp_cut_tool, tp_cat, tp_sort_header_tool, mergeCols1, pampa_plotglm, tp_easyjoin_tool, Count1 UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr 0 1217 1594 11.800000 0
Ecology Obis marine indicators https://training.galaxyproject.org//topics/ecology/tutorials/obisindicators/tutorial.html Biodiversity, Ecology, Data mining 2023-04-11 2026-05-19 10 True False False True obis_data, obisindicators, tp_cut_tool UseGalaxy.eu UseGalaxy.be 0 440 535 13.516667 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 2026-05-07 3 True False False True cshl_fastq_to_fasta, fastp, ncbi_blastn_wrapper, Count1 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 853 1030 7.800000 0
Ecology Metabarcoding/eDNA through Obitools https://training.galaxyproject.org//topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html Sequencing quality control, Statistical calculation, Sequence composition calculation 2022-02-28 2026-05-07 13 True False True True fastqc, obi_clean, obi_illumina_pairend, wc_gnu, obi_uniq, ncbi_blastn_wrapper, join1, Filter1, Cut1, obi_tab, obi_ngsfilter, obi_stat, seq_filter_by_id, fastq_groomer, unzip, obi_grep, obi_annotate UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no UseGalaxy.cz, UseGalaxy.fr 0 5188 7121 4.333333 0
Ecology Phylodiversity analysis quick tutorial https://training.galaxyproject.org//topics/ecology/tutorials/phylodiversity_workflow/tutorial.html 2025-06-06 2026-05-07 2 True False False False phylogenetic_occupancy_matcher, estimate_endem, phylo_index, crsconverter UseGalaxy.eu 0 178 212 32.466667 0
Ecology Marine Omics identifying biosynthetic gene clusters https://training.galaxyproject.org//topics/ecology/tutorials/marine_omics_bgc/tutorial.html Protein feature detection, Genome annotation, Sequence motif recognition 2024-08-19 2025-06-03 3 True False False True regex1, prodigal, sanntis_marine, SanntiS_marine, interproscan 0 355 395 19.816667 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 Expression analysis, Cross-assembly, Statistical calculation, Taxonomic classification 2024-03-04 2026-04-08 6 True False False True upload1, est_abundance, kraken2, recentrifuge UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main) 0 1107 1465 9.650000 0
Ecology Life Traits Ecoregionalization workflow https://training.galaxyproject.org//topics/ecology/tutorials/ecoregiolifetraits/tutorial.html 2025-06-02 2026-05-07 4 True False False False regexColumn1, Filter1, ecoregion_taxa_seeker, ecoregion_eco_map, tp_cut_tool, ClaraGuess, column_remove_by_header, ecoregion_brt_analysis, unzip, ecoregion_GeoNearestNeighbor, WormsMeasurements UseGalaxy.eu 0 108 113 41.300000 0
Ecology Ecoregionalization workflow tutorial https://training.galaxyproject.org//topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html 2024-09-16 2026-05-22 8 True False False True filter_tabular, interactive_tool_jupyter_notebook, regexColumn1, unzip, ecoregion_taxa_seeker, ecoregion_cluster_estimate, ecoregion_eco_map, tp_cut_tool, mergeCols1, ecoregion_brt_analysis, ecoregion_clara_cluster, ecoregion_GeoNearestNeighbor UseGalaxy.eu 0 493 609 12.683333 0
Ecology Regional GAM https://training.galaxyproject.org//topics/ecology/tutorials/regionalGAM/tutorial.html Ecology Visualisation 2019-07-04 2026-05-07 19 True False False True tp_awk_tool, regionalgam_gls, Remove beginning1, Filter1, regexColumn1, regionalgam_autocor_acf, csv2tab_R, ggplot2_point, tab2csv_R, Paste1, regionalgam_glmmpql, mergeCols1, regionalgam_ab_index, flight-curve, regionalgam_plot_trend, regionalgam_flight_curve, Count1 0 419 537 16.233333 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 Filter1, spocc_occ, gdal_ogr2ogr, Summary_Statistics1, Count1 UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no 0 905 1084 6.100000 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 2026-05-07 9 True False False False interactive_tool_metashark UseGalaxy.eu, UseGalaxy.fr 0 378 442 5.150000 0
Ecology SAM3 – AI-based Semantic Segmentation of marine biodiversity Images and Videos https://training.galaxyproject.org//topics/ecology/tutorials/SAM3/tutorial.html 2026-05-07 2026-05-12 3 True False False False interactive_tool_anylabeling, sam3_semantic_segmentation UseGalaxy.eu 0 227 267 18.033333 0
Ecology Species distribution modeling https://training.galaxyproject.org//topics/ecology/tutorials/species-distribution-modeling/tutorial.html 2019-07-04 2026-05-07 19 True False False True tp_find_and_replace, Filter1, interactive_tool_wallace, spocc_occ, tp_cut_tool, tabular_to_csv UseGalaxy.eu, UseGalaxy.fr 0 3582 5297 4.766667 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 graphicsmagick_image_montage, xarray_mapplot, cdo_operations, xarray_metadata_info, xarray_coords_info UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz 0 2662 3051 3.633333 0
Ecology Sentinel 2 biodiversity https://training.galaxyproject.org//topics/ecology/tutorials/remote-sensing/tutorial.html 2023-04-13 2025-12-08 7 True False False True srs_global_indices, srs_preprocess_s2, srs_pca, srs_spectral_indices, srs_process_data, srs_diversity_maps UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 741 927 10.350000 0
Ecology Preparing genomic data for phylogeny reconstruction https://training.galaxyproject.org//topics/ecology/tutorials/phylogeny-data-prep/tutorial.html Sequence assembly validation, Genetic variation analysis, Multiple sequence alignment, Sequence analysis, Sequence clustering, Genome annotation, Sequence trimming 2022-10-21 2025-06-03 5 True False False True funannotate_predict, repeatmasker_wrapper, regex1, Filter1, glimmer_gbk_to_orf, proteinortho, proteinortho_grab_proteins, collapse_dataset, clipkit, phykit_alignment_based, tp_replace_in_line, busco, clustalw UseGalaxy.be 0 2568 3472 7.000000 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 2026-05-07 15 True False False True fastqc, stacks_denovomap, stacks_populations, stacks_procrad UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no 0 2871 4486 5.900000 0
Ecology Biodiversity data exploration https://training.galaxyproject.org//topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html 2022-03-01 2026-04-24 16 True False True True tool_anonymization, Remove beginning1, regexColumn1, tp_cut_tool, ecology_beta_diversity, ecology_homogeneity_normality, ecology_link_between_var, ecology_stat_presence_abs, ecology_presence_abs_abund UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr 0 1864 2567 12.200000 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 2026-05-07 7 True False False False interactive_tool_metashrimps UseGalaxy.eu 0 182 194 10.216667 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, UseGalaxy.ca 0 141 160 18.866667 0
Ecology QGIS Web Feature Services https://training.galaxyproject.org//topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.html 2023-10-11 2026-05-07 7 True False False False interactive_tool_qgis UseGalaxy.eu, UseGalaxy.fr 0 411 461 13.000000 0
Ecology Visualize EBV cube data with Panoply netCDF viewer https://training.galaxyproject.org//topics/ecology/tutorials/panoply_ebv/tutorial.html 2022-10-28 2026-05-07 10 True False False False interactive_tool_panoply UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 349 417 11.866667 0
Ecology Cleaning GBIF data using OpenRefine https://training.galaxyproject.org//topics/ecology/tutorials/openrefine_gbif/tutorial.html 2025-01-21 2026-05-07 7 True False False False interactive_tool_openrefine, regex1 UseGalaxy.eu, UseGalaxy.fr 0 302 357 7.550000 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 2026-07-13 5 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 2238 2801 4.483333 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, UseGalaxy.ca 0 1244 1556 4.416667 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, UseGalaxy.ca 0 1800088 3166700 14.183333 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, UseGalaxy.ca 0 452 528 9.933333 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, UseGalaxy.ca 0 1800088 3166699 34.300000 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, UseGalaxy.ca 0 355 397 5.266667 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, UseGalaxy.ca 0 98 120 13.433333 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, UseGalaxy.ca 0 1800180 3166805 23.150000 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 0 158 180 32.833333 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 1446 1670 4.783333 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 1802 2107 3.133333 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 2085 2476 3.433333 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, UseGalaxy.ca 0 1334 1628 5.666667 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, UseGalaxy.ca 0 4175411 9683513 2.066667 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, UseGalaxy.ca 0 4175411 9683513 2.066667 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 Enrichment analysis, Structure visualisation, Genome visualisation, Sequence composition calculation, Read pre-processing, Sequence trimming, Mapping, Statistical calculation, Read mapping, Gene regulatory network analysis, Pathway visualisation, Primer removal, Sequencing quality control, Peak calling 2018-09-17 2026-04-13 16 True True False True jbrowse2, deeptools_plot_heatmap, trim_galore, fastqc, Filter1, cat1, deeptools_bam_coverage, bbgtobigwig, deeptools_plot_fingerprint, samtools_idxstats, bedtools_mergebed, deeptools_plot_correlation, deeptools_bam_compare, bowtie2, bedtools_sortbed, deeptools_compute_matrix, __FLATTEN__, macs2_callpeak, deeptools_multi_bam_summary UseGalaxy.eu, UseGalaxy.org (Main) 0 4182045 9696229 9.950000 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 Enrichment analysis, Generation, Sequence composition calculation, Read mapping, Mapping, Statistical calculation, Genome indexing, Gene regulatory network analysis, Sequencing quality control, Sequence alignment, Peak calling 2016-12-20 2025-04-08 11 True False False True fastqc, trimmomatic, deeptools_bam_compare, deeptools_correct_gc_bias, macs2_callpeak, bwa, deeptools_compute_matrix, bedtools_intersectbed, deeptools_plot_fingerprint, deeptools_plot_correlation, deeptools_compute_gc_bias, samtools_idxstats, deeptools_plot_heatmap, deeptools_multi_bam_summary UseGalaxy.be, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 7919 14323 7.483333 0
Epigenetics ATAC-Seq data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/atac-seq/tutorial.html Visualisation, Enrichment analysis, Formatting, Sequence composition calculation, Sequencing quality control, Read pre-processing, Read mapping, Mapping, Statistical calculation, Sequence trimming, Gene regulatory network analysis, Data handling, Primer removal, Sequence alignment analysis, Peak calling 2019-09-02 2025-12-18 24 True True True True Cut1, deeptools_plot_heatmap, bedtools_intersectbed, fastqc, Filter1, samtools_idxstats, bamFilter, wig_to_bigWig, pe_histogram, tp_sort_header_tool, picard_MarkDuplicates, bedtools_bamtobed, bowtie2, pygenomeTracks, deeptools_compute_matrix, cutadapt, __FLATTEN__, Grep1, macs2_callpeak 0 4244971 9806013 4.866667 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 Remove beginning1, Cut1, clusterprofiler_bitr, clusterprofiler_go, chipeakanno_annopeaks, minfi_analysis UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 4177692 9687016 8.916667 0
Epigenetics Hi-C analysis of Drosophila melanogaster cells using HiCExplorer https://training.galaxyproject.org//topics/epigenetics/tutorials/hicexplorer/tutorial.html Visualisation, Read mapping, Formatting 2018-02-23 2026-03-16 31 True False False True hicexplorer_hicmergematrixbins, hicexplorer_hicfindtads, hicexplorer_hiccorrectmatrix, hicexplorer_hicdetectloops, bowtie2, hicexplorer_hicbuildmatrix, hicexplorer_hicinfo, pygenomeTracks, hicexplorer_hicplotmatrix, hicexplorer_hicfindrestrictionsites, hicexplorer_hicpca UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu UseGalaxy.no, UseGalaxy.org (Main) 0 8334 13575 3.966667 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 Enrichment analysis, Sequence composition calculation, Read pre-processing, Read mapping, Sequence trimming, Statistical calculation, Gene regulatory network analysis, Primer removal, Sequencing quality control, Peak calling 2017-09-18 2025-04-08 10 True False False True fastqc, deeptools_bam_compare, deeptools_bam_coverage, bam_to_sam, bowtie2, trim_galore, macs2_callpeak, deeptools_compute_matrix, deeptools_plot_fingerprint, deeptools_plot_correlation, deeptools_compute_gc_bias, samtools_idxstats, deeptools_plot_heatmap, deeptools_multi_bam_summary UseGalaxy.be Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 2118 3058 7.033333 0
Epigenetics DNA Methylation data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/methylation-seq/tutorial.html Epigenomics Visualisation, Sequence composition calculation, Read mapping, Sequencing quality control, Statistical calculation 2017-02-16 2025-04-03 24 True False False True fastqc, bwameth, tp_awk_tool, falco, wig_to_bigWig, tp_tail_tool, deeptools_compute_matrix, metilene, deeptools_plot_profile, pileometh, replace_column_with_key_value_file 0 16497 26800 4.766667 0
Epigenetics CUT&RUN data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/cut_and_run/tutorial.html Visualisation, Enrichment analysis, Formatting, Read pre-processing, Mapping, Read mapping, Sequence trimming, Validation, Gene regulatory network analysis, Data handling, Sequence alignment analysis, Primer removal, Sequencing quality control, Peak calling 2024-03-06 2025-03-19 5 True False False True deeptools_plot_heatmap, falco, trim_galore, meme_chip, bedtools_intersectbed, datamash_transpose, Extract genomic DNA 1, deeptools_plot_fingerprint, __EXTRACT_DATASET__, bamFilter, wig_to_bigWig, pe_histogram, idr, multiqc, picard_MarkDuplicates, bedtools_bamtobed, bowtie2, deeptools_compute_matrix, __FLATTEN__, Grep1, macs2_callpeak 0 8622 10866 2.666667 0
Evolution Phylogenetics - Back to basics https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo/tutorial.html Phylogenetic analysis, Multiple sequence alignment, Phylogenetic tree analysis, Sequence analysis, Phylogenetic tree reconstruction, Phylogenetic tree generation 2024-05-10 2024-05-10 1 True False False True rbc_mafft, iqtree, fasttree, newick_display UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 8004 10179 4.033333 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, UseGalaxy.ca 0 2250206 4304817 1.666667 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, UseGalaxy.ca 0 2250206 4304817 1.666667 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, UseGalaxy.ca 0 2250206 4304817 1.666667 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, UseGalaxy.ca 0 2250206 4304817 1.666667 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, UseGalaxy.ca 0 2250206 4304817 1.666667 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, UseGalaxy.ca 0 2250206 4304817 1.666667 0
Evolution Identifying tuberculosis transmission links: from SNPs to transmission clusters https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html Genomics, Microbiology, Infectious disease, DNA polymorphism Antimicrobial resistance prediction, Phylogenetic tree visualisation, Variant calling, Phylogenetic tree generation 2022-03-16 2025-05-26 13 True False False True collapse_dataset, snp_sites, tp_cat, tp_easyjoin_tool, tp_sed_tool, tb_profiler_profile, tb_variant_filter, trimmomatic, upload1, bcftools_consensus, samtools_view, clustering_from_distmat, snp_dists, tp_grep_tool, snippy, addName, tp_replace_in_line, Grep1, __MERGE_COLLECTION__ UseGalaxy.eu 0 3869 5496 7.983333 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 raxml, interactive_tool_rstudio, upload1 UseGalaxy.eu 0 2728 3842 8.850000 0
Evolution Phylogenetic analysis for bacterial comparative genomics https://training.galaxyproject.org//topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html Genomics, Microbiology, Phylogeny 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 0 247 292 22.500000 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, UseGalaxy.ca 0 782 998 9.916667 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, UseGalaxy.ca 0 459 572 14.100000 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, UseGalaxy.ca 0 885 1017 5.883333 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, UseGalaxy.ca 0 515 620 6.000000 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, UseGalaxy.ca 0 1135 1419 10.116667 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, UseGalaxy.ca 0 258 284 7.966667 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, UseGalaxy.ca 0 169 203 7.333333 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, UseGalaxy.ca 0 2011393 3679660 13.916667 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, UseGalaxy.ca 0 501 595 14.150000 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, UseGalaxy.ca 0 342 391 11.200000 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, UseGalaxy.ca 0 358 396 13.400000 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, UseGalaxy.ca 0 402 477 14.083333 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, UseGalaxy.ca 0 242 280 21.033333 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, UseGalaxy.ca 0 166 174 8.400000 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, UseGalaxy.ca 0 520 591 13.000000 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, UseGalaxy.ca 0 131 149 10.966667 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, UseGalaxy.ca 0 182 194 21.866667 0
FAIR Data, Workflows, and Research FAIR Bioimage Metadata https://training.galaxyproject.org//topics/fair/tutorials/bioimage-metadata/tutorial.html 2023-09-13 2025-11-27 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 450 521 12.583333 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 2025-11-27 9 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 494 559 12.733333 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, UseGalaxy.ca 0 395 467 8.833333 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 2026-05-28 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 409 491 12.200000 0
FAIR Data, Workflows, and Research Data management in Medicinal Chemistry https://training.galaxyproject.org//topics/fair/tutorials/med-chem-data/tutorial.html 2026-08-16 2026-08-16 0 True False True True openbabel_svg_depiction, ctb_silicos_qed, ctb_im_rxn_maker, chembl, openbabel_compound_convert, get_pdb, md_converter UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.no 0 1 1 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, UseGalaxy.ca 0 1949896 3535120 1.516667 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, UseGalaxy.ca 0 121 128 21.200000 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, UseGalaxy.ca 0 155 164 30.983333 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 Show beginning1, Paste1, tp_tac Galaxy@AuBi, GalaxyTrakr, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) HyPhy HIV NGS Tools, MISSISSIPPI 0 6632 8196 7.600000 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 Remove beginning1, Cut1, ggplot2_point, upload1, Grouping1, datamash_ops, csv_to_tabular, tp_sorted_uniq UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz 0 1046 1396 11.500000 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 intermine, galaxy_intermine_exchange UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no 0 279 345 27.066667 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.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) HyPhy HIV NGS Tools, MISSISSIPPI 0 2191 2764 10.450000 0
Using Galaxy and Managing your Data Galaxy workflows in Dockstore https://training.galaxyproject.org//topics/galaxy-interface/tutorials/galaxy-on-dockstore/slides.html 2022-01-14 2022-10-27 4 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 3627764 7847534 1.966667 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, UseGalaxy.ca 0 4175411 9683514 2.066667 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 0 411 491 25.383333 0
Using Galaxy and Managing your Data Accessing IIIF from within Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/iiif/tutorial.html 2026-07-14 2026-08-13 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 21 22 7.883333 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 2026-07-23 9 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 3275 4203 11.150000 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) 0 2335 3651 9.950000 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, UseGalaxy.ca 0 217 250 17.000000 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, UseGalaxy.ca 0 953 1256 16.766667 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 Visualisation, Validation, Read mapping, Sequencing quality control 2025-05-26 2025-05-26 1 True False False False falco, multiqc UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr 0 501 581 8.233333 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, UseGalaxy.ca 0 341 451 12.383333 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, UseGalaxy.ca 0 509 732 22.866667 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 2026-01-23 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 8170 10703 4.433333 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, UseGalaxy.ca 0 6125 7831 10.083333 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, UseGalaxy.ca 0 1889 2476 13.050000 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, UseGalaxy.ca 0 2965 3950 11.183333 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 2026-07-23 13 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 6111 7772 10.066667 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 2025-12-17 11 True False True False interactive_tool_jupyter_notebook UseGalaxy.eu, UseGalaxy.org (Main) 0 3053 4001 8.483333 0
Using Galaxy and Managing your Data RStudio in Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/rstudio/tutorial.html 2019-10-08 2026-02-25 16 True False False False interactive_tool_rstudio UseGalaxy.eu 0 5731 8842 8.233333 0
Using Galaxy and Managing your Data Using dataset collections https://training.galaxyproject.org//topics/galaxy-interface/tutorials/collections/tutorial.html Generation, Read mapping, Sequence alignment, Genome indexing 2016-09-30 2024-12-05 20 True False True False bwa_mem, snpSift_extractFields, collapse_dataset, lofreq_call UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 17529 23709 8.733333 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, UseGalaxy.ca 0 439 555 16.583333 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, UseGalaxy.ca 0 142 154 17.566667 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 bedtools_maskfastabed, repeatmodeler, repeatmasker_wrapper, red UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 11449 14431 4.333333 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, UseGalaxy.ca 0 4175541 9683666 2.066667 0
Genome Annotation Genome annotation with Funannotate https://training.galaxyproject.org//topics/genome-annotation/tutorials/funannotate/tutorial.html Gene and protein families Sequence annotation, Formatting, Sequence motif recognition, Genome visualisation, Homology-based gene prediction, Information extraction, Query and retrieval, Genome annotation, Sequence assembly validation, Sequence alignment, Protein feature detection, Fold recognition 2021-11-29 2025-06-10 26 True False True True funannotate_compare, funannotate_predict, picard_MergeSamFiles, jbrowse, interproscan, busco, eggnog_mapper, rna_star, aegean_parseval, funannotate_annotate UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz 0 12400 17210 5.600000 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 Transcriptome assembly, Multiple sequence alignment, De-novo assembly, Database search, Coding region prediction, Sequence alignment analysis, Phylogenetic tree generation 2022-09-08 2025-06-03 10 True False False True bg_diamond_view, gops_intersect_1, bg_diamond, join1, Filter1, Cut1, cat1, regexColumn1, rapidnj, collapse_dataset, tab2fasta, Add_a_column1, orfipy, tp_split_on_column, rbc_mafft, bg_diamond_makedb UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 2178 2964 10.216667 0
Genome Annotation Genome annotation with Maker (short) https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html Sequence annotation, Genome visualisation, Genome annotation, Sequence assembly validation 2021-01-12 2024-02-29 3 True False False True gffread, jbrowse, maker, fasta-stats, busco, jcvi_gff_stats, maker_map_ids UseGalaxy.be 0 4411 6108 9.516667 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 Read pre-processing, Transposon prediction, Primer removal, Sequence trimming 2019-07-02 2024-03-18 12 True True False True __EXTRACT_DATASET__, Filter1, bowtie_wrapper, Cut1, deeptools_bam_coverage, bg_find_subsequences, Add_a_column1, tp_sort_header_tool, gff_to_prot, transit_gumbel, cutadapt, tp_easyjoin_tool UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.no UseGalaxy.cz, UseGalaxy.eu 0 4184362 9699178 5.833333 0
Genome Annotation Genome annotation with Maker https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html Sequence annotation, Homology-based gene prediction, Genome visualisation, Ab-initio gene prediction, Genome annotation, Sequence assembly validation, Operation, Gene prediction 2018-09-24 2024-02-29 14 True False False True gffread, augustus_training, jbrowse, maker, snap_training, fasta-stats, busco, jcvi_gff_stats, maker_map_ids UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz 0 14506 25262 4.450000 0
Genome Annotation Functional annotation of protein sequences https://training.galaxyproject.org//topics/genome-annotation/tutorials/functional/tutorial.html Function analysis, Protein sites, features and motifs Sequence motif recognition, Homology-based gene prediction, Information extraction, Protein feature detection, Genome annotation, Sequence alignment analysis, Fold recognition, Query and retrieval 2022-07-20 2025-06-03 12 True False False True interproscan, eggnog_mapper, ncbi_blastp_wrapper, bg_diamond UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.no 0 5283 6900 6.233333 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 jbrowse, create_or_update, iframe UseGalaxy.no UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu 0 1811 2609 11.166667 0
Genome Annotation Long non-coding RNAs (lncRNAs) annotation with FEELnc https://training.galaxyproject.org//topics/genome-annotation/tutorials/lncrna/tutorial.html Classification, Sequence annotation, Annotation, RNA-Seq analysis, Transcriptome assembly 2022-09-23 2024-09-18 11 True False True True gffread, stringtie, Extract_features1, tp_cat, feelnc UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 2340 3082 9.933333 0
Genome Annotation CRISPR screen analysis https://training.galaxyproject.org//topics/genome-annotation/tutorials/crispr-screen/tutorial.html Sequence composition calculation, Read pre-processing, Sequence trimming, Validation, Statistical calculation, Genetic variation analysis, Primer removal, Sequencing quality control 2021-10-15 2024-08-08 12 True True True True fastqc, mageck_count, mageck_mle, tp_awk_tool, volcanoplot, mageck_test, cutadapt, multiqc UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3785946 8322318 4.750000 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 Coding region prediction, Genome annotation, Gene prediction, Genome visualisation 2018-03-06 2026-01-23 27 True True True True jbrowse, prokka UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 4195505 9716897 7.150000 0
Genome Annotation Secondary metabolite discovery https://training.galaxyproject.org//topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html Gene prediction, Data handling, Service invocation, Differential gene expression analysis, Sequence clustering 2024-02-21 2024-09-27 2 True False False True edu.tamu.cpt.gff3.customGbkToGff, tp_awk_tool, interactive_tool_jupyter_notebook, Remove beginning1, ncbi_acc_download, ctb_simsearch, ctb_silicos_qed, collapse_dataset, openbabel_remDuplicates, bp_genbank2gff3, ctb_chemfp_mol2fps, antismash, ctb_np-likeness-calculator UseGalaxy.eu 0 1012 1249 3.966667 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 clustalw, chromeister, tp_awk_tool, gecko UseGalaxy.org.au, UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz 0 4131336 9523734 10.333333 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, Gene prediction, Genome visualisation, Differential protein expression profiling, Genome annotation, Sequence assembly validation, Sequence alignment 2025-03-17 2026-07-30 5 True False False True omark, gffread, jbrowse, fasta-stats, busco, rna_star, braker3 0 2485 2983 4.766667 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, Gene prediction, Genome visualisation, Differential protein expression profiling, Genome annotation, Sequence assembly validation 2024-08-21 2025-06-04 8 True False False True omark, gffread, jbrowse, busco, jcvi_gff_stats, helixer 0 1826 2149 6.800000 0
Genome Annotation Bacterial Genome Annotation https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements Sequence motif recognition, Multilocus sequence typing, Genome visualisation, Structural variation detection, Genome annotation, Nucleic acid feature detection, Genome assembly, Protein feature detection, Scaffolding 2024-02-01 2024-10-15 6 True False True True tbl2gff3, plasmidfinder, tp_replace_in_column, jbrowse, integron_finder, upload1, Grouping1, tp_tail_tool, bakta, isescan UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main) 0 9152 12508 8.100000 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 jbrowse, create_or_update, list_organism, iframe, create_account UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3950891 8907559 13.533333 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 Genome annotation, Read mapping, Antimicrobial resistance prediction, Genome visualisation 2024-01-23 2025-12-18 10 True False True True tbl2gff3, jbrowse, upload1, bowtie2, bakta, staramr_search, Grep1 Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.org (Main) 0 4781 6459 9.233333 0
Genome Annotation Comparison of two annotation tools - Helixer and Braker3 https://training.galaxyproject.org//topics/genome-annotation/tutorials/comparison-braker-helixer-annotation/tutorial.html Sequence assembly, Genomics Sequence annotation, Genome visualisation, Genome annotation, Sequence assembly validation, Gene prediction, Differential protein expression profiling, Sequence alignment 2025-06-20 2025-06-25 2 True False False True omark, gffread, jbrowse, busco, rna_star, helixer, braker3 0 933 1068 7.916667 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, UseGalaxy.ca 0 71 77 17.200000 0
Genome Annotation Bacterial genome quality control https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html Genomics, Microbiology Sequence assembly validation, Sequence composition calculation, Validation, Sequencing quality control, Statistical calculation, Genome comparison 2025-03-14 2025-03-14 1 True False False False checkm2, drep_dereplicate, upload1 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz 0 248 288 21.783333 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 upload1, ppanggolin_all, ppanggolin_msa UseGalaxy.eu, UseGalaxy.fr 0 198 227 18.466667 0
Genome Annotation Pangenome analysis with Roary https://training.galaxyproject.org//topics/genome-annotation/tutorials/pangenome-annotation-with-roary/tutorial.html Genomics Phylogenetic analysis, Genome annotation, Gene prediction, Genome assembly, Sequence analysis, Coding region prediction 2026-07-21 2026-07-21 1 True False False False iqtree, upload1, roary, prokka GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, UseGalaxy.fr, UseGalaxy.no 0 104 116 5.350000 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, UseGalaxy.ca 0 35513 64415 2.116667 0
Genome Annotation Dataset construction for bacterial comparative genomics https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html Genomics, Microbiology Sequence database search, Data retrieval, Data handling 2025-03-14 2026-04-13 2 True False False False Remove beginning1, bg_uniq, Cut1, cat1, upload1, datasets_download_genome, sort1 UseGalaxy.fr UseGalaxy.cz 0 156 174 38.400000 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 visualisation, Variant calling, Genome visualisation, Phylogenetic tree generation 2018-02-26 2026-01-23 25 True False False True jbrowse, snippy UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 16597 26086 5.033333 0
Visualisation Genomic Data Visualisation with JBrowse https://training.galaxyproject.org//topics/visualisation/tutorials/jbrowse/tutorial.html Genome visualisation 2020-01-10 2026-04-29 17 True True False False jbrowse Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz 0 4181049 9690871 10.783333 0
Visualisation Genomic Data Visualisation with JBrowse2 https://training.galaxyproject.org//topics/visualisation/tutorials/jbrowse2/tutorial.html Pathway visualisation, Structure visualisation, Genome visualisation 2026-04-29 2026-04-29 1 True False False False jbrowse2 UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@Pasteur, UseGalaxy.org.au 0 310 319 3.883333 0
Imaging Using BioImage.IO models for image analysis in Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/process-image-bioimageio/tutorial.html Image analysis 2025-04-09 2026-06-23 10 True False False True __EXTRACT_DATASET__, ip_binary_to_labelimage, image_math, ip_threshold, ip_split_image, bioimage_inference, ip_overlay_images UseGalaxy.be, UseGalaxy.eu 0 348 397 11.666667 0
Imaging Content Tracking and Verification in Galaxy Workflows with ISCC-SUM https://training.galaxyproject.org//topics/imaging/tutorials/iscc-suite/tutorial.html Image analysis 2026-02-14 2026-02-16 2 True False False True __EXTRACT_DATASET__, iscc_sum, iscc_sum_similarity, param_value_from_file, ip_threshold, ip_split_image, iscc_sum_verify UseGalaxy.eu, UseGalaxy.org (Main) 0 71 71 59.716667 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 2025-11-26 9 True False False True ip_convertimage, gate_finder, celesta, squidpy_spatial, basic_illumination, palom, ashlar, quantification, mesmer, scimap_mcmicro_to_anndata, vitessce_spatial, scimap_phenotyping, scanpy_compute_graph, rename_tiff_channels, unet_coreograph 0 1779 2346 4.783333 0
Imaging Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/parameter-tuning/tutorial.html Visualisation, Image analysis, Data handling, Image annotation 2025-04-28 2026-01-21 4 True False False True ip_filter_standard, ip_segmetrics, collapse_dataset, param_value_from_file, ip_threshold, tp_split_on_column, ip_histogram_equalization UseGalaxy.be UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 195 210 19.983333 0
Imaging Nucleoli segmentation and feature extraction using CellProfiler https://training.galaxyproject.org//topics/imaging/tutorials/tutorial-CP/tutorial.html Image analysis, Quantification, Parsing 2020-07-01 2025-11-26 12 True True False True cp_measure_object_size_shape, cp_mask_image, cp_enhance_or_suppress_features, cp_display_data_on_image, cp_cellprofiler, cp_relate_objects, idr_download_by_ids, cp_convert_objects_to_image, cp_measure_texture, cp_measure_image_area_occupied, cp_image_math, cp_measure_granularity, cp_identify_primary_objects, cp_save_images, cp_common, cp_measure_object_intensity, cp_measure_image_intensity, cp_gray_to_color, cp_export_to_spreadsheet, cp_measure_image_quality UseGalaxy.be, UseGalaxy.eu Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 4179656 9689591 6.066667 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 Visualisation, Image analysis, Data handling, Image annotation 2025-03-20 2025-11-26 5 True False False True __EXTRACT_DATASET__, ip_points_to_label, ip_binary_to_labelimage, idr_download_by_ids, ip_overlay_images, ip_spot_detection_2d, unzip, ip_histogram_equalization UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu UseGalaxy.org (Main) 0 326 383 10.983333 0
Imaging Voronoi segmentation https://training.galaxyproject.org//topics/imaging/tutorials/voronoi-segmentation/tutorial.html Visualisation, Image analysis, Data handling, Image annotation 2025-05-13 2026-02-20 8 True False False True ip_count_objects, ip_binary_to_labelimage, ip_filter_standard, image_math, colorize_labels, repeat_channels, ip_imageinfo, voronoi_tessellation, ip_threshold, ip_2d_feature_extraction, ip_convertimage, unzip, ip_overlay_images UseGalaxy.be, UseGalaxy.eu UseGalaxy.org (Main) 0 585 774 6.966667 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 2026-04-28 9 True False False True Convert characters1, omero_metadata_import, split_file_to_collection, omero_filter, omero_import, omero_get_id, tp_replace_in_line, param_value_from_file, omero_roi_import, omero_get_value UseGalaxy.eu UseGalaxy.org (Main) 0 382 498 14.566667 0
Imaging Execute a BiaPy workflow in Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/biapy/tutorial.html Image analysis 2026-02-11 2026-02-17 2 True False False True __EXTRACT_DATASET__, biapy, ip_binary_to_labelimage, libcarna_render, ip_convertimage, ip_overlay_images UseGalaxy.eu 0 92 101 15.450000 0
Imaging Training Custom YOLO Models for Segmentation of Bioimages https://training.galaxyproject.org//topics/imaging/tutorials/yolo-segmentation-training/tutorial.html Visualisation, Image analysis, Image annotation, Data handling 2025-07-25 2025-11-26 7 True False False True graphicsmagick_image_convert, interactive_tool_anylabeling, json2yolosegment, yolo_training, unzip, ip_histogram_equalization UseGalaxy.eu 0 521 595 3.000000 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 2025-11-26 5 True False False True ip_points_association_nn, ip_spot_detection_2d, ip_curve_fitting UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 314 357 7.300000 0
Imaging Analyse HeLa fluorescence siRNA screen https://training.galaxyproject.org//topics/imaging/tutorials/hela-screen-analysis/tutorial.html Visualisation, Image analysis, Data handling, Image annotation 2019-08-13 2026-01-18 16 True False False True ip_binary_to_labelimage, ip_filter_standard, collapse_dataset, ip_threshold, ip_2d_feature_extraction, unzip, ip_2d_filter_segmentation_by_features UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu UseGalaxy.no, UseGalaxy.org (Main) 0 912 1166 17.166667 0
Imaging Object tracking using CellProfiler https://training.galaxyproject.org//topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html Image analysis, Quantification, Parsing 2021-03-17 2026-06-23 12 True False False True cp_cellprofiler, cp_color_to_gray, cp_tile, cp_export_to_spreadsheet, cp_measure_object_size_shape, cp_overlay_outlines, cp_save_images, cp_common, cp_track_objects, unzip, cp_measure_object_intensity, cp_identify_primary_objects UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org (Main) 0 2391 2938 5.550000 0
Imaging Introduction to Image Analysis using Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/imaging-introduction/tutorial.html Visualisation, Image analysis, Data handling, Image annotation 2019-08-13 2026-01-18 18 True False False True ip_count_objects, ip_filter_standard, ip_binary_to_labelimage, ip_imageinfo, ip_overlay_images, ip_threshold, unzip, ip_histogram_equalization UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu UseGalaxy.org (Main) 0 3021 4146 9.166667 0
Imaging Where to start with bioimage analysis in Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html Visualisation, Image analysis, Formatting, Data handling, Quantification, Image annotation, Parsing 2026-02-17 2026-02-19 4 True False False False ip_histogram_equalization, ip_imageinfo, cellposesam, cellpose, ip_filter_standard, idr_download_by_ids, interactive_tool_cellprofiler, ip_split_image, interactive_tool_cellpose, ip_threshold, libcarna_render, ip_convertimage, bf2raw, interactive_tool_ilastik, interactive_tool_qupath, cp_overlay_outlines, bioimage_inference, ip_overlay_images, ip_color_deconvolution 0 302 360 8.450000 0
Imaging Segmentation of Anatomical Structures in Medical 3-D Images https://training.galaxyproject.org//topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html Visualisation, Image analysis, Data handling, Image annotation 2026-02-26 2026-02-26 1 True False False True Convert characters1, ip_concat_channels, param_value_from_file, ridge_filter_skimage, add_line_to_file, ip_2d_filter_segmentation_by_features, tp_text_file_with_recurring_lines, clip_image, Add_a_column1, compose_text_param, ip_2d_feature_extraction, ip_scale_image, highdicom_dicom2tiff, ip_threshold, tp_sort_header_tool, libcarna_render, unzip, ip_binary_to_labelimage, tp_replace_in_line, query_tabular UseGalaxy.eu UseGalaxy.org (Main) 0 189 211 17.933333 0
Imaging Quantitative Analysis of Histological Staining Using Color Deconvolution https://training.galaxyproject.org//topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html Visualisation, Image analysis, Data handling, Image annotation 2026-06-15 2026-06-21 2 True False False True Cut1, collection_element_identifiers, collapse_dataset, ip_imageinfo, tp_cat, Show tail1, tp_sed_tool, cat1, tp_text_file_with_recurring_lines, Add_a_column1, imagej2_analyze_particles_binary, ip_split_image, ip_2d_feature_extraction, __EXTRACT_DATASET__, Paste1, ip_threshold, Grep1, Show beginning1, ip_histogram_equalization, ip_color_deconvolution 0 117 137 27.316667 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 Visualisation, Image analysis, Data handling, Image annotation 2025-08-11 2026-06-01 4 True False False True __EXTRACT_DATASET__, interactive_tool_qupath, graphicsmagick_image_convert, ip_points_to_label, ip_imageinfo, ip_split_image, ip_2d_feature_extraction UseGalaxy.eu 0 591 681 3.933333 0
Imaging AI pipeline for annotating marine species (Project Moorev - Marine) https://training.galaxyproject.org//topics/imaging/tutorials/Annotation_AI_Pipeline/tutorial.html 2026-07-24 2026-07-27 2 True False False False coco_annotation_visualizer, edit_coco_annotation, sam3_semantic_segmentation UseGalaxy.eu 0 30 35 65.533333 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, UseGalaxy.ca 0 4175541 9683666 2.066667 0
Introduction to Galaxy Analyses A short introduction to Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-short/tutorial.html Sequencing quality control, Statistical calculation, Sequence composition calculation 2018-08-27 2026-01-23 44 True True True True fastqc, cshl_fastq_quality_filter UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 4238104 9780514 12.150000 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 Remove beginning1, Cut1, ggplot2_point, upload1, Grouping1, datamash_ops, csv_to_tabular, tp_sorted_uniq UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz 0 28516 44549 10.050000 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 2026-07-23 69 True False True True upload1, comp1, datamash_ops, bedtools_intersectbed, tp_sort_header_tool, tp_head_tool UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.no 0 56575 89670 8.550000 0
Introduction to Galaxy Analyses Introduction to Galaxy as an RDM platform https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-rdm/tutorial.html Visualisation 2026-03-19 2026-07-23 3 True False False True export_remote, Add_a_column1, imagemagick_image_montage, column_remove_by_header, unzip, Summary_Statistics1, ggplot2_histogram UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.org (Main) 0 427 533 11.416667 0
Introduction to Galaxy Analyses Very Short Introductions: QC https://training.galaxyproject.org//topics/introduction/tutorials/vsi_qc/tutorial.html Sequence contamination filtering, Validation, Sequencing quality control 2024-03-26 2024-06-25 4 True False False False multiqc, fastp Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 456 531 11.366667 0
Introduction to Galaxy Analyses From peaks to genes https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html 2016-03-29 2026-03-30 69 True False True True gops_intersect_1, tp_replace_in_column, Cut1, get_flanks1, upload1, CONVERTER_interval_to_bed_0, Grouping1, tp_tail_tool, Add_a_column1, tp_sort_header_tool UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no 0 21525 35166 10.550000 0
Introduction to Galaxy Analyses NGS data logistics https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html SNP detection, Formatting, Generation, Read mapping, Validation, Genome indexing, Sequence contamination filtering, Data handling, Sequencing quality control, Sequence alignment 2017-02-22 2026-01-06 40 True False True True picard_MarkDuplicates, bwa_mem, samtools_stats, fastp, lofreq_call, Filter1, multiqc, snpEff, snpSift_extractFields, snpEff_build_gb, collapse_dataset, samtools_view, bwa, lofreq_indelqual, lofreq_viterbi, fasterq_dump, snpeff_sars_cov_2, bwa_mem2 UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz 0 21968 36814 9.400000 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 2026-07-23 13 True False False True Remove beginning1, Cut1, ggplot2_point, upload1, Grouping1, datamash_ops, csv_to_tabular, tp_sorted_uniq Galaxy@AuBi, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2472 3256 17.116667 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 2026-05-17 43 True False True True gops_intersect_1, Filter1, cat1, gene2exon1, tp_sort_header_tool, tp_cat UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) MISSISSIPPI, UseGalaxy.no 0 21440 33408 9.716667 0
Introduction to Galaxy Analyses Data Manipulation Olympics https://training.galaxyproject.org//topics/introduction/tutorials/data-manipulation-olympics/tutorial.html 2022-07-20 2026-07-23 17 True False False True {{version_split}}, {{version_cut_columns}}, Cut1, Grouping1, {{version_count}}, {{version_paste}}, tp_cat, tp_sorted_uniq, tabular_to_csv, Count1, {{version_compute}}, {{version_remove_columns_by_header}}, {{version_replace_text_line}}, join1, Filter1, {{version_remove_beginning}}, cat1, datamash_ops, Add_a_column1, tp_split_on_column, {{version_cat}}, {{version_datamash}}, {{version_replace_text_column}}, {{version_join}}, {{version_sort}}, {{version_wc}}, upload1, {{version_filter}}, tp_sort_header_tool, {{version_select_first}}, wc_gnu, regexColumn1, Remove beginning1, {{version_unique}}, Show beginning1, {{version_cut_advanced}} 0 7071 10107 11.583333 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, UseGalaxy.ca 0 4175541 9683670 2.066667 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, UseGalaxy.ca 0 8766 12165 5.316667 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, UseGalaxy.ca 0 590 667 9.750000 0
Introduction to Galaxy Analyses Introduction to the Dataverse Integration in Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-dataverse/tutorial.html 2026-06-25 2026-06-25 1 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 46 49 35.150000 0
Introduction to Galaxy Analyses Best Practices for Citing Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-cite/tutorial.html 2025-11-06 2026-07-24 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 398 428 10.383333 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_uep_opt, pm_muairss_read UseGalaxy.cz, UseGalaxy.eu UseGalaxy.be 0 426 520 12.666667 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, UseGalaxy.ca 0 4175541 9683672 2.066667 0
Metabolomics Predicting EI+ mass spectra with QCxMS https://training.galaxyproject.org//topics/metabolomics/tutorials/qcxms-predictions/tutorial.html Metabolomics 2024-10-01 2026-07-23 2 True True False True qcxms_neutral_run, split_file_to_collection, tp_cut_tool, qcxms_production_run, qcxms_getres, xtb_molecular_optimization, param_value_from_file, openbabel_compound_convert, tp_cat, ctb_im_conformers, __FILTER_FAILED_DATASETS__ UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be 0 2049905 3795160 5.966667 0
Metabolomics Molecular formula assignment and mass recalibration with MFAssignR package https://training.galaxyproject.org//topics/metabolomics/tutorials/mfassignr/tutorial.html Metabolomics Visualisation, Mass spectra calibration, Deisotoping, Annotation 2025-05-19 2026-07-23 2 True False False True mfassignr_mfassign, mfassignr_kmdnoise, mfassignr_findRecalSeries, mfassignr_recal, mfassignr_recallist, mfassignr_snplot, mfassignr_mfassignCHO, mfassignr_isofiltr, mfassignr_histnoise 0 377 440 11.616667 0
Metabolomics Mass spectrometry imaging: Finding differential analytes https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html Metabolomics 2019-04-13 2026-07-23 10 True False False True Filter1, cardinal_quality_report, cardinal_segmentations, cardinal_preprocessing, maldi_quant_peak_detection, maldi_quant_preprocessing, join_files_on_column_fuzzy, Grep1, cardinal_mz_images, Summary_Statistics1, cardinal_combine, cardinal_classification UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2304 3201 9.200000 0
Metabolomics Mass spectrometry: LC-MS analysis https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms/tutorial.html Metabolomics Label-free quantification, Peak detection, Data filtering, Validation, Chromatographic alignment, Mass spectrum visualisation, Annotation, Chromatogram visualisation, Spectral analysis 2019-07-02 2026-07-23 14 True False False True abims_xcms_retcor, abims_CAMERA_annotateDiffreport, abims_xcms_fillPeaks, xcms_export_samplemetadata, msnbase_readmsdata, xcms_merge, Batch_correction, Univariate, generic_filter, xcms_plot_chromatogram, abims_xcms_group, wsdl_hmdb, quality_metrics, abims_xcms_xcmsSet UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no 0 14198 22744 3.650000 0
Metabolomics Mass spectrometry imaging: Examining the spatial distribution of analytes https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html Metabolomics 2019-02-21 2026-07-23 19 True False False True cardinal_data_exporter, Filter1, cardinal_quality_report, cardinal_spectra_plots, cardinal_filtering, cardinal_mz_images UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3483 4832 9.666667 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 Metabolomics Label-free quantification, Peak detection, Chromatographic alignment, Mass spectrum visualisation, Correlation, Chromatogram visualisation, Format validation, Formatting, Spectral library search, Data filtering, Validation, Imputation, Standardisation and normalisation, Clustering, Filtering 2023-05-08 2026-07-23 6 True False False True abims_xcms_retcor, matchms_formatter, xcms_merge, msconvert, abims_xcms_fillPeaks, msnbase_readmsdata, waveica, matchms_similarity, ramclustr_define_experiment, abims_xcms_group, ramclustr, matchms_filtering, abims_xcms_xcmsSet, riassigner UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr 0 3373 4249 3.966667 0
Metabolomics Mass spectrometry: LC-MS preprocessing with XCMS https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html Metabolomics Label-free quantification, Peak detection, Data filtering, Validation, Chromatographic alignment, Mass spectrum visualisation, Annotation, Chromatogram visualisation, Spectral analysis 2020-02-04 2026-07-23 15 True True False False abims_xcms_retcor, abims_CAMERA_annotateDiffreport, abims_xcms_fillPeaks, xcms_export_samplemetadata, msnbase_readmsdata, xcms_merge, xcms_plot_chromatogram, abims_xcms_group, idchoice, abims_xcms_summary, abims_xcms_xcmsSet, intens_check UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 4182420 9694337 7.350000 0
Metabolomics Mass spectrometry: GC-MS analysis with the metaMS package https://training.galaxyproject.org//topics/metabolomics/tutorials/gcms/tutorial.html Metabolomics Label-free quantification, Peak detection, Data filtering, Validation, Chromatographic alignment, Mass spectrum visualisation, Chromatogram visualisation 2021-09-22 2026-07-23 9 True False False False xcms_merge, abims_xcms_fillPeaks, xcms_export_samplemetadata, msnbase_readmsdata, metams_runGC, xcms_plot_chromatogram, abims_xcms_group, abims_xcms_xcmsSet UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.no 0 2026 3009 4.000000 0
Metabolomics Mass spectrometry: LC-MS data processing https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html Metabolomics 2021-12-14 2026-07-23 9 True False False False normalization, Batch_correction, generic_filter, quality_metrics, Multivariate, intens_check UseGalaxy.fr UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3509 4646 6.516667 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, UseGalaxy.ca 0 4175541 9683672 2.066667 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 Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding 2017-06-22 2024-08-09 4 True False False True humann2_regroup_table, mothur_make_group, mothur_classify_seqs, mothur_make_biom, metaphlan2, krona-text, mothur_screen_seqs, mothur_filter_seqs, humann2_renorm_table, mothur_summary_seqs, mothur_count_seqs, metaphlan2krona, mothur_pre_cluster, mothur_make_shared, mothur_classify_otu, mothur_merge_files, taxonomy_krona_chart, mothur_cluster_split, humann2, mothur_unique_seqs, mothur_align_seqs UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.no 0 11823 15892 5.733333 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 Visualisation, Statistical calculation, Genome annotation, Taxonomic classification, Aggregation 2023-05-03 2026-05-11 8 True False True True krakentools_kreport2krona, est_abundance, interactive_tool_pavian, metaphlan, interactive_tool_phinch, __UNZIP_COLLECTION__, kraken2, kraken_biom, taxonomy_krona_chart UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 16071 21259 5.683333 0
Microbiome MGnify v5.0 Amplicon Pipeline https://training.galaxyproject.org//topics/microbiome/tutorials/mgnify-amplicon/tutorial.html Metagenomics, Taxonomy, Sequence analysis Visualisation, Read pre-processing, Mapping, Sequence trimming, Statistical calculation, Sequence contamination filtering, Nucleic acid feature detection, Comparison, Nucleic acid design, Analysis, Sequence feature detection, k-mer counting, Sequencing quality control, Formatting, Alignment, Sequence composition calculation, Validation, DNA barcoding 2025-07-30 2025-11-18 3 True False False True collection_element_identifiers, Grouping1, collapse_dataset, cshl_fasta_formatter, bedtools_getfastabed, param_value_from_file, mgnify_seqprep, seqprep, query_tabular, fastqc, __FILTER_FROM_FILE__, tp_awk_tool, fastq_to_fasta_python, CONVERTER_uncompressed_to_gz, fastq_filter, Add_a_column1, CONVERTER_gz_to_uncompressed, lotus2, trimmomatic, infernal_cmsearch, ampvis2_heatmap, prinseq, fastq_dl, bedtools_maskfastabed, collection_column_join, biom_convert, multiqc, taxonomy_krona_chart, filter_tabular, wc_gnu, fastp, mapseq, __FILTER_EMPTY_DATASETS__, cmsearch_deoverlap, __UNZIP_COLLECTION__, ampvis2_load, __MERGE_COLLECTION__, tp_find_and_replace, gops_concat_1 0 535 702 14.600000 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 Pairwise sequence alignment, Visualisation 2025-01-07 2026-04-13 2 True False False True join1, Filter1, tp_replace_in_column, Cut1, cat1, add_column_headers, minimap2, Grouping1, sort1, tp_tail_tool, Add_a_column1, count_gff_features, histogram_rpy, tab2fasta, MQoutputfilter, tp_sorted_uniq, CONVERTER_fasta_to_tabular, ggplot2_histogram UseGalaxy.fr 0 566 641 7.866667 0
Microbiome Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Sequence file editing, Visualisation, Read pre-processing, Sequence assembly validation, Sequence trimming, Statistical calculation, Sequence contamination filtering, Primer removal, Sequence assembly visualisation, Sequencing quality control, Formatting, Variant calling, Sequence composition calculation, Read mapping, Local alignment, Genome assembly, Data handling, Sequence alignment analysis 2022-12-05 2026-05-11 11 True False True True fastqc, bandage_info, filter_tabular, quast, metaspades, bandage_image, random_lines1, bg_uniq, coverm_contig, bowtie2, collection_column_join, megahit, megahit_contig2fastg, bamtools, seqtk_subseq, cutadapt, tp_cat, ngsutils_bam_filter UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 5859 8035 10.400000 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 2026-08-16 2026-08-16 0 True False True True msstatstmt, unipept, Grep1 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 0 0 0.000000 0
Microbiome Clinical Metaproteomics 4: Quantitation https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-4-quantitation/tutorial.html Visualisation, Heat map generation, Imputation, Statistical calculation, Standardisation and normalisation, Clustering, Protein quantification, Principal component plotting 2026-08-16 2026-08-16 0 True False True True Cut1, Grouping1, Grep1, maxquant UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) 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 Visualisation, Aggregation 2024-08-01 2025-06-17 7 True False True True krakentools_beta_diversity, krakentools_alpha_diversity Galaxy@Pasteur, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr 0 10667 12772 4.166667 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 Visualisation, Phylogenetic tree analysis, Multiple sequence alignment, Multilocus sequence typing, Pairwise sequence alignment, Mapping, Statistical calculation, Aggregation, Sequence contamination filtering, Box-Whisker plot plotting, De-novo assembly, Base-calling, Sequence assembly visualisation, Sequencing quality control, Scatter plot plotting, Mapping assembly, Phylogenetic tree generation, Taxonomic classification, Variant calling, Sequence composition calculation, Phylogenetic tree reconstruction, Sequence assembly, Validation, Cross-assembly, Genome assembly, Data handling, Antimicrobial resistance prediction, Sequence alignment analysis 2023-01-26 2025-11-18 12 True False True True porechop, __BUILD_LIST__, bandage_image, Cut1, newick_display, collection_element_identifiers, Grouping1, tp_cut_tool, fasta2tab, samtools_coverage, collapse_dataset, bedtools_getfastabed, param_value_from_file, krakentools_kreport2krona, clustalw, add_line_to_file, tp_head_tool, tp_sorted_uniq, Count1, tp_multijoin_tool, fastqc, fasttree, nanoplot, mlst, barchart_gnuplot, medaka_consensus_pipeline, Add_a_column1, compose_text_param, snpSift_filter, tp_split_on_column, CONVERTER_gz_to_uncompressed, flye, clair3, ggplot2_heatmap, regex1, minimap2, krakentools_extract_kraken_reads, bcftools_consensus, Paste1, tab2fasta, collection_column_join, kraken2, samtools_depth, multiqc, fasta_merge_files_and_filter_unique_sequences, taxonomy_krona_chart, regexColumn1, Remove beginning1, tp_replace_in_column, split_file_to_collection, bcftools_norm, fastp, snpSift_extractFields, __FILTER_EMPTY_DATASETS__, Grep1, table_compute, samtools_fastx, tp_find_and_replace, bamtools_split_mapped, __FILTER_FAILED_DATASETS__, abricate UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz 0 6135 8799 8.550000 0
Microbiome Remove contamination and host reads https://training.galaxyproject.org//topics/microbiome/tutorials/host-removal/tutorial.html Validation, Sequencing quality control, Read mapping 2025-12-18 2026-05-12 3 True False True True __ZIP_COLLECTION__, multiqc, bowtie2 Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 553 664 10.850000 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 analysis, Pairwise sequence alignment, Aggregation, Box-Whisker plot plotting, De-novo assembly, Genome assembly, Antimicrobial resistance prediction, Sequence assembly visualisation, Scatter plot plotting, Mapping assembly 2019-06-25 2024-06-14 4 True False True True nanoplot, minimap2, bandage_image, miniasm, racon, staramr_search, unicycler, gfa_to_fa, PlasFlow UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 4501 6082 7.783333 0
Microbiome Clinical Metaproteomics 2: Discovery https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html Visualisation, Formatting, Heat map generation, Imputation, Statistical calculation, Standardisation and normalisation, Clustering, Protein quantification, Filtering, Principal component plotting 2026-08-16 2026-08-16 0 True False True True maxquant, filter_tabular, Remove beginning1, Filter1, msconvert, Cut1, ident_params, peptide_shaker, Grouping1, fasta2tab, fasta_cli, dbbuilder, Grep1, search_gui, tp_cat, fasta_merge_files_and_filter_unique_sequences, query_tabular UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.fr 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 Sequence contamination filtering, Visualisation, Taxonomic classification, Sequence composition calculation, Sequencing quality control, Statistical calculation, Aggregation 2022-09-29 2024-11-29 5 True False True True fastqc, fastp, porechop, Filter1, kraken2, krakentools_kreport2krona, taxonomy_krona_chart UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3610 5203 8.900000 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, Expression analysis, Target-Decoy, Protein identification, de Novo sequencing 2026-08-16 2026-08-16 0 True False True True uniprotxml_downloader, dbbuilder, fasta_merge_files_and_filter_unique_sequences, metanovo UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu UseGalaxy.be, UseGalaxy.org (Main) 0 0 0 0.000000 0
Microbiome Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2 https://training.galaxyproject.org//topics/microbiome/tutorials/lotus2-identifying-fungi/tutorial.html Sequence feature detection, DNA barcoding 2024-09-30 2024-09-30 2 True False False True lotus2 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 1118 1367 8.033333 0
Microbiome Clinical Metaproteomics 3: Verification https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html 2026-08-16 2026-08-16 0 True False True True uniprotxml_downloader, Remove beginning1, Filter1, Cut1, Grouping1, collapse_dataset, dbbuilder, pepquery2, tp_cat, fasta_merge_files_and_filter_unique_sequences, query_tabular UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.org (Main) 0 2 2 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 Sequence contamination filtering, Visualisation, Taxonomic classification, Sequence composition calculation, Validation, Sequencing quality control, Statistical calculation 2020-11-24 2024-07-31 5 True False False True fastqc, fastp, Remove beginning1, porechop, tp_replace_in_line, kraken2, datamash_reverse, multiqc, taxonomy_krona_chart UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr 0 10664 14677 5.816667 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 Conversion, Visualisation, Read pre-processing, Sequence trimming, Sequence comparison, Statistical calculation, Primer removal, Sequencing quality control, Taxonomic classification, Phylogenetic analysis, Phylogenetic inference, Species frequency estimation, Sequence composition calculation, Validation, Sequence similarity search, Sequence alignment analysis, Phylogenetic tree editing, Phylogenetic tree visualisation 2020-02-13 2025-06-16 6 True False True True Cut1, export2graphlan, fastqc, humann_rename_table, humann_regroup_table, graphlan_annotate, fastq_paired_end_interlacer, tp_sort_header_tool, bg_sortmerna, multiqc, taxonomy_krona_chart, humann_split_stratified_table, graphlan, metaphlan, humann_renorm_table, cutadapt, Grep1, humann_unpack_pathways, humann, combine_metaphlan2_humann2, tp_find_and_replace UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no 0 1172 1471 11.666667 0
Microbiome Binning of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html Metagenomics, Sequence assembly Sequence assembly, Sequence clustering, Read binning, Sequence composition calculation, Genome comparison, Validation, Sequence assembly validation, Statistical calculation, Read mapping, Genome annotation, Sequencing quality control 2023-12-05 2026-04-09 9 True False True True Fasta_to_Contig2Bin, drep_dereplicate, concoct_cut_up_fasta, maxbin2, __BUILD_LIST__, concoct, samtools_sort, das_tool, checkm_lineage_wf, bowtie2, concoct_coverage_table, concoct_extract_fasta_bins, metabat2_jgi_summarize_bam_contig_depths, binette, semibin, metabat2, concoct_merge_cut_up_clustering UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr GalaxyTrakr, UseGalaxy.org.au, UseGalaxy.org (Main) 0 7785 9510 5.666667 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 Conversion, Visualisation, Read pre-processing, Sequence trimming, Sequence comparison, Statistical calculation, Aggregation, Primer removal, Sequencing quality control, Taxonomic classification, Phylogenetic analysis, Phylogenetic inference, Species frequency estimation, Sequence composition calculation, Validation, Sequence similarity search, Sequence alignment analysis, Phylogenetic tree editing, Phylogenetic tree visualisation 2019-11-21 2025-06-16 6 True True True True Cut1, Grouping1, export2graphlan, fastqc, humann_rename_table, humann_regroup_table, graphlan_annotate, combine_metaphlan_humann, fastq_paired_end_interlacer, tp_sort_header_tool, bg_sortmerna, multiqc, taxonomy_krona_chart, humann_split_stratified_table, graphlan, metaphlan, humann_renorm_table, cutadapt, Grep1, humann_unpack_pathways, humann, tp_find_and_replace UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.eu 0 4183784 9694339 6.950000 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 Visualisation, Variant calling, Analysis, Deposition, DNA barcoding 2024-06-05 2026-04-13 12 True False True True dada2_makeSequenceTable, dada2_assignTaxonomyAddspecies, collection_element_identifiers, Grouping1, dada2_filterAndTrim, dada2_plotQualityProfile, tp_head_tool, phyloseq_from_dada2, cat1, Add_a_column1, __SORTLIST__, dada2_learnErrors, dada2_removeBimeraDenovo, interactive_tool_phyloseq, tp_replace_in_column, tp_replace_in_line, dada2_mergePairs, __UNZIP_COLLECTION__, dada2_seqCounts, dada2_dada UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 10409 14841 5.783333 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, UseGalaxy.ca 0 581 931 14.083333 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, UseGalaxy.ca 0 165 177 27.583333 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 2026-02-18 2 external False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.ca 0 868 1292 10.216667 0
Microbiome Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads https://training.galaxyproject.org//topics/microbiome/tutorials/mags-building/tutorial.html Metagenomics, Sequence assembly Sequence composition calculation, Genome annotation, Validation, Genome comparison, Sequence assembly validation, Statistical calculation, Data handling, Sequencing quality control 2025-12-18 2026-05-18 6 True False True False __EXTRACT_DATASET__, drep_dereplicate, kmetashot, Remove beginning1, join1, tp_replace_in_column, Cut1, cat1, multiqc, Grouping1, checkm_lineage_wf, collapse_dataset, collection_column_join, bakta, tp_sort_header_tool, fasterq_dump, Summary_Statistics1 UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 1630 2142 7.216667 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 Visualisation, Phylogenetic analysis, Phylogenetic tree analysis, Sequence clustering, Phylogenetic tree reconstruction, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding, Phylogenetic tree generation 2019-05-13 2025-12-18 6 True False True True newick_display, collapse_dataset, mothur_chimera_vsearch, mothur_classify_seqs, mothur_dist_seqs, mothur_remove_lineage, mothur_filter_seqs, mothur_screen_seqs, mothur_cluster, mothur_summary_seqs, mothur_summary_single, mothur_count_seqs, mothur_pre_cluster, mothur_rarefaction_single, mothur_count_groups, mothur_make_shared, XY_Plot_1, mothur_classify_otu, mothur_sub_sample, mothur_dist_shared, mothur_cluster_split, mothur_heatmap_sim, mothur_venn, mothur_remove_groups, mothur_tree_shared, mothur_unique_seqs, mothur_remove_seqs UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.fr 0 6944 11643 8.066667 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 Visualisation, Phylogenetic analysis, Phylogenetic tree analysis, Sequence clustering, Phylogenetic tree reconstruction, Sequence read processing, Sequencing quality control, Taxonomic classification, DNA barcoding, Phylogenetic tree generation 2017-02-12 2025-12-18 5 True False False True newick_display, mothur_chimera_vsearch, mothur_classify_seqs, mothur_make_biom, mothur_dist_seqs, mothur_make_contigs, mothur_remove_lineage, mothur_filter_seqs, mothur_screen_seqs, mothur_cluster, mothur_summary_seqs, mothur_summary_single, mothur_count_seqs, mothur_pre_cluster, mothur_rarefaction_single, mothur_seq_error, mothur_count_groups, mothur_get_groups, mothur_make_shared, mothur_classify_otu, mothur_sub_sample, mothur_dist_shared, taxonomy_krona_chart, mothur_taxonomy_to_krona, mothur_cluster_split, mothur_heatmap_sim, mothur_venn, mothur_remove_groups, mothur_remove_seqs, mothur_tree_shared, mothur_unique_seqs, mothur_align_seqs, XY_Plot_1 UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 14710 21601 5.150000 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 Sequence analysis, Sequence composition calculation, Variant calling, Genome visualisation, Validation, Statistical calculation, Sequence contamination filtering, Local alignment, Global alignment, Taxonomic classification, Phylogenetic tree visualisation, Sequence alignment analysis, Sequencing quality control, Sequence alignment, Antimicrobial resistance prediction, Phylogenetic tree generation 2020-07-25 2026-01-06 32 True False True True qualimap_bamqc, fastqc, tp_awk_tool, tp_sed_tool, jvarkit_wgscoverageplotter, EMBOSS: seqret84, tb_profiler_profile, tb_variant_filter, upload1, bcftools_consensus, EMBOSS:%20seqret84, kraken2, mosdepth, multiqc, samtools_stats, fastp, snippy, jbrowse, tbvcfreport, __FLATTEN__ 0 8868 13346 7.750000 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 Multiple sequence alignment, Generation, Sequence analysis, Sequencing quality control, Read mapping, Genome indexing, Sequence contamination filtering, Local alignment, Global alignment, Primer removal, Sequence alignment analysis, Sequence alignment 2023-05-15 2024-03-20 4 True False False True qualimap_bamqc, samtools_merge, Cut1, EMBOSS: maskseq51, param_value_from_file, datamash_ops, ivar_trim, Add_a_column1, compose_text_param, rbc_mafft, ivar_consensus, fasta_compute_length, bwa_mem, fasta_regex_finder, upload1, samtools_view, fatovcf, fastp, __APPLY_RULES__, __ZIP_COLLECTION__, mimodd_info, Grep1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org (Main) 0 1324 1544 7.966667 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 Sequence file editing, Phylogenetic analysis, Data retrieval, Generation, Multiple sequence alignment, Sequence analysis, Read mapping, Genome indexing, Sequence contamination filtering, De-novo assembly, Data handling, Sequence alignment analysis, Primer removal, Sequencing quality control, Sequence alignment 2022-11-21 2024-10-04 10 True False False False qualimap_bamqc, bwa_mem, fastp, __RELABEL_FROM_FILE__, iqtree, upload1, collapse_dataset, samtools_view, vapor, bamtools_split_ref, seqtk_subseq, Grep1, ivar_consensus, Show beginning1, rbc_mafft, tp_find_and_replace UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 2547 3609 8.166667 0
Single Cell Analysis of plant scRNA-Seq Data with Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-plant/tutorial.html Expression profile clustering, Principal component visualisation, Differential gene expression analysis 2021-04-08 2026-06-25 8 True False True True anndata_import, anndata_manipulate, scanpy_remove_confounders, scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_normalize, scanpy_inspect, scanpy_plot UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3295 4091 7.233333 0
Sequence analysis Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants https://training.galaxyproject.org//topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html Phylogenetic analysis, Multiple sequence alignment, Sequence analysis, Phylogenetic inference (from molecular sequences) 2025-03-26 2025-04-27 2 True False True True filter_by_fasta_ids, quicktree, Remove beginning1, tapscan_classify, Filter1, Cut1, iqtree, trimal, rbc_mafft, ete_treeviewer UseGalaxy.be, UseGalaxy.eu 0 501 634 16.233333 0
Transcriptomics Whole transcriptome analysis of Arabidopsis thaliana https://training.galaxyproject.org//topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html Visualisation, RNA-Seq analysis, Sequence composition calculation, RNA-Seq quantification, Read pre-processing, Read mapping, Sequence trimming, Validation, Gene expression analysis, Differential gene expression analysis, Primer removal, Sequencing quality control 2021-04-08 2026-07-07 20 True True True True deseq2, filter_by_fasta_ids, Filter1, Cut1, cat1, salmon, falco, trim_galore, rbc_mirdeep2_mapper, sort1, sample_seqs, targetfinder, __MERGE_COLLECTION__, multiqc, rbc_mirdeep2_quantifier UseGalaxy.cz 0 4037561 9182291 8.916667 0
Sequence analysis NCBI BLAST+ against the MAdLand https://training.galaxyproject.org//topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.html Sequence alignment analysis 2023-01-16 2024-07-31 9 True False False False ncbi_blastx_wrapper, ncbi_blastp_wrapper, bg_diamond Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@Pasteur, IPK Galaxy Blast Suite, UseGalaxy.no 0 2009 2534 10.300000 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, UseGalaxy.ca 0 4175541 9683681 2.066667 0
Proteomics Statistical analysis of DIA data https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.html Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling 2020-12-02 2023-11-09 9 True False False True histogram_rpy, msstats, Grep1, Filter1 UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz 0 1584 2179 9.966667 0
Proteomics metaQuantome 1: Data creation https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Visualisation, Formatting, Prediction and recognition, Label-free quantification, Filtering 2020-10-16 2024-03-14 20 True False False True unipept, Remove beginning1, tp_replace_in_column, Filter1, Cut1, msconvert, peptide_shaker, regex1, flashlfq, tp_replace_in_line, Grep1, search_gui, query_tabular UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 979 1601 9.500000 0
Proteomics Neoantigen 2: Database merge and FragPipe discovery https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.html 2025-01-14 2025-12-03 4 True False False False Remove beginning1, collapse_dataset, fragpipe, Grep1, fragpipe_manifest_generator, fasta_merge_files_and_filter_unique_sequences, query_tabular, validate_fasta_database UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) 0 495 574 12.266667 0
Proteomics Detection and quantitation of N-termini (degradomics) via N-TAILS https://training.galaxyproject.org//topics/proteomics/tutorials/ntails/tutorial.html Proteomics 2017-02-14 2025-04-08 16 True False False True FileFilter, IDMapper, IDConflictResolver, IDFilter, FeatureFinderMultiplex, HighResPrecursorMassCorrector, PeptideIndexer, ConsensusID, FalseDiscoveryRate, MSGFPlusAdapter, MzTabExporter, IDMerger, FileMerger 0 1012 1343 7.500000 0
Proteomics Neoantigen 3: PepQuery2 Verification https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-peptide-verification/tutorial.html Filtering, Formatting 2025-01-14 2025-12-03 4 True False False False ncbi_blastp_wrapper, msconvert, tab2fasta, pepquery2, query_tabular UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz 0 239 265 14.550000 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_sequence_property_based_descriptors, pdaug_basic_plots, pdaug_merge_dataframes, pdaug_addclasslabel, pdaug_ml_models UseGalaxy.be 0 1180 1711 12.233333 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, Statistical calculation, RNA-Seq analysis, Sequence alignment, Transcriptome assembly 2025-01-14 2025-12-03 6 True False False False translate_bed, gffcompare_to_bed, freebayes, sqlite_to_tabular, hisat2, regexColumn1, concatenate, custom_pro_db, fasta2tab, CONVERTER_gz_to_uncompressed, tab2fasta, column_regex_find_and_replace, gffcompare, stringtie, fasta_merge_files_and_filter_unique_sequences, bed_to_protein_map 0 279 313 18.000000 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 msstatstmt, unipept, Grep1 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 411 512 29.866667 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 Visualisation, Tag-based peptide identification, Heat map generation, Imputation, Statistical calculation, Standardisation and normalisation, Clustering, Spectrum calculation, Protein quantification, Differential protein expression profiling, Principal component plotting 2021-02-17 2025-09-22 19 True False True True maxquant, tp_replace_in_column, Filter1, Cut1, uniprot, fasta2tab, msstats, datamash_ops, Grep1, Summary_Statistics1, tp_easyjoin_tool, ggplot2_heatmap2 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) 0 9429 14874 6.316667 0
Proteomics Clinical Metaproteomics 4: Quantitation https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.html Visualisation, Heat map generation, Imputation, Statistical calculation, Standardisation and normalisation, Clustering, Protein quantification, Principal component plotting 2024-02-06 2025-08-10 5 True False True True Cut1, Grouping1, Grep1, maxquant UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 286 358 25.833333 0
Proteomics Proteogenomics 2: Database Search https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html Conversion, Peptide database search 2018-11-20 2026-04-22 25 True False True True ident_params, peptide_shaker, tab2fasta, search_gui, mz_to_sqlite, query_tabular UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 1770 2569 12.483333 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 2026-07-23 19 True False False True cardinal_data_exporter, cardinal_quality_report, tp_sort_header_tool, Grep1 UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3176 4700 6.400000 0
Proteomics Library Generation for DIA Analysis https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html Visualisation, Heat map generation, Imputation, Statistical calculation, Standardisation and normalisation, Clustering, Protein quantification, Principal component plotting 2020-12-02 2025-06-02 12 True False False True maxquant, OpenSwathDecoyGenerator, Filter1, TargetedFileConverter, OpenSwathAssayGenerator, diapysef UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 5001 6446 4.666667 0
Proteomics DIA Analysis using OpenSwathWorkflow https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html Filtering, Formatting 2020-12-02 2025-05-20 12 True False False True OpenSwathWorkflow, msconvert, pyprophet_protein, pyprophet_peptide, pyprophet_export, Grep1, pyprophet_merge, pyprophet_score UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 3639 5048 8.100000 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 2025-12-03 4 True False False False tp_awk_tool, regex1, rna_star, arriba_get_filters, tab2fasta, CONVERTER_gz_to_uncompressed, arriba, query_tabular UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 390 488 11.716667 0
Proteomics Neoantigen 5a: Predicting HLA Binding https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-predicting-hla-binding/tutorial.html Genetic variation analysis, Read mapping 2025-01-14 2025-12-03 4 True False False False optitype, tp_awk_tool, seq2hla, query_tabular UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 244 268 17.683333 0
Proteomics EncyclopeDIA https://training.galaxyproject.org//topics/proteomics/tutorials/encyclopedia/tutorial.html Filtering, Formatting 2021-06-21 2025-05-19 12 True False True True encyclopedia_searchtolib, encyclopedia_quantify, msconvert UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 2242 2992 8.950000 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 FidoAdapter, IDMapper, IDPosteriorErrorProbability, TextExporter, IDScoreSwitcher, IDConflictResolver, FileInfo, FeatureFinderMultiplex, PeptideIndexer, histogram_rpy, tp_tail_tool, ProteinQuantifier, FalseDiscoveryRate, Grep1, XTandemAdapter, Summary_Statistics1, MultiplexResolver UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 1542 2083 9.983333 0
Proteomics Clinical Metaproteomics 2: Discovery https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html Visualisation, Formatting, Heat map generation, Imputation, Statistical calculation, Standardisation and normalisation, Clustering, Protein quantification, Filtering, Principal component plotting 2024-02-06 2025-08-10 5 True False True True maxquant, filter_tabular, Remove beginning1, Filter1, msconvert, Cut1, ident_params, peptide_shaker, Grouping1, fasta2tab, fasta_cli, dbbuilder, Grep1, search_gui, tp_cat, fasta_merge_files_and_filter_unique_sequences, query_tabular UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.fr 0 474 596 24.316667 0
Proteomics metaQuantome 3: Taxonomy https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy Visualisation, Principal component visualisation, Differential protein expression analysis, Functional clustering, Quantification, Query and retrieval, Heat map generation, Statistical inference, Indexing, Filtering 2020-10-29 2024-03-15 14 True False False True metaquantome_expand, metaquantome_viz, metaquantome_db, metaquantome_sample, metaquantome_filter, metaquantome_stat UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 521 662 18.900000 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, Expression analysis, Target-Decoy, Protein identification, de Novo sequencing 2024-02-06 2025-07-30 7 True False True True uniprotxml_downloader, dbbuilder, fasta_merge_files_and_filter_unique_sequences, metanovo UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu UseGalaxy.be, UseGalaxy.org (Main) 0 786 1112 21.083333 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 2025-12-03 5 True False False False Filter1, iedb_api, fasta_to_tabular, table_compute, query_tabular 0 219 239 10.666667 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 reactome_analysis, Jvenn, cluter_profiler, retrieve_from_hpa, MQoutputfilter, rna_abbased_data, IDconverter UseGalaxy.be UseGalaxy.fr 0 3336 4765 8.666667 0
Proteomics Neoantigen 4: Variant Annotation https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-variant-annotation/tutorial.html 2025-01-14 2025-12-03 5 True False False False Convert characters1, regexColumn1, select, tab2fasta, column_regex_find_and_replace, pep_pointer, query_tabular, cut 0 231 258 14.866667 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, pep_pointer, ncbi_blastp_wrapper, query_tabular UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no 0 1955 2761 13.700000 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 DecoyDatabase, addValue, fasta2tab, tab2fasta, dbbuilder, fasta_merge_files_and_filter_unique_sequences UseGalaxy.org.au, UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 5143 8014 8.600000 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 uniprotxml_downloader, Remove beginning1, Filter1, Cut1, Grouping1, collapse_dataset, dbbuilder, pepquery2, tp_cat, fasta_merge_files_and_filter_unique_sequences, query_tabular UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.org (Main) 0 307 392 29.683333 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.org.au, UseGalaxy.eu 0 550 622 9.816667 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 Convert characters1, Filter1, bg_uniq, uniprot, tp_cut_tool, comp1, Grep1, wolf_psort, get_subontology_from, tp_easyjoin_tool, tp_sorted_uniq, term_id_vs_term_name 0 716 1037 8.066667 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 2026-05-11 42 True False True True sqlite_to_tabular, unipept, peptide_shaker, search_gui, query_tabular UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3247 5047 10.083333 0
Proteomics Peptide and Protein ID using OpenMS tools https://training.galaxyproject.org//topics/proteomics/tutorials/protein-id-oms/tutorial.html Filtering, Formatting 2017-10-16 2025-04-08 32 True False False True FidoAdapter, IDPosteriorErrorProbability, TextExporter, msconvert, IDScoreSwitcher, IDFilter, PeakPickerHiRes, FileInfo, PeptideIndexer, XTandemAdapter, ConsensusID, FalseDiscoveryRate, Grep1, MSGFPlusAdapter, IDMerger UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3817 6262 8.133333 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, tp_cut_tool, prot_features, retrieve_from_hpa, MQoutputfilter, retr_pepatlas1, rna_abbased_data, IDconverter UseGalaxy.be, UseGalaxy.fr 0 1939 2629 9.916667 0
Proteomics Multiomics data analysis using MultiGSEA https://training.galaxyproject.org//topics/proteomics/tutorials/multiGSEA-tutorial/tutorial.html Pathway analysis, Gene-set enrichment analysis, Aggregation 2025-03-10 2025-03-11 2 True False False True tp_grep_tool, multigsea, Filter1 UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz 0 661 740 6.416667 0
Proteomics metaQuantome 2: Function https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics Visualisation, Principal component visualisation, Differential protein expression analysis, Functional clustering, Quantification, Query and retrieval, Heat map generation, Statistical inference, Indexing, Filtering 2020-10-29 2024-03-15 14 True False False True metaquantome_expand, metaquantome_viz, metaquantome_db, metaquantome_sample, metaquantome_filter, metaquantome_stat UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 497 672 16.266667 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_sequence_property_based_descriptors, pdaug_fishers_plot, pdaug_basic_plots, pdaug_peptide_data_access, pdaug_tsvtofasta, pdaug_merge_dataframes, pdaug_addclasslabel, pdaug_peptide_sequence_analysis UseGalaxy.be 0 873 1147 11.050000 0
Proteomics Label-free data analysis using MaxQuant https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-label-free/tutorial.html Visualisation, Tag-based peptide identification, Heat map generation, Imputation, Statistical calculation, Standardisation and normalisation, Clustering, Spectrum calculation, Protein quantification, Differential protein expression profiling, Principal component plotting 2020-04-29 2025-05-21 14 True False False True maxquant, Filter1, Cut1, msstats, histogram_rpy, Add_a_column1, tp_sort_header_tool, Grep1 UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz 0 21290 30808 3.733333 0
Proteomics MaxQuant and MSstats for the analysis of TMT data https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.html Visualisation, Heat map generation, Imputation, Statistical calculation, Standardisation and normalisation, Clustering, Protein quantification, Principal component plotting 2021-08-13 2025-01-08 11 True False False True msstatstmt, maxquant UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org (Main) 0 4621 6139 4.416667 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 peptide_shaker, PeakPickerHiRes, FileConverter, Grep1, search_gui 0 3540 5483 6.233333 0
Proteomics Proteogenomics 1: Database Creation https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html Sequence annotation, Variant calling, Statistical calculation, RNA-Seq analysis, Sequence alignment, Transcriptome assembly 2018-11-20 2026-04-20 30 True False True True translate_bed, gffcompare_to_bed, freebayes, filter_tabular, hisat2, regexColumn1, tp_replace_in_column, sqlite_to_tabular, custom_pro_db, fasta2tab, cat_multi_datasets, tab2fasta, gffcompare, stringtie, fasta_merge_files_and_filter_unique_sequences, bed_to_protein_map, query_tabular UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz 0 6543 10497 6.900000 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, UseGalaxy.ca 0 7875 12598 2.616667 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 Visualisation, Read mapping, Statistical calculation, Cross-assembly, Sequence contamination filtering, Expression analysis, Sequencing quality control, Taxonomic classification 2024-07-15 2025-12-18 5 True False True True est_abundance, recentrifuge, fastp, falco, upload1, kraken2 GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 2298 3002 10.216667 0
Sequence analysis Quality Control https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-control/tutorial.html Sequence composition calculation, Read pre-processing, Sequence trimming, Validation, Statistical calculation, Box-Whisker plot plotting, Primer removal, Sequencing quality control, Scatter plot plotting 2016-10-04 2026-03-30 49 True True True True fastqc, nanoplot, pycoqc, fastqe, cutadapt, multiqc UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr 0 4293318 9893615 9.066667 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.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz 0 2630 3455 3.850000 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 Local alignment, Global alignment, Sequence alignment, Sequence analysis, Multiple sequence alignment, Sequence alignment analysis, PCR primer design 2025-03-20 2025-11-20 3 True False False True varvamp, split_file_to_collection, EMBOSS: degapseq20, rbc_mafft, fasta_compute_length, ncbi_makeblastdb UseGalaxy.be, UseGalaxy.eu 0 1288 1523 2.966667 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 Sequence file editing, Visualisation, Phylogenetic analysis, Sequence clustering, Sequence read processing, Data handling, Demultiplexing, Sequencing quality control, Taxonomic classification, DNA barcoding 2024-01-08 2024-03-05 2 True False False True filter_by_fasta_ids, fastq_to_tabular, qiime_align_seqs, collection_element_identifiers, cshl_fastx_reverse_complement, __FILTER_FROM_FILE__, cshl_fastq_to_fasta, __SORTLIST__, ncbi_blastn_wrapper, regex1, seqtk_mergepe, aligned_to_consensus, seqtk_trimfq, tab2fasta, mothur_merge_files, fastq_groomer, unzip, fastq_masker_by_quality, ab1_fastq_converter, mothur_degap_seqs UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 4363 5368 6.666667 0
Sequence analysis Mapping https://training.galaxyproject.org//topics/sequence-analysis/tutorials/mapping/tutorial.html Mapping Genome visualisation, Sequence composition calculation, Sequencing quality control, Read pre-processing, Read mapping, Sequence trimming, Statistical calculation, Validation, Data handling, Primer removal, Sequence alignment analysis 2016-10-04 2026-03-30 46 True True True True fastqc, samtools_stats, jbrowse, bamFilter, bowtie2, trim_galore, __FLATTEN__, multiqc UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 4246608 9800745 9.500000 0
Single Cell Converting between common single cell data formats https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-data-ingest/tutorial.html Community profiling, Loading 2024-02-13 2026-06-25 5 True False False True anndata_ops, datamash_transpose, regexColumn1, join1, Filter1, dropletutils_read_10x, Cut1, monocle3_create, seurat_read10x, tp_cut_tool, sceasy_convert, scanpy_filter_cells, dropletutils, tp_tail_tool, tabular_to_fastq, anndata_inspect, fastq_to_tabular UseGalaxy.org (Main) 0 3263 3809 4.150000 0
Single Cell Pre-processing of 10X Single-Cell RNA Datasets https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html Community profiling, Loading, Validation, Sequencing quality control, Sequence alignment 2019-09-11 2025-04-29 13 True False True True rna_starsolo, dropletutils, multiqc UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.fr, UseGalaxy.no 0 14532 18784 5.950000 0
Single Cell Bulk RNA Deconvolution with MuSiC https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music/tutorial.html 2022-02-11 2026-06-25 11 True False True True music_deconvolution, music_inspect_eset, music_construct_eset UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 4684 5812 4.033333 0
Single Cell Pre-processing of Single-Cell RNA Data https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing/tutorial.html Data handling, Sequencing quality control, Read summarisation, RNA-Seq quantification, Validation, Sequence alignment analysis, Sequence alignment 2019-02-22 2025-04-08 5 True True False True samtools_stats, tp_sed_tool, umi_tools_count, bamFilter, featurecounts, collection_column_join, __FLATTEN__, rna_star, multiqc, umi_tools_extract UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 4182605 9692822 8.983333 0
Single Cell Single-cell quality control with scater https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scater-qc/tutorial.html Sequence visualisation, Read pre-processing, Sequencing quality control 2019-10-23 2025-02-14 6 True False False True scater_plot_dist_scatter, scater_create_qcmetric_ready_sce, scater_plot_pca, scater_filter UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no UseGalaxy.cz 0 829 925 7.216667 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, Gene expression analysis, Sequence composition calculation 2021-03-03 2025-11-18 25 True False True True anndata_manipulate, _dropletBarcodePlot, join1, dropletutils_read_10x, Cut1, _ensembl_gtf2gene_list, sceasy_convert, alevin, dropletutils_empty_drops, anndata_inspect, _salmon_kallisto_mtx_to_10x UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 4002 6004 10.916667 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 Visualisation, Enrichment analysis, Generation, Principal component visualisation, Sequence composition calculation, Expression profile clustering, Read mapping, Imputation, Genome indexing, Statistical calculation, Mapping, Gene regulatory network analysis, Differential gene expression analysis, Sequencing quality control, Sequence alignment, Peak calling 2023-04-24 2025-10-16 10 True False False True fastqc, bwa_mem, episcanpy_build_matrix, sinto_fragments, falco, bedtools_sortbed, anndata_inspect, episcanpy_preprocess, sinto_barcode, tp_sorted_uniq, scanpy_plot, macs2_callpeak UseGalaxy.org.au, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz 0 6860 8065 2.450000 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, UseGalaxy.ca 0 4143137 9569644 2.066667 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, UseGalaxy.ca 0 810 1065 9.900000 0
Single Cell Understanding Barcodes https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-umis/tutorial.html Sequencing quality control, Statistical calculation, Sequence composition calculation 2019-02-20 2026-06-25 12 True False True True fastqc, seq_filter_by_id, umi_tools_extract UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, UseGalaxy.no 0 7111 8804 5.483333 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, UseGalaxy.ca 0 3981 4501 3.383333 0
Single Cell Removing the effects of the cell cycle https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html Expression profile clustering, Principal component visualisation, Differential gene expression analysis 2023-01-25 2026-06-25 16 True False False True anndata_manipulate, scanpy_cluster_reduce_dimension, cat1, addValue, scanpy_inspect, sort1, anndata_inspect, table_compute, tp_easyjoin_tool, scanpy_regress_variable, scanpy_plot 0 2470 2886 3.150000 0
Single Cell Downstream Single-cell RNA analysis with RaceID https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-raceid/tutorial.html Molecular dynamics, Expression analysis, Expression profile clustering 2019-03-25 2025-02-14 7 True False False True datamash_transpose, raceid_filtnormconf, raceid_inspectclusters, raceid_trajectory, tp_sed_tool, raceid_inspecttrajectory, raceid_clustering, datamash_ops, tp_head_tool UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz 0 1237 1450 7.700000 0
Single Cell Clustering 3K PBMCs with Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html Expression profile clustering, Principal component visualisation, Differential gene expression analysis 2019-12-19 2026-07-28 18 True True True True anndata_import, anndata_manipulate, scanpy_remove_confounders, scanpy_cluster_reduce_dimension, celltypist, scanpy_filter, scanpy_normalize, scanpy_inspect, datamash_ops, anndata_inspect, scanpy_plot UseGalaxy.eu 0 4185001 9696909 8.433333 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 2026-06-25 11 True False False True music_compare UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 403 557 12.016667 0
Single Cell Single-cell ATAC-seq standard processing with SnapATAC2 https://training.galaxyproject.org//topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html Generation, Principal component visualisation, Expression profile clustering, Read mapping, Genome indexing, Gene expression profiling, Essential dynamics, Differential gene expression analysis, Dimensionality reduction, Sequence alignment 2024-07-11 2025-07-02 5 True False False True anndata_ops, bwa_mem, anndata_manipulate, scanpy_plot, snapatac2_peaks_and_motif, scanpy_filter, Cut1, scanpy_normalize, snapatac2_plotting, snapatac2_preprocessing, scanpy_inspect, anndata_inspect, snapatac2_clustering, fasta_compute_length, replace_column_with_key_value_file 0 2461 2853 4.200000 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_ops, anndata_manipulate, tp_replace_in_column, Cut1, Paste1, anndata_inspect UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org (Main) 0 2833 3916 11.416667 0
Single Cell Importing files from public atlases https://training.galaxyproject.org//topics/single-cell/tutorials/EBI-retrieval/tutorial.html 2023-11-14 2026-06-25 9 True False True True tp_grep_tool, hca_matrix_downloader, anndata_ops, regexColumn1, scanpy_read_10x, seurat_read10x, sceasy_convert, retrieve_scxa, tp_find_and_replace 0 742 936 12.916667 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, UseGalaxy.ca 0 3929 4618 4.700000 0
Single Cell Evaluating Reference Data for Bulk RNA Deconvolution https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html Visualisation, Annotation 2025-02-02 2026-06-25 4 True False False True Cut1, tp_cut_tool, collapse_dataset, tp_easyjoin_tool, Count1, tp_multijoin_tool, datamash_transpose, ggplot2_violin, tp_awk_tool, join1, tp_sed_tool, Add_a_column1, music_construct_eset, Paste1, collection_column_join, bg_column_arrange_by_header, Remove beginning1, ggplot2_point, annotatemyids, music_deconvolution, __DUPLICATE_FILE_TO_COLLECTION__, table_compute UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz 0 251 281 16.850000 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_filter_cells, seurat_run_pca, seurat_find_neighbours, seurat_find_clusters, seurat_normalise_data, seurat_plot, seurat_read10x, retrieve_scxa, seurat_scale_data, seurat_find_markers, seurat_run_umap, seurat_find_variable_genes UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 2909 3444 6.133333 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 Expression profile clustering, Principal component visualisation, Differential gene expression analysis 2021-03-24 2025-04-23 24 True False True True scanpy_filter_genes, Cut1, scanpy_find_cluster, scanpy_filter_cells, scanpy_find_variable_genes, scanpy_plot, anndata_ops, scanpy_run_pca, anndata_manipulate, scanpy_cluster_reduce_dimension, join1, scanpy_scale_data, scanpy_inspect, scanpy_compute_graph, scanpy_plot_embed, scanpy_run_umap, anndata_inspect, scanpy_filter, scanpy_normalize, interactive_tool_cellxgene_vip, retrieve_scxa, scanpy_normalise_data, scanpy_find_markers, scanpy_run_tsne 0 6115 9443 7.700000 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 2026-06-25 8 True False True True anndata_ops, anndata_import, anndata_manipulate, tp_replace_in_column, Cut1, scanpy_filter_cells, Paste1, anndata_inspect, unzip UseGalaxy.org.au, UseGalaxy.be UseGalaxy.cz, UseGalaxy.org (Main) 0 631 740 15.016667 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 Gene expression profiling, Essential dynamics, Dimensionality reduction 2025-02-28 2025-07-02 2 True False False True __EXTRACT_DATASET__, anndata_manipulate, __FILTER_FROM_FILE__, snapatac2_peaks_and_motif, snapatac2_plotting, collection_element_identifiers, snapatac2_preprocessing, anndata_inspect, snapatac2_clustering, Show beginning1, fasta_compute_length UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) 0 857 951 5.350000 0
Single Cell Clustering 3K PBMCs with Seurat https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-seurat-pbmc3k/tutorial.html 2025-01-23 2025-05-09 5 True False True True seurat_data, seurat_clustering, seurat_create, Filter1, seurat_plot, Cut1, seurat_preprocessing, seurat_reduce_dimension, csv_to_tabular UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) MISSISSIPPI 0 2766 3365 5.116667 0
Single Cell Scanpy Parameter Iterator https://training.galaxyproject.org//topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.html 2023-07-19 2026-06-25 9 True False False True scanpy_find_cluster, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_run_umap, scanpy_compute_graph, scanpy_run_tsne UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main) 0 391 428 12.400000 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, UseGalaxy.ca 0 4175541 9683688 2.066667 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, UseGalaxy.ca 0 5292 6160 4.000000 0
Single Cell Batch Correction and Integration with Seurat or Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna_batch_correction/tutorial.html Expression profile clustering, Principal component visualisation, Differential gene expression analysis 2026-07-09 2026-07-09 1 True False False True scanpy_remove_confounders, seurat_data, scanpy_cluster_reduce_dimension, seurat_clustering, scanpy_filter, scanpy_normalize, seurat_plot, seurat_preprocessing, seurat_reduce_dimension, scanpy_inspect, anndata_inspect, seurat_integrate, scanpy_plot, Count1 UseGalaxy.org.au, UseGalaxy.eu UseGalaxy.org (Main) 0 97 105 5.766667 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 2026-06-25 9 True False False True datamash_transpose, music_construct_eset, tp_awk_tool, join1, tp_sed_tool, regex1, Cut1, scanpy_read_10x, tp_cut_tool, retrieve_scxa, annotatemyids, sort1, music_manipulate_eset, anndata_inspect, add_line_to_file, table_compute, tp_easyjoin_tool UseGalaxy.cz 0 861 1369 7.866667 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 anndata_manipulate, scanpy_plot_trajectory, scanpy_run_paga, scanpy_find_cluster, scanpy_run_dpt, scanpy_run_diffmap, scanpy_plot_embed, scanpy_run_fdg, scanpy_compute_graph UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main) 0 1612 1989 7.600000 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, UseGalaxy.ca 0 2142027 4028460 1.616667 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, UseGalaxy.ca 0 7741 8706 1.650000 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 2026-06-25 9 True False False True music_construct_eset, tp_awk_tool, regex1, tp_sed_tool, tp_cut_tool, annotatemyids, sort1, music_manipulate_eset, column_remove_by_header, table_compute, tp_easyjoin_tool UseGalaxy.cz 0 901 1326 10.900000 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_topmarkers, monocle3_plotCells, datamash_transpose, regexColumn1, monocle3_create, join1, Filter1, Cut1, tp_cut_tool, monocle3_learnGraph, monocle3_orderCells, monocle3_preprocess, anndata_inspect, monocle3_diffExp, monocle3_partition, monocle3_reduceDim UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) 0 4500 5520 4.333333 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, UseGalaxy.ca 0 3220508 6597373 1.866667 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, UseGalaxy.ca 0 2613901 5149365 1.766667 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, Expression profile clustering, Principal component visualisation 2025-02-12 2025-05-09 8 True False True True __EXTRACT_DATASET__, anndata_manipulate, tp_awk_tool, tp_replace_in_column, decoupler_pseudobulk, scanpy_filter, volcanoplot, tp_replace_in_line, column_remove_by_header, anndata_inspect, edger UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz 0 2588 2926 2.850000 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 2026-06-25 9 True True False True goenrichment, Cut1, gprofiler_gost, tp_split_on_column UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) 0 2075781 3858155 5.733333 0
Statistics and machine learning Machine learning: classification and regression https://training.galaxyproject.org//topics/statistics/tutorials/classification_regression/tutorial.html 2019-03-07 2025-04-08 13 True False False True sklearn_ensemble, sklearn_svm_classifier, plotly_ml_performance_plots, plotly_regression_performance_plots UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) 0 5928 10490 2.933333 0
Statistics and machine learning Clustering in Machine Learning https://training.galaxyproject.org//topics/statistics/tutorials/clustering_machinelearning/tutorial.html Visualisation 2020-05-08 2025-04-08 14 True False False True sklearn_numeric_clustering, csv_to_tabular, ggplot2_point UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.fr 0 8870 14476 2.716667 0
Statistics and machine learning Classification in Machine Learning https://training.galaxyproject.org//topics/statistics/tutorials/classification_machinelearning/tutorial.html 2020-04-30 2025-05-14 18 True True True True sklearn_svm_classifier, plotly_ml_performance_plots, Remove beginning1, sklearn_generalized_linear, sklearn_build_pipeline, sklearn_ensemble, sklearn_searchcv, sklearn_nn_classifier UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.no 0 4178663 9688170 11.233333 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 model_prediction, keras_train_and_eval, keras_model_builder, sklearn_to_categorical, tp_cut_tool, keras_model_config, ml_visualization_ex UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.fr 0 3694642 8055113 5.833333 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 Cut1, interactive_tool_ml_jupyter_notebook, Filter1 UseGalaxy.eu 0 1395 1724 8.383333 0
Statistics and machine learning Text-mining with the SimText toolset https://training.galaxyproject.org//topics/statistics/tutorials/text-mining_simtext/tutorial.html 2021-04-05 2025-05-07 8 True False False True pubmed_by_queries, interactive_tool_simtext_app, pmids_to_pubtator_matrix UseGalaxy.eu 0 587 784 14.833333 0
Statistics and machine learning GTEx Tissue Modeling with Galaxy Image Learner https://training.galaxyproject.org//topics/statistics/tutorials/GTEx_Tissue_modeling/tutorial.html 2026-07-24 2026-07-24 1 True True False True image_learner UseGalaxy.eu, UseGalaxy.org (Main) 0 187742 343085 56.616667 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 2026-05-11 20 True True True True model_prediction, keras_train_and_eval, keras_model_builder, sklearn_to_categorical, keras_model_config, ml_visualization_ex UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.fr 0 4034435 9152868 4.100000 0
Statistics and machine learning Basics of machine learning https://training.galaxyproject.org//topics/statistics/tutorials/machinelearning/tutorial.html 2018-11-05 2026-05-12 16 True True True True sklearn_svm_classifier UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.fr, UseGalaxy.no 0 4178800 9688088 13.016667 0
Statistics and machine learning Gleam Multimodal Learner - Head and Neck cancer Recurrence Prediction with HANCOCK https://training.galaxyproject.org//topics/statistics/tutorials/multimodal_learner/tutorial.html 2026-03-25 2026-05-18 4 True True True True multimodal_learner UseGalaxy.org (Main) UseGalaxy.eu 0 596584 1045229 12.233333 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, sklearn_ensemble, sklearn_searchcv, plotly_regression_performance_plots, plotly_parallel_coordinates_plot UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.no 0 13614 21801 2.166667 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 0 326 391 13.700000 0
Statistics and machine learning Modeling Breast Cancer Subtypes with Flexynesis https://training.galaxyproject.org//topics/statistics/tutorials/flexynesis_classification/tutorial.html 2025-08-13 2026-05-18 7 True False True True __EXTRACT_DATASET__, datamash_transpose, tabpfn, join1, flexynesis, tp_cut_tool, tp_sort_header_tool, Show beginning1, table_compute, tp_easyjoin_tool, flexynesis_plot UseGalaxy.be, UseGalaxy.eu UseGalaxy.fr 0 325 434 24.316667 0
Statistics and machine learning Galaxy Tabular Learner - Building a Model using Chowell clinical data https://training.galaxyproject.org//topics/statistics/tutorials/loris_model/tutorial.html 2024-12-13 2026-05-15 4 True True True True PyCaret_Model_Comparison, tabular_learner 0 1931754 3488260 15.966667 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 2026-05-11 13 True True True True model_prediction, keras_train_and_eval, keras_model_builder, keras_model_config, plotly_regression_performance_plots UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.fr, UseGalaxy.no 0 4039136 9142102 3.450000 0
Statistics and machine learning GLEAM Image Learner - Validating Skin Lesion Classification on HAM10000 https://training.galaxyproject.org//topics/statistics/tutorials/image_learner/tutorial.html 2026-01-28 2026-05-18 4 True True True True image_learner UseGalaxy.eu, UseGalaxy.org (Main) 0 897196 1467182 20.800000 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 __EXTRACT_DATASET__, flexynesis, flexynesis_utils, flexynesis_plot UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.org (Main) 0 114 125 36.866667 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_external_sample_status_prediction, pancancer_pathway_count_heatmaps, pancancer_targene_summary_figures, pancancer_targene_cell_line_predictions, pancancer_targene_pharmacology, pancancer_compare_within_models, pancancer_visualize_decisions, pancancer_map_mutation_class, pancancer_within_disease_analysis, pancancer_classifier, pancancer_apply_weights, pancancer_alternative_genes_pathwaymapper 0 936 1386 10.633333 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 model_prediction, keras_train_and_eval, keras_model_builder, keras_model_config, ml_visualization_ex UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.fr, UseGalaxy.no 0 4109017 9433744 5.333333 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 model_prediction, keras_train_and_eval, keras_model_builder, keras_model_config, ml_visualization_ex UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.fr 0 2679 3382 7.233333 0
Statistics and machine learning Interval-Wise Testing for omics data https://training.galaxyproject.org//topics/statistics/tutorials/iwtomics/tutorial.html Genome annotation, Comparison, Differentially-methylated region identification, Differential gene expression analysis, Peak calling 2018-06-14 2023-11-09 17 True False False True iwtomics_testandplot, iwtomics_loadandplot, iwtomics_plotwithscale UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) 0 443 566 14.933333 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__, tp_replace_in_column, flexynesis, datamash_ops, Add_a_column1, flexynesis_plot UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.org (Main) 0 183 216 21.933333 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__, tp_cut_tool, tp_sort_header_tool, flexynesis_cbioportal_import, table_compute, flexynesis_utils UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main) 0 153 168 7.450000 0
Statistics and machine learning Regression in Machine Learning https://training.galaxyproject.org//topics/statistics/tutorials/regression_machinelearning/tutorial.html 2020-01-25 2026-05-12 20 True True True True Remove beginning1, sklearn_generalized_linear, sklearn_build_pipeline, sklearn_ensemble, plotly_regression_performance_plots, sklearn_searchcv UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.no 0 4179122 9688203 7.783333 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 2199777 4170990 6.433333 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) UseGalaxy.eu 0 568 677 9.133333 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 0 4883 7480 5.083333 0
Synthetic Biology Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools https://training.galaxyproject.org//topics/synthetic-biology/tutorials/retrosynthesis_analysis/tutorial.html 2022-06-23 2024-06-14 8 True False True True rp2paths, rpextractsink, get_sbml_model, rpcompletion, rrparser, retropath2 UseGalaxy.be 0 744 1027 14.300000 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, rpthermo, rpfba, rpscore UseGalaxy.be 0 762 1078 10.050000 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 selenzy-wrapper, rpbasicdesign, dnabot UseGalaxy.be UseGalaxy.fr 0 1202 1793 13.233333 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 4175541 9683695 2.066667 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 3231092 6624411 1.866667 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 0 405 643 18.500000 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 0 379 408 21.266667 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 58 58 19.383333 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 0 466 517 15.883333 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 0 219 241 23.850000 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 0 212 239 17.050000 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 0 355 555 21.533333 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 47 47 104.550000 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 59 61 19.666667 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 0 143 147 22.416667 0
Teaching and Hosting Galaxy training Running a workshop as an instructor https://training.galaxyproject.org//topics/teaching/tutorials/running-workshop/tutorial.html 2018-11-15 2025-12-18 7 True False False False 0 277 409 22.833333 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, UseGalaxy.ca 0 4175541 9683698 2.066667 0
Transcriptomics Reference-based RNA-Seq data analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/ref-based/tutorial.html Visualisation, Enrichment analysis, RNA-Seq quantification, Read pre-processing, Pathway or network visualisation, Sequence trimming, Differential gene expression analysis, Read summarisation, Gene functional annotation, Primer removal, RNA-Seq analysis, Pathway or network analysis, Sequencing quality control, Sequence alignment, Structure visualisation, Formatting, Genome visualisation, Read mapping, Validation, Data handling, Pathway visualisation, Exonic splicing enhancer prediction 2016-10-05 2026-04-13 110 True False True True rseqc_geneBody_coverage, jbrowse2, Cut1, falco, collection_element_identifiers, Grouping1, __TAG_FROM_FILE__, tp_cat, gtftobed12, ggplot2_heatmap2, table_compute, __FILTER_FROM_FILE__, join1, Filter1, goseq, cat1, length_and_gc_content, rseqc_infer_experiment, Add_a_column1, ChangeCase, dexseq_count, rna_star, samtools_idxstats, __EXTRACT_DATASET__, deseq2, dexseq, deg_annotate, samtools_view, featurecounts, tp_sort_header_tool, pathview, rseqc_read_distribution, multiqc, tp_grep_tool, picard_MarkDuplicates, Remove beginning1, tp_replace_in_line, pygenomeTracks, cutadapt, __FLATTEN__, __MERGE_COLLECTION__ UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz 0 214454 387977 4.400000 0
Transcriptomics Pathway analysis with the MINERVA Platform https://training.galaxyproject.org//topics/transcriptomics/tutorials/minerva-pathways/tutorial.html Annotation, Sequence composition calculation, Sequencing quality control, RNA-Seq quantification, Read pre-processing, Validation, Sequence trimming, Statistical calculation, Data handling, Read summarisation, Gene functional annotation, Primer removal, RNA-Seq analysis, Sequence alignment 2024-03-28 2024-07-26 3 True False False True rseqc_geneBody_coverage, Cut1, tp_sorted_uniq, fastqc, join1, goseq, fasterq_dump, Add_a_column1, limma_voom, __EXTRACT_DATASET__, featurecounts, collection_column_join, tp_sort_header_tool, rseqc_read_distribution, multiqc, annotatemyids, tp_replace_in_line, cutadapt, Grep1, hisat2 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 841 975 14.816667 0
Transcriptomics De novo transcriptome reconstruction with RNA-Seq https://training.galaxyproject.org//topics/transcriptomics/tutorials/de-novo/tutorial.html Sequence annotation, Sequence composition calculation, Sequencing quality control, RNA-Seq quantification, Statistical calculation, Read summarisation, Differential gene expression analysis, RNA-Seq analysis, Sequence alignment, Transcriptome assembly 2017-02-19 2024-06-14 36 True False True True fastqc, deseq2, hisat2, trimmomatic, Filter1, deeptools_bam_coverage, featurecounts, gffcompare, stringtie, stringtie_merge Galaxy@AuBi, UseGalaxy.be, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 18012 30379 6.733333 0
Transcriptomics Genome-wide alternative splicing analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html Visualisation, Sequence annotation, Formatting, RNA-Seq analysis, Sequence analysis, Sequence composition calculation, Protein sequence analysis, Sequence assembly validation, Sequence comparison, Statistical calculation, Validation, Sequence contamination filtering, Data handling, De-novo assembly, Sequencing quality control, Sequence alignment, Transcriptome assembly 2023-05-17 2026-04-13 13 True True False True rseqc_geneBody_coverage, rseqc_junction_saturation, gffread, Cut1, collection_element_identifiers, addValue, stringtie, tp_cat, gtftobed12, fastqc, __FILTER_FROM_FILE__, tp_awk_tool, Filter1, rna_quast, cat1, rseqc_infer_experiment, isoformswitchanalyzer, sort1, Add_a_column1, rna_star, stringtie_merge, regex1, rseqc_junction_annotation, pfamscan, rseqc_read_distribution, multiqc, rseqc_inner_distance, tp_grep_tool, cpat, fastp, Remove beginning1, gene2exon1, tp_uniq_tool, pygenomeTracks, __FLATTEN__, gffcompare UseGalaxy.cz, UseGalaxy.fr 0 2820859 5591991 7.400000 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.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 162651 262152 2.100000 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 deseq2, Cut1, heinz_scoring, heinz_visualization, heinz, heinz_bum UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 4177765 9687076 12.416667 0
Transcriptomics 1: RNA-Seq reads to counts https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html Formatting, Sequence composition calculation, RNA-Seq quantification, Read pre-processing, Sequence trimming, Validation, Statistical calculation, Data handling, Read summarisation, Primer removal, Sequencing quality control, Sequence alignment 2018-09-23 2026-07-24 34 True False False True fastqc, picard_MarkDuplicates, rseqc_geneBody_coverage, rseqc_infer_experiment, featurecounts, collection_column_join, cutadapt, hisat2, rseqc_read_distribution, multiqc, samtools_idxstats UseGalaxy.eu MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 84866 151283 5.300000 0
Transcriptomics CLIP-Seq data analysis from pre-processing to motif detection https://training.galaxyproject.org//topics/transcriptomics/tutorials/clipseq/tutorial.html Sequence composition calculation, Read pre-processing, Mapping, Sequence trimming, Statistical calculation, Primer removal, Sequencing quality control, Sequence alignment 2018-08-17 2023-11-09 23 True False False True bedtools_genomecoveragebed_bedgraph, rcas, meme_chip, umi_tools_dedup, fastqc, Extract genomic DNA 1, tp_awk_tool, bctools_extract_alignment_ends, sort1, deeptools_plot_fingerprint, bedtools_slopbed, rna_star, __SORTLIST__, wig_to_bigWig, peakachu, deeptools_plot_correlation, cutadapt, __MERGE_COLLECTION__, umi_tools_extract, deeptools_multi_bam_summary 0 9021 17164 3.633333 0
Transcriptomics Differential abundance testing of small RNAs https://training.galaxyproject.org//topics/transcriptomics/tutorials/srna/tutorial.html Sequence composition calculation, Sequencing quality control, RNA-Seq quantification, Read pre-processing, Sequence trimming, Statistical calculation, Gene expression analysis, Differential gene expression analysis, Primer removal, RNA-Seq analysis, Sequence alignment 2017-06-29 2023-11-09 26 True False False True fastqc, deseq2, fastq_manipulation, Filter1, bedtools_bamtofastq, salmon, trim_galore, hisat2, samtool_filter2 UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 7489 12812 5.583333 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, goslimmer, Filter1 Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 24321 38883 3.400000 0
Transcriptomics De novo transcriptome assembly, annotation, and differential expression analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/full-de-novo/tutorial.html Sequence composition calculation, Coding region prediction, Validation, Statistical calculation, de Novo sequencing, De-novo assembly, Gene functional annotation, Sequencing quality control, Transcriptome assembly 2020-02-13 2023-11-09 8 True False False True fastqc, trimmomatic, trinity_define_clusters_by_cutting_tree, trinity_samples_qccheck, trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_filter_low_expr_transcripts, trinity_contig_exn50_statistic, trinity_run_de_analysis, trinity, describe_samples, trinity_analyze_diff_expr, transdecoder, multiqc, trinotate UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no 0 15838 27950 4.133333 0
Transcriptomics RNA-RNA interactome data analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-interactome/tutorial.html Sequence composition calculation, Read pre-processing, Primer removal, Sequencing quality control, Statistical calculation, Sequence trimming 2020-03-23 2023-11-09 12 True False False True fastqc, chira_quantify, chira_extract, chira_collapse, cutadapt, chira_merge, query_tabular, chira_map UseGalaxy.be, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu 0 1652 2416 12.400000 0
Transcriptomics 3: RNA-seq genes to pathways https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html Gene set testing, Gene functional annotation, Gene-set enrichment analysis 2018-12-31 2023-11-09 13 True False False True fgsea, join1, goseq, Cut1, egsea, tp_cut_tool, Add_a_column1, tp_sort_header_tool UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz 0 29558 46010 5.816667 0
Transcriptomics RNA-Seq data analysis, clustering and visualisation tutorial https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html Differential gene expression analysis, Gene functional annotation, RNA-Seq analysis 2025-05-28 2026-06-08 9 True False False True deseq2, Filter1, goseq, Cut1, cat1, deg_annotate, length_and_gc_content, Grouping1, volcanoplot, Add_a_column1, tp_sort_header_tool, Show beginning1, table_compute, tp_easyjoin_tool, Multivariate, ggplot2_heatmap2 UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 3205 3784 3.833333 0
Transcriptomics 2: RNA-seq counts to genes https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html Annotation, RNA-Seq analysis 2018-12-31 2024-04-10 21 True False False True tp_cut_tool, annotatemyids, tp_replace_in_line, mergeCols1, limma_voom UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr 0 51572 83202 5.700000 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.org.au, UseGalaxy.cz, UseGalaxy.no 0 1159 1546 14.516667 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 2026-04-13 15 True False False True datamash_transpose, ggplot2_heatmap2, join1, Filter1, Cut1, cat1, tp_sort_header_tool, Show beginning1, Show tail1 GalaxyTrakr, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.no 0 80721 131272 2.666667 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, UseGalaxy.ca 0 4178282 9687751 12.166667 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, UseGalaxy.ca 0 4176701 9685146 18.383333 0
Transcriptomics Visualization of RNA-Seq results with Volcano Plot in R https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot-r/tutorial.html 2021-06-14 2024-06-14 8 True False True False interactive_tool_rstudio, volcanoplot UseGalaxy.eu 0 31705 43111 3.733333 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, UseGalaxy.ca 0 12413 15104 3.316667 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, UseGalaxy.ca 0 22982 35607 4.233333 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 0 4556 5801 11.050000 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, UseGalaxy.ca 0 4175541 9683703 2.066667 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, Genetic variation analysis, Database search 2024-08-06 2024-09-27 3 True False False False beacon2_cnv UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr 0 294 334 10.033333 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 Service discovery, Database search, Genetic variation analysis 2024-08-06 2026-01-12 4 True False False False beacon2_cnv, cnv_vcf2json, beacon2_import, cnv_phenopacket UseGalaxy.eu 0 483 529 4.600000 0
Variant Analysis Calling very rare variants https://training.galaxyproject.org//topics/variant-analysis/tutorials/dunovo/tutorial.html Generation, Variant calling, Sequence composition calculation, Read mapping, Genome indexing, Statistical calculation, Sequencing quality control, Sequence alignment 2017-02-22 2024-12-09 21 True False False True fastqc, bwa_mem, correct_barcodes, make_families, Filter1, naive_variant_caller, bamleftalign, dunovo, allele_counts_1, align_families, sequence_content_trimmer UseGalaxy.be, UseGalaxy.org (Main) 0 2599 3766 5.516667 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 mimodd_varextract, snpEff_download, snpEff, mimodd_vcf_filter, mimodd_varreport, mimodd_map, tp_find_and_replace, mimodd_varcall UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 4874 6969 10.733333 0
Variant Analysis Trio Analysis using Synthetic Datasets from RD-Connect GPAP https://training.galaxyproject.org//topics/variant-analysis/tutorials/trio-analysis/tutorial.html Genetic variation analysis, Sequence analysis 2022-05-19 2024-09-17 13 True False True True tp_grep_tool, gemini_inheritance, gene_iobio_display_generation_iframe, pyega3, regexColumn1, CONVERTER_uncompressed_to_gz, Filter1, bcftools_norm, snpEff, CONVERTER_gz_to_uncompressed, gemini_load, bcftools_merge UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz 0 2288 3860 9.966667 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, Visualisation, Generation, Variant calling, Sequence composition calculation, Read mapping, Validation, Genome indexing, Statistical calculation, Genome alignment, Sequencing quality control, Sequence alignment, Copy number estimation 2022-10-05 2025-03-20 14 True False False True __EXTRACT_DATASET__, fastqc, bwa_mem, trimmomatic, __BUILD_LIST__, circos, bamleftalign, tp_text_file_with_recurring_lines, falco, samtools_view, samtools_calmd, tp_replace_in_line, Grep1, control_freec, samtools_rmdup, multiqc, __RELABEL_FROM_FILE__ UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 2181 2748 8.183333 0
Variant Analysis Exome sequencing data analysis for diagnosing a genetic disease https://training.galaxyproject.org//topics/variant-analysis/tutorials/exome-seq/tutorial.html Visualisation, Generation, Sequence analysis, Sequence composition calculation, Variant calling, Read mapping, Validation, Statistical calculation, Genome indexing, Genetic variation analysis, Sequencing quality control, Sequence alignment 2016-08-19 2026-03-09 30 True False True True fastqc, gemini_inheritance, bwa_mem, freebayes, trimmomatic, bcftools_norm, snpEff, snpEff_download, falco, samtools_view, gemini_load, samtools_rmdup, multiqc UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.fr 0 41045 72196 5.216667 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 Visualisation, Generation, Read pre-processing, Read mapping, Sequence trimming, Genome indexing, Data handling, Primer removal, Sequence alignment 2025-02-24 2025-02-24 1 True False False True bwa_mem, tp_awk_tool, tp_replace_in_column, Filter1, ncbi_acc_download, ggplot2_point, collapse_dataset, trim_galore, bcftools_mpileup, tp_replace_in_line, bcftools_call, fastq_dump, vcf2tsv UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz 0 567 685 5.766667 0
Variant Analysis Calling variants in diploid systems https://training.galaxyproject.org//topics/variant-analysis/tutorials/dip/tutorial.html Genetic variation analysis, Statistical calculation, Variant calling, Sequence analysis 2017-02-20 2025-04-28 17 True False False True freebayes, snpEff, gemini_db_info, vcfallelicprimitives, gemini_query, gemini_load UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.no 0 17365 29222 8.800000 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 Formatting, Generation, Variant calling, Sequence composition calculation, Read mapping, Statistical calculation, Genome indexing, Data handling, Sequence alignment analysis, Sequencing quality control, Sequence alignment 2017-02-16 2024-03-15 23 True False False True fastqc, picard_MarkDuplicates, bwa_mem, freebayes, picard_MergeSamFiles, Cut1, bamleftalign, vcffilter2, bamFilter, vcf2tsv UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no 0 10190 17330 5.683333 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 Visualisation, Generation, Variant calling, Sequence composition calculation, Read mapping, Validation, Genome indexing, Statistical calculation, Data handling, Sequence alignment analysis, Sequencing quality control, Sequence alignment 2019-03-13 2025-03-20 16 True False False True fastqc, bwa_mem, trimmomatic, multiqc, snpEff, bamleftalign, falco, bamFilter, samtools_calmd, gemini_annotate, gemini_query, gemini_load, samtools_rmdup, tp_easyjoin_tool, bg_column_arrange_by_header, varscan_somatic UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.fr 0 16219 28383 5.883333 0
Variant Analysis Calculating CHEK2 variant effect scores from MAVE data with CountESS https://training.galaxyproject.org//topics/variant-analysis/tutorials/countess-mave-chek2/tutorial.html Visualisation 2026-07-30 2026-07-30 1 True False False False join1, Cut1, ggplot2_point, countess, ggplot2_histogram UseGalaxy.eu 0 48 58 12.483333 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, UseGalaxy.ca 0 4175541 9683704 2.066667 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 circos_interval_to_text, circos_gc_skew, circos, Cut1, deeptools_bam_coverage, circos_interval_to_tile, circos_wiggle_to_scatter, gff2bed1 UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr Galaxy@AuBi, MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) 0 1949 2406 8.300000 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 Remove beginning1, random_lines1, Cut1, circos, upload1, Grep1 Galaxy@AuBi, Galaxy@Pasteur, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.no 0 4207531 9734052 4.716667 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, UseGalaxy.ca 0 2528291 4965402 1.750000 0