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 3581008 8642235 2.150000 0
Galaxy Server administration Reference Data with Data Managers https://training.galaxyproject.org//topics/admin/tutorials/reference-genomes/tutorial.html Sequence alignment, Genome indexing, Read mapping, Generation 2019-01-28 2026-01-23 7 True True False False bwa_mem_index_builder_data_manager, bwa, data_manager_fetch_genome_all_fasta_dbkey 0 3581686 8643096 15.733333 0
Galaxy Server administration Reference Data with CVMFS https://training.galaxyproject.org//topics/admin/tutorials/cvmfs/tutorial.html 2019-01-27 2026-01-23 55 True True True False 0 3583316 8645591 11.366667 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 3581008 8642235 2.150000 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 3581008 8642235 2.150000 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 3581754 8643384 8.650000 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 3583696 8646595 9.683333 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 3581008 8642237 2.150000 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 3582417 8644418 7.550000 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 3581008 8642237 2.150000 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 2725868 5821826 9.400000 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 1576346 3046322 1.633333 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 3581008 8642237 2.150000 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 3581008 8642237 2.150000 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 3587629 8653962 7.666667 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 3581008 8642237 2.150000 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 3585196 8649378 10.283333 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 3581951 8643694 14.483333 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 3581008 8642240 2.150000 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 3581008 8642240 2.150000 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 3582962 8644984 12.316667 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 3581008 8642240 2.150000 0
Galaxy Server administration Galaxy Monitoring with Telegraf and Grafana https://training.galaxyproject.org//topics/admin/tutorials/monitoring/tutorial.html 2019-01-31 2026-03-04 55 True True True False 0 3583987 8647685 5.850000 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 3606984 8690263 5.700000 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 3581008 8642240 2.150000 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 3581008 8642240 2.150000 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 3581643 8643075 16.533333 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 3565235 8579646 8.616667 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 3583438 8645848 9.166667 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 0 258 307 13.850000 0
Galaxy Server administration Reference Data with CVMFS without Ansible https://training.galaxyproject.org//topics/admin/tutorials/cvmfs-manual/tutorial.html 2020-06-17 2026-01-23 10 True False False False 0 471 618 9.500000 0
Galaxy Server administration Use Apptainer containers for running Galaxy jobs https://training.galaxyproject.org//topics/admin/tutorials/apptainer/tutorial.html 2021-01-08 2025-11-24 19 True False True False 0 1166 1475 9.400000 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 0 933 1344 13.866667 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 0 644 784 13.800000 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 75 93 8.216667 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 0 173 191 16.183333 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 70 79 6.550000 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 8365 16517 1.283333 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 95 114 10.183333 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 0 550 720 15.150000 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 1777 2738 11.183333 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 0 231 273 7.316667 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 3100 5033 2.416667 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 1319 1785 7.766667 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 0 779 1172 7.533333 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 96 107 8.066667 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 0 718 821 4.050000 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 0 604 793 12.483333 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 1672 2727 5.066667 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 0 704 1017 6.650000 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 0 118 138 5.183333 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 0 112 120 4.100000 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 1153 1308 0.866667 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 2440 3130 1.000000 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 3597150 8672521 3.266667 0
Image analysis using Deep Learning BioImage Model Zoo: Advanced models in one-click https://training.galaxyproject.org//topics/ai4life/tutorials/getting-started/slides.html 2023-04-18 2023-05-24 4 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 2277366 4669864 1.866667 0
Image analysis using Deep Learning Contribute to the BioImage.IO models https://training.galaxyproject.org//topics/ai4life/tutorials/contribute-materials/slides.html 2023-05-18 2023-05-24 3 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 2215265 4534092 1.866667 0
Image analysis using Deep Learning Welcome to the BioImage Model Zoo https://training.galaxyproject.org//topics/ai4life/tutorials/welcome-bioimageio/slides.html 2023-05-11 2023-05-18 3 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 2230191 4566468 1.866667 0
Assembly An Introduction to Genome Assembly https://training.galaxyproject.org//topics/assembly/tutorials/general-introduction/tutorial.html Formatting, De-novo assembly, Visualisation, Sequence composition calculation, Sequence assembly validation, Sequencing quality control, Statistical calculation, Validation 2017-05-23 2026-01-23 30 True True True True velvetg, multiqc, fastqc, quast, fastq_paired_end_interlacer, velveth Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 3618623 8703531 9.050000 0
Assembly Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Formatting, Read mapping, Genome assembly, Visualisation, Sequence contamination filtering, Statistical calculation, Data handling, Primer removal, Local alignment, Sequence assembly visualisation, Sequence composition calculation, Sequencing quality control, Read pre-processing, Sequence assembly validation, Sequence file editing, Sequence alignment analysis, Variant calling, Sequence trimming 2026-03-24 2026-03-24 0 True False True True coverm_contig, metaspades, bamtools, fastqc, bandage_image, random_lines1, bg_uniq, megahit, ngsutils_bam_filter, megahit_contig2fastg, quast, cutadapt, bowtie2, seqtk_subseq, tp_cat, filter_tabular, collection_column_join, bandage_info UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 5 6 0.450000 0
Assembly Assembly of the mitochondrial genome from PacBio HiFi reads https://training.galaxyproject.org//topics/assembly/tutorials/mitochondrion-assembly/tutorial.html Genomics, Sequence assembly, Biodiversity, Mitochondria 2024-09-03 2025-06-04 4 True False True True mitohifi, compress_file UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 1107 1319 11.033333 0
Assembly Large genome assembly and polishing https://training.galaxyproject.org//topics/assembly/tutorials/largegenome/tutorial.html Genomics, Sequence assembly, Biodiversity Genome assembly, Visualisation, Sequence contamination filtering, Statistical calculation, Variant calling, Box-Whisker plot plotting, Sequence assembly, Mapping assembly, Sequence assembly visualisation, De-novo assembly, Sequence composition calculation, Sequencing quality control, Validation, Sequence assembly validation, Cross-assembly, Pairwise sequence alignment, Scatter plot plotting, Base-calling 2023-03-06 2026-01-23 15 True False True True multiqc, bandage_image, racon, fastqc, genomescope, medaka_consensus_pipeline, nanoplot, fasta-stats, fastp, meryl, minimap2, quast, busco, barchart_gnuplot, flye UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz 0 8137 10482 5.233333 0
Assembly Unicycler Assembly https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html Sequence assembly, Genomics, Microbiology Gene prediction, Genome annotation, Aggregation, Genome assembly, Sequence composition calculation, Sequencing quality control, Validation, Visualisation, Statistical calculation, Sequence assembly validation, Coding region prediction 2017-10-11 2026-01-23 25 True True False True multiqc, fastqc, prokka, quast, unicycler UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3594287 8664791 7.133333 0
Assembly Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data https://training.galaxyproject.org//topics/assembly/tutorials/vgp_workflow_training/tutorial.html Sequence assembly, Chromosome conformation capture Visualisation, Sequence assembly validation 2022-04-06 2025-09-09 26 True False True False quast Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 3969 5433 7.450000 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 Read mapping, Sequencing error detection, Genome assembly, Visualisation, Sequence contamination filtering, Statistical calculation, Sequence alignment, Box-Whisker plot plotting, Mapping assembly, Sequence assembly visualisation, De-novo assembly, Sequence composition calculation, Sequencing quality control, Sequence assembly validation, Cross-assembly, Filtering, Scatter plot plotting 2021-03-24 2026-01-05 16 True False False True fastqc, bandage_image, bwa_mem2, filtlong, polypolish, nanoplot, __FLATTEN__, fastp, CONVERTER_bz2_to_uncompressed, porechop, __EXTRACT_DATASET__, quast, upload1, flye UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr 0 11108 16515 7.600000 0
Assembly Chloroplast genome assembly https://training.galaxyproject.org//topics/assembly/tutorials/chloroplast-assembly/tutorial.html Gene prediction, Genome annotation, Mapping assembly, Read alignment, Read mapping, Sequence assembly visualisation, Generation, Genome assembly, Analysis, Genome visualisation, Genome indexing, De-novo assembly, Sequence assembly, Cross-assembly, Sequence alignment, Box-Whisker plot plotting, Coding region prediction, Scatter plot plotting 2020-12-04 2026-01-23 22 True False True True bandage_image, prokka, pilon, nanoplot, fasta-stats, bwa_mem, upload1, jbrowse, bandage_info, flye UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 8452 13034 7.916667 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 Read mapping, Sequence assembly visualisation, Genome assembly, Visualisation, Sequencing quality control, Sequence assembly validation, Sequence contamination filtering 2021-03-24 2026-01-05 18 True False True True bandage_image, falco, quast, fastp, shovill, upload1, bandage_info UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 11060 16854 9.533333 0
Assembly Genome assembly using PacBio data https://training.galaxyproject.org//topics/assembly/tutorials/hifi-assembly/tutorial.html Genomics, Sequence assembly, Biodiversity Mapping assembly, Genome assembly, De-novo assembly, Visualisation, Sequence assembly validation, Cross-assembly 2021-11-29 2025-06-04 2 True False False True hifiasm, fasta-stats, quast, busco, gfa_to_fa, flye UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no 0 1236 1483 6.466667 0
Assembly Genome Assembly Quality Control https://training.galaxyproject.org//topics/assembly/tutorials/assembly-quality-control/tutorial.html Biodiversity, Sequence assembly, Data quality management Phasing, Genome assembly, Scaffolding, De-novo assembly, Visualisation, Sequence assembly validation, k-mer counting 2022-08-26 2025-06-04 6 True True False True chromeister, quast, merqury, meryl, busco UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.cz 0 2680807 5689105 10.383333 0
Assembly Making sense of a newly assembled genome https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html Sequence assembly, Genomics, Microbiology Sequence alignment, Mapping, Read mapping, Sequence visualisation, Genome visualisation 2018-06-14 2024-06-24 29 True False False True tp_sed_tool, random_lines1, tp_sort_header_tool, upload1, mergeCols1, jbrowse, lastz_wrapper_2, tp_replace_in_line, addValue, circos_interval_to_tiles, Cut1, datamash_ops, fasta_compute_length, bedtools_intersectbed, tp_grep_tool, cat1, join1, tp_replace_in_column, bedtools_complementbed, bedtools_sortbed, circos, fasta_filter_by_length, circos_aln_to_links, Filter1, tp_cat, collapse_dataset, Grep1 0 6877 13146 8.050000 0
Assembly Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step https://training.galaxyproject.org//topics/assembly/tutorials/vgp_genome_assembly/tutorial.html Genomics, Sequence assembly, Biodiversity Mapping, Phasing, Genome assembly, Scaffolding, De-novo assembly, Visualisation, Read pre-processing, Sequence assembly validation, k-mer counting, Sequence alignment, Primer removal, Pairwise sequence alignment, Sequence trimming, Read binning, Data handling 2021-06-04 2026-01-23 58 True False True True pretext_snapshot, tp_find_and_replace, hifiasm, bedtools_bamtobed, gfa_to_fa, purge_dups, yahs, Convert characters1, gfastats, pretext_map, tp_cut_tool, collection_column_join, bellerophon, sort1, bwa_mem2, tp_grep_tool, genomescope, cat1, salsa, quast, merqury, busco, Add_a_column1, meryl, minimap2, cutadapt, bionano_scaffold, collapse_dataset UseGalaxy.cz 0 17204 25683 3.416667 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 tp_sed_tool, parse_mito_blast, Cut1, Filter1, gfastats, kraken2, tp_cat, ncbi_dustmasker_wrapper, ncbi_blastn_wrapper UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 1956 2393 8.800000 0
Assembly ERGA post-assembly QC https://training.galaxyproject.org//topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html Genomics, Sequence assembly, Biodiversity Sequence assembly visualisation, Genome assembly, Phasing, Scaffolding, De-novo assembly, Visualisation, Sequence assembly validation, k-mer counting, Sequence alignment, Genotyping, Pairwise sequence alignment, Sequence alignment analysis, Sequence trimming, Data deposition, Data parsing, Data handling 2023-06-23 2025-06-04 8 True False True True bg_diamond, bandage_image, pretext_snapshot, tp_find_and_replace, samtools_stats, blobtoolkit, gfastats, __EXTRACT_DATASET__, pretext_map, interactive_tool_blobtoolkit, bellerophon, genomescope, bwa_mem2, CONVERTER_gz_to_uncompressed, merqury, smudgeplot, busco, meryl, minimap2, collapse_dataset UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.org (Main) 0 2257 2897 8.366667 0
Assembly De Bruijn Graph Assembly https://training.galaxyproject.org//topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html Formatting, Sequence assembly visualisation, Optimisation and refinement, Genome assembly, Sequence assembly, De-novo assembly 2017-05-24 2026-01-07 26 True True False True velvetg, bandage_image, velvetoptimiser, fasta-stats, spades, velveth UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz 0 3587868 8653051 10.650000 0
Assembly Hybrid genome assembly - Nanopore and Illumina https://training.galaxyproject.org//topics/assembly/tutorials/hybrid_denovo_assembly/tutorial.html Mapping assembly, Read alignment, Read mapping, Generation, Aggregation, Genome assembly, Analysis, De-novo assembly, Genome indexing, Visualisation, Sequencing quality control, Sequence assembly validation, Validation, Sequence alignment, Cross-assembly, Sequence assembly 2025-11-03 2025-11-06 2 True False False True multiqc, pilon, quast, bwa_mem, unicycler, busco, flye UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.no 0 932 1117 4.283333 0
Assembly Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads https://training.galaxyproject.org//topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html Read mapping, Sequence assembly visualisation, Aggregation, Genome assembly, Sequencing quality control, Validation, Sequence contamination filtering, Sequence file editing, Pairwise sequence alignment, Box-Whisker plot plotting, Scatter plot plotting, Data handling 2020-04-21 2025-05-15 14 True True True True samtools_stats, bandage_image, multiqc, fasterq_dump, collapse_dataset, seqtk_sample, fasta_filter_by_length, nanoplot, samtools_view, fastp, minimap2, bowtie2, unicycler, __ZIP_COLLECTION__, bandage_info, samtools_fastx UseGalaxy.org.au, UseGalaxy.eu Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 3587409 8652768 10.666667 0
Assembly An introduction to get started in genome assembly and annotation https://training.galaxyproject.org//topics/assembly/tutorials/get-started-genome-assembly/slides.html 2021-11-30 2023-10-23 7 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3099445 7017189 2.050000 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 0 1126808 1933263 1.250000 0
Assembly Deeper look into Genome Assembly algorithms https://training.galaxyproject.org//topics/assembly/tutorials/algorithms-introduction/slides.html 2021-01-12 2021-01-12 1 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3560228 8573707 2.150000 0
Climate Ocean's variables study https://training.galaxyproject.org//topics/climate/tutorials/ocean-variables/tutorial.html 2023-11-29 2025-05-10 5 True False False True interactive_tool_divand, divand_full_analysis, interactive_tool_odv UseGalaxy.eu 0 264 311 11.750000 0
Climate Nitrate DMQC for autonomous platforms such as Argo floats https://training.galaxyproject.org//topics/climate/tutorials/ocean_qcv_analysis/tutorial.html 2025-08-08 2025-09-16 3 True False False True harmonize_insitu_to_netcdf, tool_odv_history, interactive_tool_odv, tool_odv, tool_biogeochemical_calibration UseGalaxy.eu 0 91 104 10.683333 0
Climate Analyse Argo data https://training.galaxyproject.org//topics/climate/tutorials/argo_pangeo/tutorial.html 2024-03-24 2025-05-10 2 True False False True argo_getdata, timeseries_extraction, interactive_tool_odv, xarray_coords_info, xarray_metadata_info UseGalaxy.eu 0 361 423 8.900000 0
Climate Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools https://training.galaxyproject.org//topics/climate/tutorials/pangeo/tutorial.html Visualisation 2022-02-18 2025-05-10 6 True True True True xarray_netcdf2netcdf, regexColumn1, climate_stripes, xarray_coords_info, ggplot2_point, __EXTRACT_DATASET__, xarray_select, __MERGE_COLLECTION__, xarray_mapplot, graphicsmagick_image_montage, xarray_metadata_info UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 2974279 6617354 11.966667 0
Climate Functionally Assembled Terrestrial Ecosystem Simulator (FATES) https://training.galaxyproject.org//topics/climate/tutorials/fates/tutorial.html Visualisation 2020-10-25 2025-05-10 18 True True True True ctsm_fates, tp_find_and_replace, ggplot2_point, __EXTRACT_DATASET__, xarray_select, interactive_tool_panoply, xarray_metadata_info UseGalaxy.eu, UseGalaxy.org (Main) 0 3582553 8644643 8.116667 0
Climate Pangeo Notebook in Galaxy - Introduction to Xarray https://training.galaxyproject.org//topics/climate/tutorials/pangeo-notebook/tutorial.html 2022-02-18 2025-05-10 11 True True True True interactive_tool_pangeo_notebook UseGalaxy.eu 0 2974553 6617926 8.666667 0
Climate Sentinel 5P data visualisation https://training.galaxyproject.org//topics/climate/tutorials/sentinel5_data/tutorial.html 2024-01-26 2025-05-10 2 True False False True interactive_tool_copernicus, interactive_tool_panoply, interactive_tool_copernicus_notebook 0 358 406 5.033333 0
Climate Getting your hands-on climate data https://training.galaxyproject.org//topics/climate/tutorials/climate-101/tutorial.html Visualisation 2020-04-30 2025-05-10 14 True False False True cds_essential_variability, tp_awk_tool, psy_maps, climate_stripes, ggplot2_point, datamash_ops, interactive_tool_panoply, Grep1 UseGalaxy.eu 0 1137 1548 6.900000 0
Climate Introduction to climate data https://training.galaxyproject.org//topics/climate/tutorials/introduction/slides.html 2020-10-11 2025-05-10 2 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3581008 8642245 2.150000 0
Climate Collaboration with JupyterGIS https://training.galaxyproject.org//topics/climate/tutorials/jupytergis_collaboration/tutorial.html 2025-04-03 2025-05-10 4 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 223 270 6.516667 0
Climate Getting your hands-on earth data https://training.galaxyproject.org//topics/climate/tutorials/earth_system/tutorial.html 2024-10-04 2025-05-10 2 True False False False argo_getdata, c3s, obis_data, spocc_occ UseGalaxy.eu UseGalaxy.be 0 159 197 9.666667 0
Climate Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab https://training.galaxyproject.org//topics/climate/tutorials/fates-jupyterlab/tutorial.html 2020-10-25 2025-05-10 16 True False False False interactive_tool_jupyter_notebook UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) 0 584 994 8.600000 0
Climate Ocean Data View (ODV) https://training.galaxyproject.org//topics/climate/tutorials/ocean-data-view/tutorial.html 2023-11-27 2025-05-10 2 True False False False interactive_tool_odv UseGalaxy.eu, UseGalaxy.fr 0 503 603 4.366667 0
Climate Visualize Climate data with Panoply netCDF viewer https://training.galaxyproject.org//topics/climate/tutorials/panoply/tutorial.html 2020-03-05 2025-05-10 18 True False False False interactive_tool_panoply UseGalaxy.eu, UseGalaxy.org (Main) 0 6696 10732 1.633333 0
Galaxy Community Building Creation of a Galaxy tutorial table for your community https://training.galaxyproject.org//topics/community/tutorials/community-tutorial-table/tutorial.html 2025-09-17 2025-10-28 2 True False False False 0 48 52 7.300000 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 2026-01-28 4 True False False False 0 84 105 8.500000 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 36 38 6.916667 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 0 152 192 8.700000 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 0 114 130 9.766667 0
Galaxy Community Building Creation of resources listing all the tools and their metadata relevant to your community https://training.galaxyproject.org//topics/community/tutorials/community-tool-table/tutorial.html 2024-03-13 2025-10-28 5 True False False False 0 130 155 7.600000 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 63 78 8.016667 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 0 190 205 7.716667 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 vmd_hbonds, ambertools_acpype, gmx_setup, tp_grep_tool, openbabel_compound_convert, bio3d_rmsf, gmx_energy, mdanalysis_cosine_analysis, gmx_em, bio3d_rmsd, gmx_sim, gmx_merge_topology_files, gmx_editconf, md_converter, gmx_solvate, bio3d_pca_visualize, get_pdb, bio3d_pca UseGalaxy.org.au, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 11464 19825 4.866667 0
Computational chemistry Protein target prediction of a bioactive ligand with Align-it and ePharmaLib https://training.galaxyproject.org//topics/computational-chemistry/tutorials/zauberkugel/tutorial.html 2022-02-15 2024-06-14 10 True False False True openbabel_addh, sort1, ctb_alignit, split_file_to_collection, rdconf, tp_cat UseGalaxy.cz 0 1349 1920 7.300000 0
Computational chemistry Data management in Medicinal Chemistry https://training.galaxyproject.org//topics/computational-chemistry/tutorials/med-chem-data/tutorial.html 2024-01-08 2024-09-13 4 True False True True ctb_silicos_qed, ctb_im_rxn_maker, openbabel_compound_convert, chembl, md_converter, openbabel_svg_depiction, get_pdb UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.no 0 549 652 9.016667 0
Computational chemistry Protein-ligand docking https://training.galaxyproject.org//topics/computational-chemistry/tutorials/cheminformatics/tutorial.html 2019-10-19 2025-12-04 17 True False False True ctb_remDuplicates, sdf_to_tab, openbabel_compound_convert, tp_find_and_replace, ctb_np-likeness-calculator, ctb_remIons, prepare_receptor, ctb_compound_convert, openbabel_svg_depiction, ctb_chemfp_nxn_clustering, ctb_chemfp_butina_clustering, tp_grep_tool, docking, fpocket, ctb_filter, ctb_online_data_fetch, ctb_obgrep, prepare_box, ctb_change_title, ctb_chemfp_mol2fps, chembl, tp_cat, get_pdb, collapse_dataset UseGalaxy.org (Main) 0 20673 34892 3.166667 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, openbabel_compound_convert, ctb_frankenstein_ligand, rxdock_rbcavity, enumerate_charges, rdock_rbcavity, split_file_to_collection, rxdock_rbdock, xchem_pose_scoring, rdock_rbdock, sucos_max_score, collapse_dataset 0 3277 5335 8.200000 0
Computational chemistry Running molecular dynamics simulations using NAMD https://training.galaxyproject.org//topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.html 2019-06-03 2023-11-09 9 True False False True setup, namd_npt, namd_nvt, minimizer 0 4367 7231 3.850000 0
Computational chemistry Running molecular dynamics simulations using GROMACS https://training.galaxyproject.org//topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.html 2019-06-03 2023-11-09 15 True False False True gmx_setup, tp_grep_tool, gmx_em, gmx_sim, gmx_solvate, get_pdb, gmx_editconf UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 27840 49139 2.450000 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 mdanalysis_ramachandran_plot, mdanalysis_dihedral, bio3d_rmsf, mdanalysis_cosine_analysis, bio3d_rmsd, mdanalysis_distance, mdanalysis_rdf, bio3d_pca UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no 0 33188 58409 2.333333 0
Computational chemistry Setting up molecular systems https://training.galaxyproject.org//topics/computational-chemistry/tutorials/setting-up-molecular-systems/tutorial.html 2019-06-03 2023-11-09 14 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1906 2551 9.566667 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 3581008 8642246 2.150000 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 3581175 8642433 12.550000 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 0 359 668 8.650000 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 5601 6717 1.483333 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 68 74 3.483333 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 0 587 779 13.466667 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 0 290 377 13.550000 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 0 295 378 14.150000 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 0 672 884 9.616667 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 89 131 11.650000 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 1286 1746 3.533333 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 0 325 483 12.850000 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 92 110 18.450000 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 0 708 1060 12.600000 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 0 522 697 10.850000 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 0 134 150 10.366667 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, Read mapping, Data handling, Read pre-processing, Sequence trimming 2018-06-20 2025-11-20 33 True False True True fastq_to_tabular, tp_sed_tool, random_lines1, Cut1, Filter1, cutadapt, bowtie2, seqtk_subseq, tp_cut_tool, tp_cat, bam_to_sam, tp_sorted_uniq, c3s 0 1922 2794 12.833333 0
Contributing to the Galaxy Training Material FAIR Galaxy Training Material https://training.galaxyproject.org//topics/contributing/tutorials/fair-gtn/tutorial.html 2026-03-24 2026-03-24 0 True False False False 0 0 0 0.000000 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 68 68 7.583333 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 96 100 6.183333 0
Contributing to the Galaxy Training Material Creating content in Markdown https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-content/tutorial.html Sequencing quality control, Validation 2017-06-25 2025-04-08 85 True False False False upload1, multiqc 0 3861 9905 7.050000 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 3581008 8642248 2.150000 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 0 138 159 14.500000 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 Methylation analysis, Tree-based sequence alignment, Variant calling, Variant classification 2021-06-30 2025-03-28 18 True False True False pangolin, fasta_regex_finder, Filter1, upload1, datamash_ops, nextclade UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 7638 13546 7.400000 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 Formatting, Read mapping, Generation, SNP detection, Genome indexing, Sequencing quality control, Validation, Sequence contamination filtering, Sequence alignment, Data handling 2020-06-24 2024-06-14 16 True False True True samtools_stats, lofreq_indelqual, multiqc, snpSift_extractFields, fasterq_dump, lofreq_call, snpeff_sars_cov_2, Filter1, bwa_mem, fastp, picard_MarkDuplicates, tp_cut_tool, lofreq_viterbi, Grep1 UseGalaxy.eu, UseGalaxy.org (Main) MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 14016 20984 6.450000 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 3260261 7551859 6.516667 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 Read mapping, Variant classification, Tree-based sequence alignment, Visualisation, Sequencing quality control, Validation, Sequence contamination filtering 2021-06-08 2025-12-18 11 True False True True multiqc, compose_text_param, falco, pangolin, snpSift_filter, fastp, bcftools_consensus, collapse_dataset UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr 0 3104 3828 8.416667 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 alignment, Sequence file editing, Read mapping, Generation, Genome indexing, Data handling 2021-08-04 2023-11-09 5 True False False True tp_replace_in_line, trimmomatic, bwa_mem, seqtk_subseq, __UNZIP_COLLECTION__, __ZIP_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 4188 5909 9.183333 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 fasterq_dump, snpeff_sars_cov_2, jq, fastq_to_fasta_python, query_tabular, tp_cat, fastq_dump UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3361781 7887921 11.866667 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 Sequence alignment, Statistical calculation, Read mapping, Generation, Genome visualisation, Genome indexing, Sequence composition calculation, Sequencing quality control 2023-07-10 2024-02-29 2 True False False False bwa_mem, jbrowse, fastqc UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@AuBi, Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz 0 1442 1869 11.916667 0
Foundations of Data Science Data Manipulation Olympics https://training.galaxyproject.org//topics/data-science/tutorials/data-manipulation-olympics/tutorial.html 2026-03-24 2026-03-24 0 True False False True tabular_to_csv, tp_sort_header_tool, upload1, {{version_cut_columns}}, {{version_datamash}}, {{version_remove_columns_by_header}}, {{version_cut_advanced}}, {{version_join}}, {{version_replace_text_line}}, {{version_select_first}}, {{version_remove_beginning}}, Grouping1, Count1, Cut1, datamash_ops, Show beginning1, cat1, {{version_paste}}, {{version_sort}}, {{version_compute}}, join1, tp_split_on_column, Add_a_column1, wc_gnu, {{version_cat}}, {{version_filter}}, {{version_unique}}, regexColumn1, {{version_replace_text_column}}, Remove beginning1, Filter1, tp_cat, {{version_split}}, tp_sorted_uniq, {{version_count}}, {{version_wc}} 0 4 4 1.366667 0
Foundations of Data Science Learning about one gene across biological resources and formats https://training.galaxyproject.org//topics/data-science/tutorials/online-resources-gene/tutorial.html 2023-09-07 2026-03-09 3 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, MISSISSIPPI, PepSimili, PhagePromotor, UseGalaxy.no 0 2019937 4091614 7.850000 0
Foundations of Data Science A (very) brief history of genomics https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture1/tutorial.html 2024-01-09 2024-02-20 2 True True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1864243 3741237 19.550000 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 2026-03-09 5 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 545 585 5.166667 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 0 9717 12679 4.033333 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 0 191 437 12.483333 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 0 1586 2047 8.683333 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 0 1472 1837 2.650000 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 0 530 714 4.666667 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 0 657 818 3.333333 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.org.au, UseGalaxy.eu 0 2890 3895 8.866667 0
Foundations of Data Science CLI Educational Game - Bashcrawl https://training.galaxyproject.org//topics/data-science/tutorials/cli-bashcrawl/tutorial.html 2021-09-30 2024-10-15 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 2253 2549 1.766667 0
Foundations of Data Science Python - Warm-up for statistics and machine learning https://training.galaxyproject.org//topics/data-science/tutorials/python-warmup-stat-ml/tutorial.html 2025-03-11 2025-03-11 1 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 200 235 8.016667 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.org.au, UseGalaxy.eu 0 363 596 5.433333 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 0 3522 4520 2.116667 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 0 1050 1294 9.066667 0
Foundations of Data Science Introduction to SQL https://training.galaxyproject.org//topics/data-science/tutorials/sql-basic/tutorial.html 2021-10-11 2024-12-13 8 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 658 808 9.833333 0
Foundations of Data Science SQL Educational Game - Murder Mystery https://training.galaxyproject.org//topics/data-science/tutorials/sql-game/tutorial.html 2021-10-11 2023-11-23 6 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 736 798 2.750000 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 0 1257 1739 8.550000 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 0 1028 1294 9.466667 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 0 699 796 7.066667 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.org.au, UseGalaxy.eu 0 1686 2614 10.016667 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 0 1008 1180 4.750000 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 0 310 373 3.366667 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 0 584 764 11.866667 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 0 426 705 12.016667 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 0 901 1001 1.950000 0
Foundations of Data Science Introduction to sequencing with Python (part two) https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture3/tutorial.html 2024-01-23 2024-02-20 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 166 179 3.916667 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 0 678 869 6.850000 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 0 617 739 9.066667 0
Foundations of Data Science Python - Lists & Strings & Dictionaries https://training.galaxyproject.org//topics/data-science/tutorials/python-iterables/tutorial.html 2022-04-25 2024-06-25 6 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 2273 2661 2.300000 0
Foundations of Data Science Data Manipulation Olympics - JQ https://training.galaxyproject.org//topics/data-science/tutorials/data-manipulation-olympics-jq/tutorial.html 2023-06-16 2024-05-07 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 440 492 5.650000 0
Foundations of Data Science Introduction to sequencing with Python (part three) https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture4/tutorial.html 2024-02-06 2024-02-20 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 179 194 1.033333 0
Foundations of Data Science Python - Flow Control https://training.galaxyproject.org//topics/data-science/tutorials/python-flow/tutorial.html 2022-04-25 2023-02-13 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 308 359 9.733333 0
Foundations of Data Science Introduction to sequencing with Python (part four) https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture5/tutorial.html 2024-02-13 2024-02-20 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 174 188 3.650000 0
Foundations of Data Science Data manipulation with Pandas https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture6/tutorial.html 2024-02-20 2025-02-27 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 75 81 9.716667 0
Foundations of Data Science Python - Loops https://training.galaxyproject.org//topics/data-science/tutorials/python-loops/tutorial.html 2022-04-25 2023-02-13 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 436 511 7.133333 0
Foundations of Data Science Versioning your code and data with git https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture7/tutorial.html 2024-03-12 2024-03-12 1 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 19 19 15.566667 0
Foundations of Data Science Python - Files & CSV https://training.galaxyproject.org//topics/data-science/tutorials/python-files/tutorial.html 2022-04-25 2023-02-13 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 594 684 4.983333 0
Foundations of Data Science Python - Try & Except https://training.galaxyproject.org//topics/data-science/tutorials/python-exceptions/tutorial.html 2022-04-25 2023-02-13 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 640 726 3.700000 0
Foundations of Data Science Python - Introductory Graduation https://training.galaxyproject.org//topics/data-science/tutorials/python-basics-recap/tutorial.html 2022-04-25 2023-02-13 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 255 299 11.433333 0
Foundations of Data Science Python - Testing https://training.galaxyproject.org//topics/data-science/tutorials/python-testing/tutorial.html 2022-10-19 2023-02-13 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 254 277 6.466667 0
Foundations of Data Science Python - Type annotations https://training.galaxyproject.org//topics/data-science/tutorials/python-typing/tutorial.html 2022-10-19 2023-02-13 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 653 690 2.650000 0
Foundations of Data Science Python - Argparse https://training.galaxyproject.org//topics/data-science/tutorials/python-argparse/tutorial.html 2022-04-25 2023-01-24 5 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1381 1498 2.000000 0
Foundations of Data Science Virtual Environments For Software Development https://training.galaxyproject.org//topics/data-science/tutorials/python-venv/tutorial.html 2022-10-19 2023-05-18 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 247 269 7.183333 0
Foundations of Data Science Conda Environments For Software Development https://training.galaxyproject.org//topics/data-science/tutorials/python-conda/tutorial.html 2022-10-19 2023-05-18 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 752 806 3.950000 0
Foundations of Data Science Python - Globbing https://training.galaxyproject.org//topics/data-science/tutorials/python-glob/tutorial.html 2022-04-25 2023-02-13 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 571 614 5.033333 0
Foundations of Data Science Python - Subprocess https://training.galaxyproject.org//topics/data-science/tutorials/python-subprocess/tutorial.html 2022-04-25 2023-02-13 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1203 1390 1.983333 0
Foundations of Data Science Python - Coding Style https://training.galaxyproject.org//topics/data-science/tutorials/python-linting/tutorial.html 2022-11-03 2023-05-18 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 241 256 9.866667 0
Foundations of Data Science Python - Multiprocessing https://training.galaxyproject.org//topics/data-science/tutorials/python-multiprocessing/tutorial.html 2022-10-19 2023-11-16 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 923 988 3.016667 0
Development in Galaxy Architecture 08 - Galaxy Application Components: Models, Managers, and Services https://training.galaxyproject.org//topics/dev/tutorials/architecture-application-components/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165864 1.333333 0
Development in Galaxy Tool Shed: sharing Galaxy tools https://training.galaxyproject.org//topics/dev/tutorials/toolshed/slides.html 2017-06-12 2022-10-18 15 False True False False 0 3581008 8642255 2.150000 0
Development in Galaxy Scripting Galaxy using the API and BioBlend https://training.galaxyproject.org//topics/dev/tutorials/bioblend-api/tutorial.html 2017-01-17 2023-11-16 22 True True True False 0 3581809 8643286 12.800000 0
Development in Galaxy Architecture 09 - Galaxy Plugin Architecture https://training.galaxyproject.org//topics/dev/tutorials/architecture-plugins/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165864 1.333333 0
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 3581008 8642255 2.150000 0
Development in Galaxy Architecture 05 - Galaxy Web Frameworks https://training.galaxyproject.org//topics/dev/tutorials/architecture-frameworks/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165864 1.333333 0
Development in Galaxy Architecture 14 - Galaxy Startup Process https://training.galaxyproject.org//topics/dev/tutorials/architecture-startup/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165864 1.333333 0
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 3581387 8642785 12.183333 0
Development in Galaxy Architecture 16 - Galaxy Testing https://training.galaxyproject.org//topics/dev/tutorials/architecture-tests/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165864 1.333333 0
Development in Galaxy Tool development and integration into Galaxy https://training.galaxyproject.org//topics/dev/tutorials/tool-integration/slides.html 2016-09-30 2025-04-08 30 external True False False 0 3581013 8642262 10.450000 0
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 3581750 8643134 6.733333 0
Development in Galaxy Architecture 13 - Galaxy Dependencies Management https://training.galaxyproject.org//topics/dev/tutorials/architecture-dependencies/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165864 1.333333 0
Development in Galaxy Architecture 04 - Galaxy Files and Directory Structure https://training.galaxyproject.org//topics/dev/tutorials/architecture-files/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165864 1.333333 0
Development in Galaxy Tool Dependencies and Containers https://training.galaxyproject.org//topics/dev/tutorials/containers/slides.html 2017-06-20 2022-10-18 14 False True False False 0 3581008 8642255 2.150000 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 3369500 7913076 9.133333 0
Development in Galaxy Tool Dependencies and Conda https://training.galaxyproject.org//topics/dev/tutorials/conda/slides.html 2017-06-20 2023-04-14 33 False True False False 0 3581008 8642255 2.150000 0
Development in Galaxy Galaxy Interactive Environments https://training.galaxyproject.org//topics/dev/tutorials/interactive-environments/slides.html 2017-02-05 2023-02-17 16 False True False False 0 3581008 8642255 2.150000 0
Development in Galaxy Architecture 06 - Dependency Injection in Galaxy https://training.galaxyproject.org//topics/dev/tutorials/architecture-dependency-injection/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165864 1.333333 0
Development in Galaxy Architecture 15 - Galaxy Production Deployment https://training.galaxyproject.org//topics/dev/tutorials/architecture-production/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165864 1.333333 0
Development in Galaxy Architecture 11 - Galaxy Markdown Architecture https://training.galaxyproject.org//topics/dev/tutorials/architecture-markdown/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165864 1.333333 0
Development in Galaxy Galaxy Interactive Tours https://training.galaxyproject.org//topics/dev/tutorials/interactive-tours/slides.html 2017-01-12 2021-07-27 14 False True False False 0 3581008 8642255 2.150000 0
Development in Galaxy Architecture 12 - Galaxy Client Architecture https://training.galaxyproject.org//topics/dev/tutorials/architecture-client/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165865 1.333333 0
Development in Galaxy Architecture 01 - Galaxy Ecosystem and Projects https://training.galaxyproject.org//topics/dev/tutorials/architecture-ecosystem/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165865 1.333333 0
Development in Galaxy Architecture 02 - Galaxy Project Management and Contribution https://training.galaxyproject.org//topics/dev/tutorials/architecture-project-management/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165865 1.333333 0
Development in Galaxy Architecture 07 - Galaxy Task Management with Celery https://training.galaxyproject.org//topics/dev/tutorials/architecture-tasks/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165865 1.333333 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 3581221 8642533 9.283333 0
Development in Galaxy Architecture 10 - Galaxy File Sources Architecture https://training.galaxyproject.org//topics/dev/tutorials/architecture-file-sources/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165865 1.333333 0
Development in Galaxy Architecture 03 - Galaxy Architecture Principles https://training.galaxyproject.org//topics/dev/tutorials/architecture-principles/slides.html 2026-02-19 2026-02-19 1 False True False False 0 96552 165865 1.333333 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 0 266 357 13.216667 0
Development in Galaxy Contributing a New Feature to Galaxy Core https://training.galaxyproject.org//topics/dev/tutorials/core-contributing/tutorial.html 2021-06-08 2026-02-19 11 True False False False 0 805 1178 11.166667 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 0 316 373 9.583333 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 56 59 2.183333 0
Development in Galaxy Creating Galaxy tools from Conda Through Deployment https://training.galaxyproject.org//topics/dev/tutorials/tool-from-scratch/tutorial.html 2021-06-15 2024-10-08 15 True False True False 0 2871 4584 6.083333 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 0 646 1251 8.966667 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 0 470 554 10.350000 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 0 251 361 12.816667 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 34 37 1.883333 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 0 303 731 8.033333 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 1340 1773 7.716667 0
Digital Humanities OpenRefine Tutorial for researching cultural data https://training.galaxyproject.org//topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html 2025-09-24 2025-10-21 2 True False False True param_value_from_file, compose_text_param, tp_grep_tool, regexColumn1, tp_head_tool, Remove beginning1, Cut1, tp_sort_header_tool, interactive_tool_openrefine, datamash_ops, filter_tabular, barchart_gnuplot, wordcloud UseGalaxy.eu 0 116 124 0.933333 0
Digital Humanities Introduction to Digital Humanities in Galaxy https://training.galaxyproject.org//topics/digital-humanities/tutorials/introduction_to_dh/tutorial.html 2025-09-11 2025-11-25 5 True False False True tp_grep_tool, tp_replace_in_line, tp_find_and_replace, Remove beginning1, diff, wc_gnu, wordcloud UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu 0 119 138 2.900000 0
Digital Humanities Text-Mining Differences in Chinese Newspaper Articles https://training.galaxyproject.org//topics/digital-humanities/tutorials/text_mining_chinese/tutorial.html 2025-02-28 2025-09-09 5 True False False True sort1, tp_replace_in_line, Cut1, diff, Filter1, datamash_ops, Add_a_column1, wordcloud UseGalaxy.cz 0 194 221 3.733333 0
Ecology Metabarcoding/eDNA through Obitools https://training.galaxyproject.org//topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html Statistical calculation, Sequence analysis, Sequence composition calculation, Sequencing quality control 2022-02-28 2025-06-03 12 True False True True obi_illumina_pairend, fastqc, fastq_groomer, obi_tab, unzip, Cut1, obi_ngsfilter, Filter1, obi_clean, join1, seq_filter_by_id, obi_uniq, obi_annotate, obi_grep, obi_stat, wc_gnu, ncbi_blastn_wrapper UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.no UseGalaxy.cz, UseGalaxy.fr 0 4791 6629 3.733333 0
Ecology Taxonomic Analysis of eDNA https://training.galaxyproject.org//topics/ecology/tutorials/eDNA-taxonomic-analysis/tutorial.html Sequencing quality control, Sequence contamination filtering 2025-06-02 2025-06-03 2 True False False True fastp, Count1, cshl_fastq_to_fasta, ncbi_blastn_wrapper UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 643 799 3.416667 0
Ecology Life Traits Ecoregionalization workflow https://training.galaxyproject.org//topics/ecology/tutorials/ecoregiolifetraits/tutorial.html 2025-06-02 2025-06-10 3 True False False False ecoregion_taxa_seeker, column_remove_by_header, regexColumn1, unzip, ecoregion_GeoNearestNeighbor, ecoregion_brt_analysis, WormsMeasurements, Filter1, ClaraGuess, ecoregion_eco_map, tp_cut_tool UseGalaxy.eu 0 66 69 12.266667 0
Ecology From NDVI data with OpenEO to time series visualisation with Holoviews https://training.galaxyproject.org//topics/ecology/tutorials/ndvi_openeo/tutorial.html 2024-01-24 2024-06-29 3 True False False True interactive_tool_copernicus_notebook, interactive_tool_holoviz UseGalaxy.eu 0 256 296 6.583333 0
Ecology Phylodiversity analysis quick tutorial https://training.galaxyproject.org//topics/ecology/tutorials/phylodiversity_workflow/tutorial.html 2025-06-06 2025-06-06 1 True False False False estimate_endem, phylo_index, crsconverter, phylogenetic_occupancy_matcher UseGalaxy.eu 0 126 152 6.966667 0
Ecology Compute and analyze biodiversity metrics with PAMPA toolsuite https://training.galaxyproject.org//topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html 2020-11-19 2025-09-03 23 True False True True datamash_transpose, pampa_glmcomm, regexColumn1, Count1, pampa_presabs, pampa_glmsp, Filter1, tp_easyjoin_tool, tp_sort_header_tool, tp_cut_tool, tp_cat, pampa_communitymetrics, mergeCols1, pampa_plotglm, regex1 UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr 0 1152 1523 10.500000 0
Ecology Cleaning GBIF data for the use in Ecology https://training.galaxyproject.org//topics/ecology/tutorials/gbif_cleaning/tutorial.html 2022-10-28 2025-06-03 6 True False False True Summary_Statistics1, Count1, spocc_occ, Filter1, gdal_ogr2ogr UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no 0 725 888 5.416667 0
Ecology RAD-Seq Reference-based data analysis https://training.galaxyproject.org//topics/ecology/tutorials/ref-based-rad-seq/tutorial.html Read mapping, Generation, Genome indexing, Sequence composition calculation, Sequencing quality control, Validation, Sequence alignment, Statistical calculation, Data handling 2017-02-14 2025-11-06 15 True False False True bwa, multiqc, fastqc, stacks_procrad, regex_replace, addValue, cat1, Convert characters1, Count1, Summary_Statistics1, Cut1, tp_replace_in_line, Filter1, tp_sort_header_tool, bwa_wrapper, stacks_populations, stacks_refmap, Grep1 0 3361 5160 4.666667 0
Ecology Data submission using ENA upload Tool https://training.galaxyproject.org//topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html Primer removal, Read mapping, Read pre-processing, Visualisation, Sequencing quality control, Validation, Sequence trimming 2024-12-13 2025-03-20 2 True False False False fastq_filter, multiqc, fastq_groomer, falco, bg_uniq, __RELABEL_FROM_FILE__, fastq_to_fasta_python, cutadapt, collection_element_identifiers, __FILTER_EMPTY_DATASETS__, ab1_fastq_converter, Paste1, regex1, ncbi_blastn_wrapper UseGalaxy.eu UseGalaxy.cz 0 320 341 3.333333 0
Ecology Visualization of Climate Data using  NetCDF xarray Map Plotting https://training.galaxyproject.org//topics/ecology/tutorials/x-array-map-plot/tutorial.html 2022-10-26 2024-06-27 9 True False False True xarray_coords_info, cdo_operations, xarray_mapplot, graphicsmagick_image_montage, xarray_metadata_info UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz 0 2483 2859 1.466667 0
Ecology Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS https://training.galaxyproject.org//topics/ecology/tutorials/Metashrimps_tutorial/tutorial.html 2024-01-22 2025-06-03 6 True False False False interactive_tool_metashrimps UseGalaxy.eu 0 138 149 7.350000 0
Ecology Champs blocs indicators https://training.galaxyproject.org//topics/ecology/tutorials/champs-blocs/tutorial.html 2023-01-04 2025-12-02 12 True False False True cb_qecb, cb_eco, cb_dissim, cb_ivr, cb_div 0 197 347 14.933333 0
Ecology Marine Omics identifying biosynthetic gene clusters https://training.galaxyproject.org//topics/ecology/tutorials/marine_omics_bgc/tutorial.html Genome annotation, Sequence motif recognition, Protein feature detection 2024-08-19 2025-06-03 3 True False False True SanntiS_marine, sanntis_marine, prodigal, interproscan, regex1 0 248 287 11.500000 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_process_data, srs_pca, srs_preprocess_s2, srs_diversity_maps, srs_global_indices, srs_spectral_indices UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 675 857 6.383333 0
Ecology Ecoregionalization workflow tutorial https://training.galaxyproject.org//topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html 2024-09-16 2025-06-03 7 True False False True ecoregion_taxa_seeker, interactive_tool_jupyter_notebook, regexColumn1, unzip, ecoregion_GeoNearestNeighbor, ecoregion_brt_analysis, ecoregion_eco_map, tp_cut_tool, ecoregion_cluster_estimate, mergeCols1, filter_tabular, ecoregion_clara_cluster UseGalaxy.eu 0 369 472 7.516667 0
Ecology RAD-Seq to construct genetic maps https://training.galaxyproject.org//topics/ecology/tutorials/genetic-map-rad-seq/tutorial.html Data handling 2017-02-14 2025-06-03 13 True False False True stacks_genotypes, stacks_denovomap UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 943 1305 8.366667 0
Ecology Species distribution modeling https://training.galaxyproject.org//topics/ecology/tutorials/species-distribution-modeling/tutorial.html 2019-07-04 2025-06-03 18 True False False True tabular_to_csv, tp_find_and_replace, spocc_occ, Filter1, tp_cut_tool, interactive_tool_wallace UseGalaxy.eu, UseGalaxy.fr 0 3359 5054 3.916667 0
Ecology Checking expected species and contamination in bacterial isolate https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Statistical calculation, Taxonomic classification, Expression analysis, Cross-assembly 2024-03-04 2025-12-18 5 True False False True est_abundance, recentrifuge, kraken2, upload1 UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main) 0 987 1320 8.450000 0
Ecology Obis marine indicators https://training.galaxyproject.org//topics/ecology/tutorials/obisindicators/tutorial.html Biodiversity, Ecology, Data mining 2023-04-11 2025-06-03 9 True False False True obis_data, tp_cut_tool, obisindicators UseGalaxy.eu UseGalaxy.be 0 340 421 11.900000 0
Ecology RAD-Seq de-novo data analysis https://training.galaxyproject.org//topics/ecology/tutorials/de-novo-rad-seq/tutorial.html Statistical calculation, Sequence composition calculation, Sequencing quality control, Data handling 2017-02-14 2025-06-03 14 True False False True stacks_denovomap, fastqc, stacks_procrad, stacks_populations UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no 0 2775 4386 5.150000 0
Ecology Preparing genomic data for phylogeny reconstruction https://training.galaxyproject.org//topics/ecology/tutorials/phylogeny-data-prep/tutorial.html Genome annotation, Sequence analysis, Sequence clustering, Genetic variation analysis, Sequence assembly validation, Multiple sequence alignment 2022-10-21 2025-06-03 5 True False False True proteinortho, clustalw, clipkit, tp_replace_in_line, phykit_alignment_based, glimmer_gbk_to_orf, Filter1, repeatmasker_wrapper, proteinortho_grab_proteins, busco, funannotate_predict, regex1, collapse_dataset 0 2389 3256 6.783333 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 2026-01-30 8 True False False False interactive_tool_metashark UseGalaxy.eu, UseGalaxy.fr 0 272 325 4.216667 0
Ecology Biodiversity data exploration https://training.galaxyproject.org//topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html 2022-03-01 2025-06-03 15 True False True True ecology_homogeneity_normality, tool_anonymization, regexColumn1, Remove beginning1, ecology_link_between_var, tp_cut_tool, ecology_stat_presence_abs, ecology_presence_abs_abund, ecology_beta_diversity UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr 0 1721 2377 10.416667 0
Ecology Regional GAM https://training.galaxyproject.org//topics/ecology/tutorials/regionalGAM/tutorial.html Ecology Visualisation 2019-07-04 2025-06-03 18 True False False True regionalgam_glmmpql, regionalgam_flight_curve, regionalgam_gls, regexColumn1, tp_awk_tool, Count1, Remove beginning1, Filter1, regionalgam_ab_index, ggplot2_point, regionalgam_autocor_acf, regionalgam_plot_trend, csv2tab_R, Paste1, tab2csv_R, mergeCols1, flight-curve 0 369 487 15.583333 0
Ecology Visualize EBV cube data with Panoply netCDF viewer https://training.galaxyproject.org//topics/ecology/tutorials/panoply_ebv/tutorial.html 2022-10-28 2024-06-27 9 True False False False interactive_tool_panoply UseGalaxy.eu, UseGalaxy.org (Main) 0 278 341 5.950000 0
Ecology QGIS Web Feature Services https://training.galaxyproject.org//topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.html 2023-10-11 2025-06-03 6 True False False False interactive_tool_qgis UseGalaxy.eu 0 333 380 7.500000 0
Ecology Audio data annotation with NEAL (Nature + Energy Audio labeler) https://training.galaxyproject.org//topics/ecology/tutorials/NEAL_tutorial/tutorial.html 2025-10-14 2025-11-06 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 68 80 1.050000 0
Ecology Cleaning GBIF data using OpenRefine https://training.galaxyproject.org//topics/ecology/tutorials/openrefine_gbif/tutorial.html 2025-01-21 2025-06-03 5 True False False False interactive_tool_openrefine, regex1 UseGalaxy.eu, UseGalaxy.fr 0 228 275 6.016667 0
Statistics and machine learning Pretraining a Large Language Model (LLM) from Scratch on DNA Sequences https://training.galaxyproject.org//topics/statistics/tutorials/genomic-llm-pretraining/tutorial.html 2025-04-17 2025-05-22 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1572 1976 3.450000 0
Statistics and machine learning Foundational Aspects of Machine Learning using Python https://training.galaxyproject.org//topics/statistics/tutorials/intro-to-ml-with-python/tutorial.html 2025-03-11 2025-05-19 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 947 1177 5.650000 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 2007 2395 2.000000 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 1688 1987 2.583333 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 1358 1577 4.050000 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 0 122 143 15.233333 0
Statistics and machine learning Fine-tuning a LLM for DNA Sequence Classification https://training.galaxyproject.org//topics/statistics/tutorials/genomic-llm-finetuning/tutorial.html 2025-04-17 2025-05-22 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 946 1163 2.633333 0
Statistics and machine learning Neural networks using Python https://training.galaxyproject.org//topics/statistics/tutorials/neural-networks-with-python/tutorial.html 2025-03-11 2025-03-11 1 True True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1206090 2125417 12.400000 0
Statistics and machine learning Predicting Mutation Impact with Zero-shot Learning using a pretrained DNA LLM https://training.galaxyproject.org//topics/statistics/tutorials/genomic-llm-zeroshot-prediction/tutorial.html 2025-04-17 2025-05-22 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 326 389 4.466667 0
Statistics and machine learning Deep Learning (without Generative Artificial Intelligence) using Python https://training.galaxyproject.org//topics/statistics/tutorials/deep-learning-without-gai-with-python/tutorial.html 2025-03-11 2025-03-11 1 True True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1206088 2125414 8.900000 0
Statistics and machine learning Generating Artificial Yeast DNA Sequences using a DNA LLM https://training.galaxyproject.org//topics/statistics/tutorials/genomic-llm-sequence-generation/tutorial.html 2025-04-17 2025-05-22 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 236 266 5.516667 0
Statistics and machine learning Optimizing DNA Sequences for Biological Functions using a DNA LLM https://training.galaxyproject.org//topics/statistics/tutorials/genomic-llm-sequence-optimization/tutorial.html 2025-04-17 2025-05-22 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 56 66 5.500000 0
Statistics and machine learning Regulations/standards for AI using DOME https://training.galaxyproject.org//topics/statistics/tutorials/dome/tutorial.html 2025-03-11 2025-05-19 3 True True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1206146 2125487 6.350000 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 Mapping, Peak calling, Enrichment analysis, Read mapping, Structure visualisation, Genome visualisation, Sequence composition calculation, Sequencing quality control, Gene regulatory network analysis, Read pre-processing, Statistical calculation, Pathway visualisation, Primer removal, Sequence trimming 2018-09-17 2025-12-18 15 True True False True fastqc, deeptools_bam_compare, deeptools_plot_heatmap, __FLATTEN__, deeptools_bam_coverage, deeptools_plot_fingerprint, cat1, deeptools_compute_matrix, samtools_idxstats, bedtools_mergebed, deeptools_plot_correlation, macs2_callpeak, deeptools_multi_bam_summary, bedtools_sortbed, trim_galore, jbrowse2, bbgtobigwig, Filter1, bowtie2 UseGalaxy.eu, UseGalaxy.org (Main) 0 3587308 8654569 9.533333 0
Epigenetics Hi-C analysis of Drosophila melanogaster cells using HiCExplorer https://training.galaxyproject.org//topics/epigenetics/tutorials/hicexplorer/tutorial.html Formatting, Read mapping, Visualisation 2018-02-23 2026-03-16 31 True False False True hicexplorer_hicfindtads, hicexplorer_hicinfo, hicexplorer_hicfindrestrictionsites, hicexplorer_hicmergematrixbins, hicexplorer_hicpca, hicexplorer_hicbuildmatrix, pygenomeTracks, bowtie2, hicexplorer_hicdetectloops, hicexplorer_hicplotmatrix, hicexplorer_hiccorrectmatrix UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu UseGalaxy.no, UseGalaxy.org (Main) 0 7853 12974 3.633333 0
Epigenetics ATAC-Seq data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/atac-seq/tutorial.html Formatting, Mapping, Peak calling, Enrichment analysis, Read mapping, Visualisation, Sequence composition calculation, Sequencing quality control, Gene regulatory network analysis, Statistical calculation, Read pre-processing, Primer removal, Sequence alignment analysis, Sequence trimming, Data handling 2019-09-02 2025-12-18 24 True True True True fastqc, bamFilter, wig_to_bigWig, tp_sort_header_tool, bedtools_bamtobed, deeptools_plot_heatmap, Cut1, __FLATTEN__, pygenomeTracks, pe_histogram, bedtools_intersectbed, deeptools_compute_matrix, picard_MarkDuplicates, samtools_idxstats, macs2_callpeak, Filter1, cutadapt, bowtie2, Grep1 0 3647702 8761201 4.950000 0
Epigenetics DNA Methylation data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/methylation-seq/tutorial.html Epigenomics Statistical calculation, Read mapping, Visualisation, Sequence composition calculation, Sequencing quality control 2017-02-16 2025-04-03 24 True False False True tp_tail_tool, fastqc, replace_column_with_key_value_file, deeptools_plot_profile, falco, wig_to_bigWig, tp_awk_tool, bwameth, pileometh, deeptools_compute_matrix, metilene 0 15710 25803 4.566667 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 Peak calling, Read mapping, Enrichment analysis, Read pre-processing, Sequence composition calculation, Sequencing quality control, Gene regulatory network analysis, Statistical calculation, Primer removal, Sequence trimming 2017-09-18 2025-04-08 10 True False False True deeptools_plot_heatmap, fastqc, deeptools_plot_fingerprint, deeptools_multi_bam_summary, trim_galore, deeptools_compute_matrix, bowtie2, samtools_idxstats, deeptools_plot_correlation, bam_to_sam, deeptools_bam_coverage, macs2_callpeak, deeptools_bam_compare, deeptools_compute_gc_bias UseGalaxy.be Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 2009 2941 6.483333 0
Epigenetics CUT&RUN data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/cut_and_run/tutorial.html Formatting, Mapping, Peak calling, Read mapping, Enrichment analysis, Visualisation, Sequencing quality control, Validation, Gene regulatory network analysis, Read pre-processing, Primer removal, Sequence alignment analysis, Sequence trimming, Data handling 2024-03-06 2025-03-19 5 True False False True multiqc, bamFilter, wig_to_bigWig, bedtools_bamtobed, deeptools_plot_heatmap, falco, __FLATTEN__, __EXTRACT_DATASET__, idr, pe_histogram, bedtools_intersectbed, deeptools_plot_fingerprint, datamash_transpose, deeptools_compute_matrix, picard_MarkDuplicates, macs2_callpeak, trim_galore, bowtie2, meme_chip, Extract genomic DNA 1, Grep1 0 7433 9459 2.400000 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 Mapping, Peak calling, Read mapping, Generation, Enrichment analysis, Genome indexing, Sequence composition calculation, Sequencing quality control, Gene regulatory network analysis, Sequence alignment, Statistical calculation 2016-12-20 2025-04-08 11 True False False True deeptools_compute_gc_bias, deeptools_plot_heatmap, bwa, bedtools_intersectbed, fastqc, deeptools_plot_fingerprint, deeptools_correct_gc_bias, trimmomatic, deeptools_compute_matrix, samtools_idxstats, macs2_callpeak, deeptools_plot_correlation, deeptools_bam_compare, deeptools_multi_bam_summary UseGalaxy.be, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 7584 13911 7.383333 0
Epigenetics Infinium Human Methylation BeadChip https://training.galaxyproject.org//topics/epigenetics/tutorials/ewas-suite/tutorial.html 2018-08-27 2024-10-15 21 True True False True clusterprofiler_go, clusterprofiler_bitr, Remove beginning1, Cut1, minfi_analysis, chipeakanno_annopeaks UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3583163 8645616 8.800000 0
Epigenetics Introduction to DNA Methylation data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/introduction-dna-methylation/slides.html 2016-10-05 2024-03-05 2 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3581008 8642262 2.150000 0
Epigenetics Introduction to ChIP-Seq data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/introduction-chip-seq/slides.html 2017-06-12 2024-03-05 2 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3581008 8642262 2.150000 0
Evolution Phylogenetics - Back to basics https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo/tutorial.html Sequence analysis, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree reconstruction, Phylogenetic tree analysis, Phylogenetic analysis, Phylogenetic tree generation, Multiple sequence alignment 2024-05-10 2024-05-10 1 True False False True rbc_mafft, newick_display, fasttree, iqtree UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 6371 8161 3.683333 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, Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation 2022-03-16 2025-05-26 13 True False False True tp_sed_tool, upload1, tp_replace_in_line, trimmomatic, samtools_view, __MERGE_COLLECTION__, snippy, snp_dists, tb_variant_filter, tp_grep_tool, clustering_from_distmat, tp_easyjoin_tool, tb_profiler_profile, bcftools_consensus, tp_cat, snp_sites, addName, collapse_dataset, Grep1 UseGalaxy.eu 0 3364 4803 7.783333 0
Evolution Tree thinking for tuberculosis evolution and epidemiology https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html Genomics, Microbiology, Phylogeny, Infectious disease Phylogenetic tree analysis, Sequence analysis 2022-03-16 2025-06-04 12 True False False True upload1, raxml, interactive_tool_rstudio UseGalaxy.eu 0 2413 3446 7.766667 0
Evolution Phylogenetics - Back to Basics - Introduction https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo-intro/slides.html 2024-05-10 2024-05-10 1 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1663653 3263565 1.700000 0
Evolution Phylogenetic analysis for bacterial comparative genomics https://training.galaxyproject.org//topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html Genomics, Microbiology, Phylogeny Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) 2025-03-14 2025-03-14 1 True False False False upload1, fasttree Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) GalaxyTrakr 0 152 177 8.533333 0
Evolution Phylogenetics - Back to Basics - Terminology https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo-terminology/slides.html 2024-05-10 2024-05-10 1 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1663653 3263565 1.700000 0
Evolution Phylogenetics - Back to Basics - Multiple Sequence Alignment https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo-msa/slides.html 2024-05-10 2024-05-10 1 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1663653 3263565 1.700000 0
Evolution Phylogenetics - Back to Basics - Building Trees https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo-trees/slides.html 2024-05-10 2024-05-10 1 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1663653 3263565 1.700000 0
Evolution Phylogenetics - Back to Basics - Estimating trees from alignments https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo-mle-trees/slides.html 2024-05-10 2024-05-10 1 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1663653 3263565 1.700000 0
Evolution Phylogenetics - Back to Basics - Phylogenetic Networks https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo-networks/slides.html 2024-05-10 2024-05-10 1 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1663653 3263565 1.700000 0
FAIR Data, Workflows, and Research Data management in Medicinal Chemistry https://training.galaxyproject.org//topics/fair/tutorials/med-chem-data/tutorial.html 2026-03-24 2026-03-24 0 True False True True ctb_silicos_qed, ctb_im_rxn_maker, openbabel_compound_convert, chembl, md_converter, openbabel_svg_depiction, get_pdb UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.no 0 2 3 3.700000 0
FAIR Data, Workflows, and Research An earth-system RO-Crate https://training.galaxyproject.org//topics/fair/tutorials/earth_system_rocrate/slides.html 2024-12-02 2024-12-02 1 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1355929 2493868 1.466667 0
FAIR Data, Workflows, and Research Introduction to Data Management Plan (DMP) for Peatland Research and PeatDataHub https://training.galaxyproject.org//topics/fair/tutorials/data-management-peatlands/tutorial.html 2024-09-13 2024-09-13 1 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 128 161 7.100000 0
FAIR Data, Workflows, and Research Making clinical datasets FAIR https://training.galaxyproject.org//topics/fair/tutorials/fair-clinical/tutorial.html 2023-10-24 2024-09-13 5 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 379 485 8.116667 0
FAIR Data, Workflows, and Research Workflow Run RO-Crate Introduction https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-workflow-run-ro-crate/tutorial.html 2023-05-11 2023-05-11 1 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 401 499 4.400000 0
FAIR Data, Workflows, and Research FAIR in a nutshell https://training.galaxyproject.org//topics/fair/tutorials/fair-intro/tutorial.html 2023-05-30 2024-04-30 6 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 962 1221 7.700000 0
FAIR Data, Workflows, and Research Uploading Data to Zenodo from Galaxy https://training.galaxyproject.org//topics/fair/tutorials/zenodo-in-galaxy/tutorial.html 2025-11-06 2025-11-06 1 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 81 84 13.350000 0
FAIR Data, Workflows, and Research RO-Crate - Introduction https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-intro/tutorial.html 2023-05-23 2025-04-08 5 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 682 886 6.183333 0
FAIR Data, Workflows, and Research Sequence data submission to ENA https://training.galaxyproject.org//topics/fair/tutorials/fair-ena/tutorial.html 2023-11-01 2024-06-25 5 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 701 810 2.250000 0
FAIR Data, Workflows, and Research FAIR and its Origins https://training.galaxyproject.org//topics/fair/tutorials/fair-origin/tutorial.html 2024-03-26 2024-03-27 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 185 204 6.450000 0
FAIR Data, Workflows, and Research Integrating InvenioRDM-compatible Repositories with Galaxy https://training.galaxyproject.org//topics/fair/tutorials/inveniordm-integration/tutorial.html 2025-11-06 2025-11-06 1 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 53 59 7.566667 0
FAIR Data, Workflows, and Research DataPLANT ARCs https://training.galaxyproject.org//topics/fair/tutorials/dataplant-arcs/tutorial.html 2024-10-22 2025-09-17 4 True True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1417399 2638316 6.183333 0
FAIR Data, Workflows, and Research FAIR data management solutions https://training.galaxyproject.org//topics/fair/tutorials/data-management/tutorial.html 2023-05-30 2025-01-16 5 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 422 513 9.383333 0
FAIR Data, Workflows, and Research Exporting Workflow Run RO-Crates from Galaxy https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-in-galaxy/tutorial.html 2023-05-11 2024-08-26 8 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 325 393 10.233333 0
FAIR Data, Workflows, and Research Metadata https://training.galaxyproject.org//topics/fair/tutorials/fair-metadata/tutorial.html 2024-03-26 2024-03-27 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 241 285 6.083333 0
FAIR Data, Workflows, and Research RO-Crate in Python https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-in-python/tutorial.html 2023-05-11 2025-04-08 5 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 283 318 4.783333 0
FAIR Data, Workflows, and Research Best practices for workflows in GitHub repositories https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-galaxy-best-practices/tutorial.html 2023-05-11 2025-04-08 6 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 437 505 8.716667 0
FAIR Data, Workflows, and Research FAIR Galaxy Training Material https://training.galaxyproject.org//topics/fair/tutorials/fair-gtn/tutorial.html 2023-05-30 2024-03-27 5 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 178 212 11.716667 0
FAIR Data, Workflows, and Research Data Registration https://training.galaxyproject.org//topics/fair/tutorials/fair-data-registration/tutorial.html 2024-03-26 2024-09-27 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 111 116 7.183333 0
FAIR Data, Workflows, and Research Access https://training.galaxyproject.org//topics/fair/tutorials/fair-access/tutorial.html 2024-03-26 2024-03-27 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 94 104 8.966667 0
FAIR Data, Workflows, and Research Submitting workflows to LifeMonitor https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-submitting-life-monitor/tutorial.html 2023-05-11 2024-09-26 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 84 102 9.083333 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 0 361 427 9.933333 0
FAIR Data, Workflows, and Research Persistent Identifiers https://training.galaxyproject.org//topics/fair/tutorials/fair-persistent-identifiers/tutorial.html 2024-03-26 2024-03-27 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 292 361 4.500000 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 0 366 422 6.816667 0
FAIR Data, Workflows, and Research FAIRification of an RNAseq dataset https://training.galaxyproject.org//topics/fair/tutorials/fair-rna/tutorial.html 2024-03-27 2024-03-27 1 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 318 377 6.700000 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 2073 2638 8.466667 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 Grouping1, Remove beginning1, Cut1, ggplot2_point, upload1, datamash_ops, csv_to_tabular, tp_sorted_uniq UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz 0 947 1294 9.250000 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 tp_tac, Paste1, Show beginning1 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 6306 7831 7.250000 0
Using Galaxy and Managing your Data InterMine integration with Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/intermine/tutorial.html 2020-12-09 2024-02-29 9 True False False True galaxy_intermine_exchange, intermine UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 225 290 20.500000 0
Using Galaxy and Managing your Data Galaxy workflows in Dockstore https://training.galaxyproject.org//topics/galaxy-interface/tutorials/galaxy-on-dockstore/slides.html 2022-01-14 2022-10-27 4 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3033188 6806283 2.050000 0
Using Galaxy and Managing your Data Getting data into Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/get-data/slides.html 2017-05-24 2022-10-18 4 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3581008 8642263 2.150000 0
Using Galaxy and Managing your Data Name tags for following complex histories https://training.galaxyproject.org//topics/galaxy-interface/tutorials/name-tags/tutorial.html 2019-04-08 2023-11-09 8 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1755 2334 10.916667 0
Using Galaxy and Managing your Data Group tags for complex experimental designs https://training.galaxyproject.org//topics/galaxy-interface/tutorials/group-tags/tutorial.html 2019-03-06 2023-11-09 11 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 2833 3811 10.383333 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 0 326 397 12.783333 0
Using Galaxy and Managing your Data Rule Based Uploader https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules/tutorial.html 2020-07-04 2024-06-14 11 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 5385 6988 10.733333 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 Read mapping, Visualisation, Sequencing quality control, Validation 2025-05-26 2025-05-26 1 True False False False multiqc, falco UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr 0 347 413 8.416667 0
Using Galaxy and Managing your Data Extracting Workflows from Histories https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history-to-workflow/tutorial.html 2017-10-18 2024-12-02 8 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3163 4076 9.916667 0
Using Galaxy and Managing your Data Onedata user-owned storage https://training.galaxyproject.org//topics/galaxy-interface/tutorials/onedata-byos/tutorial.html 2025-03-24 2025-04-08 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 148 174 11.650000 0
Using Galaxy and Managing your Data Rule Based Uploader: Advanced https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.html 2018-05-25 2024-06-14 11 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 874 1171 14.850000 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 0 7771 10225 4.316667 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.org.au, UseGalaxy.eu, UseGalaxy.org (Main) 0 2226 3526 9.483333 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.org.au, UseGalaxy.eu, UseGalaxy.org (Main) 0 2645 3481 8.050000 0
Using Galaxy and Managing your Data Exporting to Onedata remote https://training.galaxyproject.org//topics/galaxy-interface/tutorials/onedata-remote-export/tutorial.html 2025-03-24 2025-04-08 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 87 98 11.216667 0
Using Galaxy and Managing your Data Searching Your History https://training.galaxyproject.org//topics/galaxy-interface/tutorials/search/tutorial.html 2020-07-15 2023-11-16 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 452 674 18.166667 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.org.au, UseGalaxy.eu 0 5394 8375 7.766667 0
Using Galaxy and Managing your Data Using dataset collections https://training.galaxyproject.org//topics/galaxy-interface/tutorials/collections/tutorial.html Sequence alignment, Genome indexing, Read mapping, Generation 2016-09-30 2024-12-05 20 True False True False bwa_mem, collapse_dataset, lofreq_call, snpSift_extractFields UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 16804 22863 8.500000 0
Using Galaxy and Managing your Data Importing (uploading) data from Onedata https://training.galaxyproject.org//topics/galaxy-interface/tutorials/onedata-remote-import/tutorial.html 2025-03-24 2025-04-08 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 328 436 12.316667 0
Using Galaxy and Managing your Data Understanding Galaxy history system https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history/tutorial.html 2017-02-20 2025-04-28 12 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 5742 7362 9.600000 0
Using Galaxy and Managing your Data Getting started with Onedata distributed storage https://training.galaxyproject.org//topics/galaxy-interface/tutorials/onedata-getting-started/tutorial.html 2025-03-24 2025-04-08 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 254 351 8.350000 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 Gene prediction, Genome annotation, Coding region prediction, Genome visualisation 2018-03-06 2026-01-23 27 True True True True prokka, jbrowse UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3600357 8674742 7.166667 0
Genome Annotation From small to large-scale genome comparison https://training.galaxyproject.org//topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.html Multiple sequence alignment 2021-02-08 2024-07-31 8 True True False True tp_awk_tool, gecko, chromeister, clustalw UseGalaxy.org.au, UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz 0 3536555 8482128 9.700000 0
Genome Annotation Refining Genome Annotations with Apollo (prokaryotes) https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Genome visualisation 2021-06-04 2025-05-15 22 True True True True create_or_update, create_account, iframe, jbrowse, list_organism UseGalaxy.be UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3356097 7865909 13.083333 0
Genome Annotation Secondary metabolite discovery https://training.galaxyproject.org//topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html Gene prediction, Differential gene expression analysis, Sequence clustering, Service invocation, Data handling 2024-02-21 2024-09-27 2 True False False True edu.tamu.cpt.gff3.customGbkToGff, interactive_tool_jupyter_notebook, ctb_silicos_qed, ctb_simsearch, ctb_chemfp_mol2fps, tp_awk_tool, Remove beginning1, ctb_np-likeness-calculator, ncbi_acc_download, bp_genbank2gff3, collapse_dataset, antismash, openbabel_remDuplicates UseGalaxy.eu 0 831 1044 3.700000 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, Genome annotation, Gene prediction, Sequence alignment, Genome visualisation, Differential protein expression profiling, Sequence assembly validation 2025-03-17 2025-06-20 4 True False False True gffread, fasta-stats, omark, busco, braker3, rna_star, jbrowse 0 1911 2310 4.550000 0
Genome Annotation Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial resistance Genome annotation, Genome visualisation, Antimicrobial resistance prediction, Read mapping 2024-01-23 2025-12-18 10 True False True True bakta, staramr_search, tbl2gff3, bowtie2, upload1, jbrowse, Grep1 Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.org (Main) 0 4031 5464 9.283333 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 Genome annotation, Protein feature detection, Genome assembly, Genome visualisation, Scaffolding, Multilocus sequence typing, Structural variation detection, Nucleic acid feature detection, Sequence motif recognition 2024-02-01 2024-10-15 6 True False True True bakta, integron_finder, tp_tail_tool, Grouping1, isescan, tbl2gff3, upload1, plasmidfinder, tp_replace_in_column, jbrowse UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main) 0 7722 10549 7.716667 0
Genome Annotation Masking repeats with RepeatMasker https://training.galaxyproject.org//topics/genome-annotation/tutorials/repeatmasker/tutorial.html Sequence composition, complexity and repeats, Genomics Genome annotation, Mapping, Repeat sequence detection, RNA-Seq analysis, Editing 2021-11-29 2025-06-03 22 True False True True repeatmodeler, repeatmasker_wrapper, red, bedtools_maskfastabed UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 10788 13667 4.116667 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 annotation, Gene prediction, Sequence alignment, Genome visualisation, Differential protein expression profiling, Sequence assembly validation 2025-06-20 2025-06-25 2 True False False True gffread, omark, busco, braker3, helixer, rna_star, jbrowse 0 598 694 6.883333 0
Genome Annotation Genome annotation with Helixer https://training.galaxyproject.org//topics/genome-annotation/tutorials/helixer/tutorial.html Biodiversity, Genomics, Zoology, Plant biology Sequence annotation, Gene prediction, Genome annotation, Genome visualisation, Differential protein expression profiling, Sequence assembly validation 2024-08-21 2025-06-04 8 True False False True gffread, omark, busco, helixer, jcvi_gff_stats, jbrowse 0 1509 1783 6.316667 0
Genome Annotation Introduction to Genome Annotation https://training.galaxyproject.org//topics/genome-annotation/tutorials/introduction/slides.html 2019-05-13 2025-04-23 5 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3581127 8642621 2.150000 0
Genome Annotation Bacterial pangenomics https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-pangenomics/tutorial.html Genomics, Microbiology Genome annotation, Essential dynamics, Rarefaction, Sequence assembly 2025-03-14 2025-03-14 1 True False False False upload1, ppanggolin_all, ppanggolin_msa UseGalaxy.eu, UseGalaxy.fr 0 131 147 5.000000 0
Genome Annotation Genome Annotation https://training.galaxyproject.org//topics/genome-annotation/tutorials/genome-annotation/tutorial.html 2015-06-29 2025-06-10 19 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 35339 64222 2.016667 0
Genome Annotation Bacterial genome quality control https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html Genomics, Microbiology Statistical calculation, Sequence assembly validation, Sequence composition calculation, Sequencing quality control, Validation, Genome comparison 2025-03-14 2025-03-14 1 True False False False upload1, checkm2, drep_dereplicate UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz 0 159 193 6.666667 0
Genome Annotation Creating an Official Gene Set https://training.galaxyproject.org//topics/genome-annotation/tutorials/official-gene-set/tutorial.html 2023-11-02 2024-02-29 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 49 55 5.000000 0
Genome Annotation Dataset construction for bacterial comparative genomics https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html Genomics, Microbiology Data retrieval, Sequence database search, Data handling 2025-03-14 2025-03-14 1 True False False False sort1, bg_uniq, cat1, Remove beginning1, Cut1, upload1, datasets_download_genome UseGalaxy.fr UseGalaxy.cz 0 100 118 8.133333 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 Sequence alignment analysis, Database search, Coding region prediction, De-novo assembly, Phylogenetic tree generation, Transcriptome assembly, Multiple sequence alignment 2022-09-08 2025-06-03 10 True False False True tab2fasta, bg_diamond, bg_diamond_view, regexColumn1, cat1, Add_a_column1, Cut1, Filter1, join1, tp_split_on_column, rapidnj, rbc_mafft, bg_diamond_makedb, collapse_dataset, gops_intersect_1, orfipy UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 1995 2761 9.716667 0
Genome Annotation Genome annotation with Funannotate https://training.galaxyproject.org//topics/genome-annotation/tutorials/funannotate/tutorial.html Gene and protein families Genome annotation, Formatting, Query and retrieval, Protein feature detection, Genome visualisation, Homology-based gene prediction, Sequence assembly validation, Sequence annotation, Information extraction, Sequence alignment, Sequence motif recognition, Fold recognition 2021-11-29 2025-06-10 26 True False True True aegean_parseval, funannotate_annotate, picard_MergeSamFiles, funannotate_compare, eggnog_mapper, busco, funannotate_predict, rna_star, interproscan, jbrowse UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz 0 11515 16119 5.566667 0
Genome Annotation Genome annotation with Maker (short) https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html Genome annotation, Sequence annotation, Sequence assembly validation, Genome visualisation 2021-01-12 2024-02-29 3 True False False True maker_map_ids, gffread, fasta-stats, busco, jcvi_gff_stats, maker, jbrowse UseGalaxy.be 0 4187 5844 9.100000 0
Genome Annotation Essential genes detection with Transposon insertion sequencing https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html Genomics, Microbiology, Sequence analysis, Mobile genetic elements Primer removal, Transposon prediction, Read pre-processing, Sequence trimming 2019-07-02 2024-03-18 12 True True False True transit_gumbel, gff_to_prot, bowtie_wrapper, bg_find_subsequences, Cut1, Filter1, tp_easyjoin_tool, tp_sort_header_tool, __EXTRACT_DATASET__, cutadapt, deeptools_bam_coverage, Add_a_column1 UseGalaxy.org.au, UseGalaxy.no UseGalaxy.cz, UseGalaxy.eu 0 3589581 8657681 5.766667 0
Genome Annotation Genome annotation with Maker https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html Genome annotation, Gene prediction, Genome visualisation, Homology-based gene prediction, Sequence assembly validation, Sequence annotation, Operation, Ab-initio gene prediction 2018-09-24 2024-02-29 14 True False False True maker_map_ids, gffread, fasta-stats, maker, busco, jcvi_gff_stats, augustus_training, jbrowse, snap_training UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz 0 14133 24813 4.350000 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 Genome annotation, Information extraction, Protein feature detection, Sequence motif recognition, Query and retrieval, Fold recognition, Sequence alignment analysis, Homology-based gene prediction 2022-07-20 2025-06-03 12 True False False True interproscan, ncbi_blastp_wrapper, eggnog_mapper, bg_diamond UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.no 0 4778 6317 6.100000 0
Genome Annotation Refining Genome Annotations with Apollo (eukaryotes) https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo-euk/tutorial.html Genomics Genome visualisation 2022-08-22 2025-06-03 16 True False False False create_or_update, jbrowse, iframe UseGalaxy.be, UseGalaxy.no UseGalaxy.cz, UseGalaxy.eu 0 1596 2370 9.950000 0
Genome Annotation Long non-coding RNAs (lncRNAs) annotation with FEELnc https://training.galaxyproject.org//topics/genome-annotation/tutorials/lncrna/tutorial.html Sequence annotation, RNA-Seq analysis, Annotation, Classification, Transcriptome assembly 2022-09-23 2024-09-18 11 True False True True Extract_features1, gffread, stringtie, feelnc, tp_cat UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 2035 2696 9.166667 0
Genome Annotation CRISPR screen analysis https://training.galaxyproject.org//topics/genome-annotation/tutorials/crispr-screen/tutorial.html Read pre-processing, Sequence composition calculation, Sequencing quality control, Validation, Statistical calculation, Primer removal, Genetic variation analysis, Sequence trimming 2021-10-15 2024-08-08 12 True True True True multiqc, fastqc, volcanoplot, tp_awk_tool, cutadapt, mageck_mle, mageck_test, mageck_count UseGalaxy.org.au, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no 0 3190087 7279595 4.783333 0
Variant Analysis Microbial Variant Calling https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Genome visualisation, Phylogenetic tree visualisation, Variant calling, 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 15751 24927 4.900000 0
Visualisation Genomic Data Visualisation with JBrowse https://training.galaxyproject.org//topics/visualisation/tutorials/jbrowse/tutorial.html Genome visualisation 2020-01-10 2024-10-15 17 True True False False jbrowse Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz 0 3586404 8649566 10.416667 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 2026-03-05 8 True False False True param_value_from_file, tp_replace_in_line, omero_import, Convert characters1, omero_get_value, omero_get_id, split_file_to_collection, omero_roi_import, omero_filter, omero_metadata_import UseGalaxy.eu 0 260 335 7.516667 0
Imaging Introduction to Image Analysis using Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/imaging-introduction/tutorial.html Image analysis, Visualisation, Image annotation, Data handling 2019-08-13 2026-01-18 18 True False False True ip_histogram_equalization, ip_binary_to_labelimage, ip_count_objects, unzip, ip_filter_standard, ip_overlay_images, ip_threshold, ip_imageinfo UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu 0 2831 3910 8.966667 0
Imaging Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/parameter-tuning/tutorial.html Image analysis, Visualisation, Image annotation, Data handling 2025-04-28 2026-01-21 4 True False False True param_value_from_file, ip_histogram_equalization, ip_filter_standard, tp_split_on_column, ip_threshold, collapse_dataset, ip_segmetrics UseGalaxy.be UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 133 148 6.933333 0
Imaging Where to start with bioimage analysis in Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html Formatting, Quantification, Parsing, Image analysis, Visualisation, Image annotation, Data handling 2026-02-17 2026-02-19 4 True False False False ip_histogram_equalization, cp_overlay_outlines, ip_split_image, interactive_tool_ilastik, bioimage_inference, interactive_tool_cellprofiler, interactive_tool_cellpose, interactive_tool_qupath, cellposesam, ip_convertimage, ip_filter_standard, libcarna_render, ip_threshold, ip_color_deconvolution, bf2raw, idr_download_by_ids, ip_overlay_images, cellpose, ip_imageinfo 0 65 97 9.516667 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) 0 235 268 6.516667 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 ip_binary_to_labelimage, ip_convertimage, libcarna_render, ip_overlay_images, __EXTRACT_DATASET__, biapy UseGalaxy.eu 0 25 32 12.400000 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 param_value_from_file, iscc_sum_similarity, iscc_sum, iscc_sum_verify, __EXTRACT_DATASET__, ip_split_image, ip_threshold UseGalaxy.eu, UseGalaxy.org (Main) 0 21 21 26.066667 0
Imaging Segmentation of Anatomical Structures in Medical 3-D Images https://training.galaxyproject.org//topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html Image analysis, Visualisation, Image annotation, Data handling 2026-02-26 2026-02-26 1 True False False True query_tabular, tp_sort_header_tool, tp_text_file_with_recurring_lines, highdicom_dicom2tiff, tp_replace_in_line, Convert characters1, param_value_from_file, ip_2d_filter_segmentation_by_features, compose_text_param, ip_binary_to_labelimage, unzip, ridge_filter_skimage, libcarna_render, ip_threshold, Add_a_column1, add_line_to_file, ip_concat_channels, clip_image, ip_scale_image, ip_2d_feature_extraction UseGalaxy.eu 0 43 54 10.366667 0
Imaging Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines https://training.galaxyproject.org//topics/imaging/tutorials/2D-spot-detection/tutorial.html Image analysis, Visualisation, Image annotation, Data handling 2025-03-20 2025-11-26 5 True False False True ip_spot_detection_2d, ip_histogram_equalization, idr_download_by_ids, ip_binary_to_labelimage, unzip, ip_points_to_label, ip_overlay_images, __EXTRACT_DATASET__ UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu 0 256 305 4.566667 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 quantification, vitessce_spatial, scimap_phenotyping, scimap_mcmicro_to_anndata, scanpy_compute_graph, squidpy_spatial, basic_illumination, rename_tiff_channels, gate_finder, ip_convertimage, ashlar, unet_coreograph, mesmer, celesta, palom 0 1590 2144 4.650000 0
Imaging Analyse HeLa fluorescence siRNA screen https://training.galaxyproject.org//topics/imaging/tutorials/hela-screen-analysis/tutorial.html Image analysis, Visualisation, Image annotation, Data handling 2019-08-13 2026-01-18 16 True False False True ip_2d_filter_segmentation_by_features, ip_binary_to_labelimage, unzip, ip_filter_standard, ip_threshold, ip_2d_feature_extraction, collapse_dataset UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu UseGalaxy.no 0 832 1075 14.283333 0
Imaging Object tracking using CellProfiler https://training.galaxyproject.org//topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html Quantification, Parsing, Image analysis 2021-03-17 2025-11-26 11 True False False True cp_identify_primary_objects, cp_overlay_outlines, unzip, cp_common, cp_cellprofiler, cp_save_images, cp_export_to_spreadsheet, cp_measure_object_intensity, cp_color_to_gray, cp_measure_object_size_shape, cp_tile, cp_track_objects UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz 0 2259 2802 4.283333 0
Imaging Nucleoli segmentation and feature extraction using CellProfiler https://training.galaxyproject.org//topics/imaging/tutorials/tutorial-CP/tutorial.html Quantification, Parsing, Image analysis 2020-07-01 2025-11-26 12 True True False True cp_image_math, cp_measure_image_intensity, cp_mask_image, cp_convert_objects_to_image, cp_identify_primary_objects, cp_common, cp_cellprofiler, cp_gray_to_color, cp_measure_granularity, cp_measure_texture, cp_measure_object_intensity, cp_display_data_on_image, cp_measure_object_size_shape, idr_download_by_ids, cp_enhance_or_suppress_features, cp_save_images, cp_measure_image_quality, cp_export_to_spreadsheet, cp_measure_image_area_occupied, cp_relate_objects UseGalaxy.be, UseGalaxy.eu Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 3585057 8648336 5.516667 0
Imaging Training Custom YOLO Models for Segmentation of Bioimages https://training.galaxyproject.org//topics/imaging/tutorials/yolo-segmentation-training/tutorial.html Image analysis, Visualisation, Image annotation, Data handling 2025-07-25 2025-11-26 7 True False False True interactive_tool_anylabeling, ip_histogram_equalization, json2yolosegment, graphicsmagick_image_convert, unzip, yolo_training UseGalaxy.eu 0 343 413 2.233333 0
Imaging Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools https://training.galaxyproject.org//topics/imaging/tutorials/electrophoresis-gel-bands-image-analysis/tutorial.html Image analysis, Visualisation, Image annotation, Data handling 2025-08-11 2025-11-26 3 True False False True graphicsmagick_image_convert, ip_points_to_label, __EXTRACT_DATASET__, ip_split_image, interactive_tool_qupath, ip_2d_feature_extraction, ip_imageinfo UseGalaxy.eu 0 418 492 3.416667 0
Imaging Voronoi segmentation https://training.galaxyproject.org//topics/imaging/tutorials/voronoi-segmentation/tutorial.html Image analysis, Visualisation, Image annotation, Data handling 2025-05-13 2026-02-20 8 True False False True repeat_channels, ip_binary_to_labelimage, ip_count_objects, unzip, ip_convertimage, voronoi_tessellation, ip_filter_standard, colorize_labels, ip_overlay_images, image_math, ip_threshold, ip_2d_feature_extraction, ip_imageinfo UseGalaxy.be, UseGalaxy.eu 0 405 581 6.183333 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 2026-02-05 9 True False False True bioimage_inference, ip_binary_to_labelimage, ip_overlay_images, __EXTRACT_DATASET__, image_math, ip_split_image, ip_threshold UseGalaxy.be, UseGalaxy.eu 0 241 285 6.283333 0
Introduction to Galaxy Analyses From peaks to genes https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html 2016-03-29 2026-03-09 68 True False True True tp_tail_tool, Grouping1, Cut1, tp_sort_header_tool, upload1, get_flanks1, Add_a_column1, tp_replace_in_column, gops_intersect_1, CONVERTER_interval_to_bed_0 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no 0 21099 34566 10.550000 0
Introduction to Galaxy Analyses How to reproduce published Galaxy analyses https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-reproduce/tutorial.html Visualisation 2021-08-25 2024-10-15 12 True False False True Grouping1, Remove beginning1, Cut1, ggplot2_point, upload1, datamash_ops, csv_to_tabular, tp_sorted_uniq Galaxy@AuBi, UseGalaxy.eu, UseGalaxy.org (Main) MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2325 3090 16.700000 0
Introduction to Galaxy Analyses NGS data logistics https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html Formatting, Read mapping, Generation, SNP detection, Genome indexing, Sequencing quality control, Validation, Sequence contamination filtering, Sequence alignment, Data handling 2017-02-22 2026-01-06 40 True False True True bwa, samtools_stats, lofreq_indelqual, multiqc, bwa_mem2, snpSift_extractFields, fasterq_dump, snpEff_build_gb, lofreq_call, samtools_view, snpeff_sars_cov_2, Filter1, bwa_mem, fastp, picard_MarkDuplicates, snpEff, lofreq_viterbi, collapse_dataset UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) MISSISSIPPI, UseGalaxy.cz 0 21037 35644 9.350000 0
Introduction to Galaxy Analyses Introduction to Genomics and Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-strands/tutorial.html 2017-10-18 2024-10-15 41 True False True True cat1, Filter1, tp_cat, gops_intersect_1, gene2exon1 UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) MISSISSIPPI 0 21012 32911 9.600000 0
Introduction to Galaxy Analyses Data Manipulation Olympics https://training.galaxyproject.org//topics/introduction/tutorials/data-manipulation-olympics/tutorial.html 2022-07-20 2025-05-16 15 True False False True tabular_to_csv, tp_sort_header_tool, upload1, {{version_cut_columns}}, {{version_datamash}}, {{version_remove_columns_by_header}}, {{version_cut_advanced}}, {{version_join}}, {{version_replace_text_line}}, {{version_select_first}}, {{version_remove_beginning}}, Grouping1, Count1, Cut1, datamash_ops, Show beginning1, cat1, {{version_paste}}, {{version_sort}}, {{version_compute}}, join1, tp_split_on_column, Add_a_column1, wc_gnu, {{version_cat}}, {{version_filter}}, {{version_unique}}, regexColumn1, {{version_replace_text_column}}, Remove beginning1, Filter1, tp_cat, {{version_split}}, tp_sorted_uniq, {{version_count}}, {{version_wc}} 0 6540 9459 11.133333 0
Introduction to Galaxy Analyses Introduction to Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/introduction/slides.html 2016-09-30 2025-09-23 6 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3581127 8642622 2.150000 0
Introduction to Galaxy Analyses Options for using Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/options-for-using-galaxy/slides.html 2017-05-24 2022-09-23 14 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3581127 8642622 2.150000 0
Introduction to Galaxy Analyses Best Practices for Citing Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-cite/tutorial.html 2025-11-06 2026-02-24 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 168 186 7.333333 0
Introduction to Galaxy Analyses Upload data to Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/dummy/tutorial.html 2022-09-23 2023-11-09 5 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 487 550 9.666667 0
Introduction to Galaxy Analyses IGV Introduction https://training.galaxyproject.org//topics/introduction/tutorials/igv-introduction/tutorial.html 2016-03-30 2023-02-17 11 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 8417 11774 5.333333 0
Introduction to Galaxy Analyses A short introduction to Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-short/tutorial.html Statistical calculation, Sequence composition calculation, Sequencing quality control 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 3639019 8732509 12.300000 0
Introduction to Galaxy Analyses Galaxy Basics for genomics https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-101/tutorial.html Mapping 2016-12-19 2025-04-22 68 True False True True bedtools_intersectbed, tp_head_tool, comp1, tp_sort_header_tool, upload1, datamash_ops UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.no 0 52445 83932 8.483333 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 Grouping1, Remove beginning1, Cut1, ggplot2_point, upload1, datamash_ops, csv_to_tabular, tp_sorted_uniq UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz 0 25587 40215 10.116667 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 2026-03-20 2 True False False True export_remote, column_remove_by_header, imagemagick_image_montage, Summary_Statistics1, unzip, Add_a_column1, ggplot2_histogram UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz 0 59 77 3.866667 0
Introduction to Galaxy Analyses Very Short Introductions: QC https://training.galaxyproject.org//topics/introduction/tutorials/vsi_qc/tutorial.html Sequencing quality control, Validation, Sequence contamination filtering 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 0 387 458 6.166667 0
Materials Science Finding the muon stopping site with pymuon-suite in Galaxy https://training.galaxyproject.org//topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.html 2024-01-22 2024-06-14 2 True False True True pm_muairss_read, pm_uep_opt UseGalaxy.cz, UseGalaxy.eu UseGalaxy.be 0 319 406 3.933333 0
Metabolomics Mass spectrometry imaging: Examining the spatial distribution of analytes https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html 2019-02-21 2024-10-15 18 True False False True cardinal_quality_report, cardinal_data_exporter, cardinal_mz_images, cardinal_filtering, Filter1, cardinal_spectra_plots UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3178 4472 9.133333 0
Metabolomics Mass spectrometry imaging: Finding differential analytes https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html 2019-04-13 2023-11-09 9 True False False True cardinal_combine, cardinal_quality_report, join_files_on_column_fuzzy, cardinal_segmentations, Summary_Statistics1, cardinal_mz_images, cardinal_classification, cardinal_preprocessing, maldi_quant_peak_detection, Filter1, maldi_quant_preprocessing, Grep1 UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2099 2973 8.666667 0
Metabolomics Predicting EI+ mass spectra with QCxMS https://training.galaxyproject.org//topics/metabolomics/tutorials/qcxms-predictions/tutorial.html 2024-10-01 2024-10-01 1 True True False True qcxms_production_run, param_value_from_file, xtb_molecular_optimization, qcxms_getres, openbabel_compound_convert, __FILTER_FAILED_DATASETS__, split_file_to_collection, tp_cat, tp_cut_tool, qcxms_neutral_run, ctb_im_conformers UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be 0 1455833 2753885 5.750000 0
Metabolomics Molecular formula assignment and mass recalibration with MFAssignR package https://training.galaxyproject.org//topics/metabolomics/tutorials/mfassignr/tutorial.html Mass spectra calibration, Visualisation, Annotation, Deisotoping 2025-05-19 2025-05-19 1 True False False True mfassignr_mfassignCHO, mfassignr_snplot, mfassignr_recallist, mfassignr_findRecalSeries, mfassignr_kmdnoise, mfassignr_histnoise, mfassignr_mfassign, mfassignr_recal, mfassignr_isofiltr 0 209 238 3.283333 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 Formatting, Peak detection, Label-free quantification, Imputation, Standardisation and normalisation, Clustering, Mass spectrum visualisation, Chromatogram visualisation, Spectral library search, Validation, Data filtering, Chromatographic alignment, Format validation, Filtering, Correlation 2023-05-08 2023-11-09 5 True False False True abims_xcms_group, abims_xcms_fillPeaks, matchms_filtering, abims_xcms_xcmsSet, msconvert, ramclustr, msnbase_readmsdata, abims_xcms_retcor, xcms_merge, matchms_similarity, waveica, matchms_formatter, riassigner, ramclustr_define_experiment UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr 0 2973 3789 4.000000 0
Metabolomics Mass spectrometry: LC-MS analysis https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms/tutorial.html Chromatogram visualisation, Validation, Peak detection, Data filtering, Label-free quantification, Chromatographic alignment, Mass spectrum visualisation 2019-07-02 2025-09-21 13 True False False True abims_xcms_group, Univariate, abims_xcms_fillPeaks, xcms_plot_chromatogram, abims_CAMERA_annotateDiffreport, abims_xcms_xcmsSet, msnbase_readmsdata, abims_xcms_retcor, xcms_merge, quality_metrics, xcms_export_samplemetadata, generic_filter, wsdl_hmdb, Batch_correction UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no 0 13428 21762 3.633333 0
Metabolomics Introduction to Metabolomics https://training.galaxyproject.org//topics/metabolomics/tutorials/introduction/slides.html 2018-11-20 2023-01-12 1 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3581127 8642623 2.150000 0
Metabolomics Mass spectrometry: LC-MS preprocessing with XCMS https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html Chromatogram visualisation, Validation, Peak detection, Data filtering, Label-free quantification, Chromatographic alignment, Mass spectrum visualisation 2020-02-04 2024-10-15 14 True True False False abims_xcms_group, abims_xcms_summary, abims_xcms_fillPeaks, xcms_plot_chromatogram, intens_check, abims_CAMERA_annotateDiffreport, abims_xcms_xcmsSet, msnbase_readmsdata, abims_xcms_retcor, xcms_merge, idchoice, xcms_export_samplemetadata UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3587562 8652637 7.150000 0
Metabolomics Mass spectrometry: GC-MS analysis with the metaMS package https://training.galaxyproject.org//topics/metabolomics/tutorials/gcms/tutorial.html Chromatogram visualisation, Validation, Peak detection, Data filtering, Label-free quantification, Chromatographic alignment, Mass spectrum visualisation 2021-09-22 2025-10-01 8 True False False False abims_xcms_group, abims_xcms_fillPeaks, xcms_plot_chromatogram, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_merge, metams_runGC, xcms_export_samplemetadata UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.no 0 1811 2772 3.466667 0
Metabolomics Mass spectrometry: LC-MS data processing https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html 2021-12-14 2024-10-15 8 True False False False normalization, intens_check, Multivariate, quality_metrics, generic_filter, Batch_correction UseGalaxy.fr UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3144 4186 5.966667 0
Microbiome Introduction to Microbiome Analysis https://training.galaxyproject.org//topics/microbiome/tutorials/introduction/slides.html 2017-06-22 2024-08-08 5 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3581127 8642624 2.150000 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 Taxonomic classification, Sequence clustering, Phylogenetic analysis, Visualisation, Sequencing quality control, Sequence read processing, DNA barcoding 2017-06-22 2024-08-09 4 True False False True humann2_renorm_table, mothur_unique_seqs, mothur_make_shared, humann2, mothur_make_biom, metaphlan2, humann2_regroup_table, mothur_merge_files, mothur_pre_cluster, mothur_filter_seqs, mothur_make_group, metaphlan2krona, mothur_screen_seqs, mothur_count_seqs, taxonomy_krona_chart, mothur_classify_otu, mothur_classify_seqs, krona-text, mothur_summary_seqs, mothur_cluster_split, mothur_align_seqs UseGalaxy.org.au, UseGalaxy.fr, UseGalaxy.no 0 10070 13697 5.916667 0
Microbiome Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Formatting, Read mapping, Genome assembly, Visualisation, Sequence contamination filtering, Statistical calculation, Data handling, Primer removal, Local alignment, Sequence assembly visualisation, Sequence composition calculation, Sequencing quality control, Read pre-processing, Sequence assembly validation, Sequence file editing, Sequence alignment analysis, Variant calling, Sequence trimming 2022-12-05 2025-12-08 8 True False True True coverm_contig, metaspades, bamtools, fastqc, bandage_image, random_lines1, bg_uniq, megahit, ngsutils_bam_filter, megahit_contig2fastg, quast, cutadapt, bowtie2, seqtk_subseq, tp_cat, filter_tabular, collection_column_join, bandage_info UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 4987 6864 10.016667 0
Microbiome Calculating α and β diversity from microbiome taxonomic data https://training.galaxyproject.org//topics/microbiome/tutorials/diversity/tutorial.html Visualisation, Aggregation 2024-08-01 2025-06-17 7 True False True True krakentools_alpha_diversity, krakentools_beta_diversity Galaxy@Pasteur, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr 0 8360 10128 3.850000 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 Species frequency estimation, Visualisation, Sequence similarity search, Sequence comparison, Statistical calculation, Primer removal, Conversion, Taxonomic classification, Phylogenetic tree visualisation, Phylogenetic tree editing, Phylogenetic analysis, Sequence composition calculation, Sequencing quality control, Validation, Read pre-processing, Sequence alignment analysis, Phylogenetic inference, Sequence trimming 2020-02-13 2025-06-16 6 True False True True multiqc, fastqc, tp_find_and_replace, tp_sort_header_tool, fastq_paired_end_interlacer, metaphlan, bg_sortmerna, Cut1, export2graphlan, humann_regroup_table, humann_renorm_table, humann_split_stratified_table, humann, graphlan, taxonomy_krona_chart, combine_metaphlan2_humann2, graphlan_annotate, humann_rename_table, humann_unpack_pathways, cutadapt, Grep1 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no 0 930 1194 9.900000 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 Deposition, Analysis, Variant calling, DNA barcoding, Visualisation 2024-06-05 2025-07-03 11 True False True True dada2_removeBimeraDenovo, phyloseq_from_dada2, dada2_assignTaxonomyAddspecies, interactive_tool_phyloseq, __SORTLIST__, tp_replace_in_line, Grouping1, dada2_filterAndTrim, dada2_makeSequenceTable, dada2_dada, __UNZIP_COLLECTION__, dada2_seqCounts, cat1, tp_head_tool, collection_element_identifiers, Add_a_column1, tp_replace_in_column, dada2_plotQualityProfile, dada2_learnErrors, dada2_mergePairs UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 8428 11998 5.416667 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 Mapping assembly, Sequence analysis, Sequence assembly visualisation, Genome assembly, Aggregation, De-novo assembly, Antimicrobial resistance prediction, Pairwise sequence alignment, Box-Whisker plot plotting, Scatter plot plotting 2019-06-25 2024-06-14 4 True False True True bandage_image, racon, nanoplot, staramr_search, minimap2, miniasm, unicycler, PlasFlow, gfa_to_fa UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 3836 5305 6.650000 0
Microbiome Taxonomic Profiling and Visualization of Metagenomic Data https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Statistical calculation, Genome annotation, Taxonomic classification, Aggregation, Visualisation 2023-05-03 2025-12-18 7 True False True True interactive_tool_pavian, est_abundance, krakentools_kreport2krona, taxonomy_krona_chart, kraken_biom, kraken2, __UNZIP_COLLECTION__, metaphlan, interactive_tool_phinch UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 13774 18313 5.550000 0
Microbiome Clinical Metaproteomics 4: Quantitation https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-4-quantitation/tutorial.html Visualisation, Heat map generation, Statistical calculation, Protein quantification, Imputation, Standardisation and normalisation, Clustering, Principal component plotting 2026-03-24 2026-03-24 0 True False True True Grouping1, Cut1, maxquant, Grep1 UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 0 0 0.000000 0
Microbiome Binning of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html Metagenomics, Sequence assembly Genome annotation, Read mapping, Sequence clustering, Sequence composition calculation, Sequence assembly, Sequencing quality control, Validation, Sequence assembly validation, Statistical calculation, Read binning, Genome comparison 2023-12-05 2026-03-18 8 True False True True Fasta_to_Contig2Bin, concoct_merge_cut_up_clustering, binette, concoct_extract_fasta_bins, semibin, metabat2, concoct, maxbin2, __BUILD_LIST__, checkm_lineage_wf, bowtie2, samtools_sort, das_tool, concoct_coverage_table, concoct_cut_up_fasta, drep_dereplicate, metabat2_jgi_summarize_bam_contig_depths UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.org.au, UseGalaxy.org (Main) 0 6448 7876 5.450000 0
Microbiome Remove contamination and host reads https://training.galaxyproject.org//topics/microbiome/tutorials/host-removal/tutorial.html Read mapping, Sequencing quality control, Validation 2025-12-18 2025-12-18 1 True False False True bowtie2, multiqc, __ZIP_COLLECTION__ Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 201 226 3.600000 0
Microbiome Metatranscriptomics analysis using microbiome RNA-seq data https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis Aggregation, Species frequency estimation, Visualisation, Sequence comparison, Sequence similarity search, Statistical calculation, Primer removal, Conversion, Taxonomic classification, Phylogenetic tree visualisation, Phylogenetic tree editing, Phylogenetic analysis, Sequence composition calculation, Sequencing quality control, Validation, Read pre-processing, Sequence alignment analysis, Phylogenetic inference, Sequence trimming 2019-11-21 2025-06-16 6 True True True True multiqc, fastqc, tp_find_and_replace, tp_sort_header_tool, fastq_paired_end_interlacer, metaphlan, combine_metaphlan_humann, Grouping1, bg_sortmerna, Cut1, export2graphlan, humann_regroup_table, humann_renorm_table, humann_split_stratified_table, humann, graphlan, taxonomy_krona_chart, graphlan_annotate, humann_rename_table, humann_unpack_pathways, cutadapt, Grep1 UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.eu 0 3588528 8652229 6.783333 0
Microbiome Clinical Metaproteomics 5: Data Interpretation https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-5-data-interpretation/tutorial.html Prediction and recognition, Visualisation 2026-03-24 2026-03-24 0 True False True True unipept, msstatstmt, Grep1 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 1 1 3.466667 0
Microbiome Clinical Metaproteomics 2: Discovery https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html Formatting, Visualisation, Heat map generation, Statistical calculation, Protein quantification, Imputation, Standardisation and normalisation, Clustering, Filtering, Principal component plotting 2026-03-24 2026-03-24 0 True False True True search_gui, ident_params, fasta2tab, maxquant, filter_tabular, msconvert, Grouping1, fasta_merge_files_and_filter_unique_sequences, Remove beginning1, Cut1, query_tabular, Filter1, tp_cat, peptide_shaker, dbbuilder, fasta_cli, Grep1 UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 0 0 0.000000 0
Microbiome Clinical Metaproteomics 1: Database-Generation https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-1-database-generation/tutorial.html Target-Decoy, Expression analysis, Protein identification, de Novo sequencing, Tag-based peptide identification 2026-03-24 2026-03-24 0 True False True True metanovo, dbbuilder, fasta_merge_files_and_filter_unique_sequences, uniprotxml_downloader UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu UseGalaxy.be, UseGalaxy.org (Main) 0 2 6 6.433333 0
Microbiome Identification of the micro-organisms in a beer using Nanopore sequencing https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Statistical calculation, Taxonomic classification, Aggregation, Visualisation, Sequence composition calculation, Sequencing quality control, Sequence contamination filtering 2022-09-29 2024-11-29 5 True False True True fastqc, krakentools_kreport2krona, taxonomy_krona_chart, fastp, Filter1, porechop, kraken2 UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3217 4688 8.083333 0
Microbiome Clinical Metaproteomics 3: Verification https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html 2026-03-24 2026-03-24 0 True False True True uniprotxml_downloader, Grouping1, Remove beginning1, Cut1, query_tabular, Filter1, pepquery2, tp_cat, dbbuilder, collapse_dataset, fasta_merge_files_and_filter_unique_sequences UseGalaxy.cz, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.org (Main) 0 0 0 0.000000 0
Microbiome MGnify v5.0 Amplicon Pipeline https://training.galaxyproject.org//topics/microbiome/tutorials/mgnify-amplicon/tutorial.html Metagenomics, Taxonomy, Sequence analysis Formatting, Mapping, Visualisation, DNA barcoding, Sequence contamination filtering, Statistical calculation, Sequence feature detection, Sequence trimming, Analysis, Sequence composition calculation, Sequencing quality control, Validation, Read pre-processing, Nucleic acid design, Comparison, Nucleic acid feature detection, Alignment, k-mer counting 2025-07-30 2025-11-18 3 True False False True multiqc, fastqc, cmsearch_deoverlap, tp_find_and_replace, biom_convert, query_tabular, __FILTER_EMPTY_DATASETS__, prinseq, lotus2, infernal_cmsearch, mapseq, Grouping1, trimmomatic, fastq_to_fasta_python, gops_concat_1, fastp, fastq_dl, __MERGE_COLLECTION__, __UNZIP_COLLECTION__, collection_column_join, fastq_filter, param_value_from_file, bedtools_maskfastabed, tp_awk_tool, CONVERTER_gz_to_uncompressed, mgnify_seqprep, CONVERTER_uncompressed_to_gz, cshl_fasta_formatter, collection_element_identifiers, Add_a_column1, filter_tabular, wc_gnu, seqprep, ampvis2_heatmap, taxonomy_krona_chart, bedtools_getfastabed, ampvis2_load, __FILTER_FROM_FILE__, collapse_dataset 0 317 403 11.600000 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 Mapping, Phylogenetic tree generation (from molecular sequences), Aggregation, Genome assembly, Scatter plot plotting, Visualisation, Sequence contamination filtering, Statistical calculation, Data handling, Base-calling, Antimicrobial resistance prediction, Box-Whisker plot plotting, Sequence assembly, Taxonomic classification, Mapping assembly, Sequence assembly visualisation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), De-novo assembly, Sequence composition calculation, Sequencing quality control, Validation, Multilocus sequence typing, Phylogenetic tree generation, Cross-assembly, Pairwise sequence alignment, Sequence alignment analysis, Phylogenetic tree reconstruction, Phylogenetic tree analysis, Variant calling, Multiple sequence alignment 2023-01-26 2025-11-18 12 True False True True multiqc, fastqc, bandage_image, tp_find_and_replace, bamtools_split_mapped, __FILTER_EMPTY_DATASETS__, fasttree, tab2fasta, mlst, barchart_gnuplot, bcftools_norm, abricate, samtools_fastx, krakentools_kreport2krona, Grouping1, Count1, Cut1, __BUILD_LIST__, fastp, porechop, tp_cut_tool, Paste1, clair3, collection_column_join, fasta_merge_files_and_filter_unique_sequences, samtools_coverage, table_compute, param_value_from_file, compose_text_param, clustalw, snpSift_extractFields, CONVERTER_gz_to_uncompressed, tp_head_tool, __FILTER_FAILED_DATASETS__, tp_multijoin_tool, collection_element_identifiers, split_file_to_collection, tp_split_on_column, ggplot2_heatmap, kraken2, Add_a_column1, tp_replace_in_column, newick_display, regex1, samtools_depth, flye, add_line_to_file, fasta2tab, regexColumn1, taxonomy_krona_chart, bedtools_getfastabed, medaka_consensus_pipeline, Remove beginning1, nanoplot, snpSift_filter, minimap2, bcftools_consensus, tp_sorted_uniq, krakentools_extract_kraken_reads, collapse_dataset, Grep1 UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz 0 5406 7938 8.483333 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 2025-01-07 1 True False False True tab2fasta, tp_tail_tool, sort1, ggplot2_histogram, count_gff_features, cat1, Grouping1, Add_a_column1, add_column_headers, Cut1, histogram_rpy, Filter1, minimap2, join1, tp_sorted_uniq, tp_replace_in_column, MQoutputfilter, CONVERTER_fasta_to_tabular UseGalaxy.fr 0 398 460 4.950000 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 0 901 1127 4.500000 0
Microbiome 16S Microbial analysis with Nanopore data https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Statistical calculation, Taxonomic classification, Visualisation, Sequence composition calculation, Sequencing quality control, Validation, Sequence contamination filtering 2020-11-24 2024-07-31 5 True False False True datamash_reverse, multiqc, fastqc, tp_replace_in_line, taxonomy_krona_chart, Remove beginning1, fastp, porechop, kraken2 UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr 0 9371 12990 5.483333 0
Microbiome QIIME 2 Cancer Microbiome Intervention https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding 2024-02-12 2024-03-14 3 external False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 466 761 9.766667 0
Microbiome Indexing and profiling microbes with MetaSBT https://training.galaxyproject.org//topics/microbiome/tutorials/metasbt/tutorial.html Microbial ecology, Taxonomy 2025-08-25 2025-08-25 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 101 110 12.966667 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 0 717 1072 6.933333 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 Genome annotation, Sequence composition calculation, Sequencing quality control, Validation, Sequence assembly validation, Statistical calculation, Genome comparison, Data handling 2025-12-18 2025-12-18 1 True False False False bakta, multiqc, fasterq_dump, cat1, Grouping1, Summary_Statistics1, Remove beginning1, Cut1, tp_sort_header_tool, checkm_lineage_wf, __EXTRACT_DATASET__, join1, collection_column_join, drep_dereplicate, tp_replace_in_column, collapse_dataset UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz 0 592 827 5.533333 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 Taxonomic classification, Sequence clustering, Phylogenetic analysis, Visualisation, Sequencing quality control, Sequence read processing, DNA barcoding, Phylogenetic tree generation, Phylogenetic tree reconstruction, Phylogenetic tree analysis 2019-05-13 2025-12-18 6 True False True True mothur_unique_seqs, XY_Plot_1, mothur_remove_lineage, mothur_make_shared, mothur_tree_shared, mothur_remove_seqs, mothur_count_groups, mothur_sub_sample, mothur_chimera_vsearch, mothur_pre_cluster, mothur_filter_seqs, mothur_summary_single, newick_display, mothur_dist_shared, mothur_screen_seqs, mothur_count_seqs, mothur_venn, mothur_classify_otu, mothur_cluster, mothur_classify_seqs, mothur_dist_seqs, mothur_heatmap_sim, mothur_summary_seqs, mothur_cluster_split, collapse_dataset, mothur_rarefaction_single, mothur_remove_groups UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.fr 0 6325 10649 7.750000 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 Taxonomic classification, Sequence clustering, Phylogenetic analysis, Visualisation, Sequencing quality control, Sequence read processing, DNA barcoding, Phylogenetic tree generation, Phylogenetic tree reconstruction, Phylogenetic tree analysis 2017-02-12 2025-12-18 5 True False False True mothur_unique_seqs, XY_Plot_1, mothur_remove_lineage, mothur_make_shared, mothur_tree_shared, mothur_remove_seqs, mothur_remove_groups, mothur_make_biom, mothur_count_groups, mothur_sub_sample, mothur_chimera_vsearch, mothur_pre_cluster, mothur_filter_seqs, mothur_summary_single, mothur_taxonomy_to_krona, newick_display, mothur_dist_shared, mothur_seq_error, mothur_screen_seqs, mothur_count_seqs, mothur_make_contigs, mothur_venn, taxonomy_krona_chart, mothur_classify_otu, mothur_classify_seqs, mothur_cluster, mothur_dist_seqs, mothur_heatmap_sim, mothur_summary_seqs, mothur_cluster_split, mothur_align_seqs, mothur_rarefaction_single, mothur_get_groups UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 13446 19857 4.983333 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 Taxonomic classification, Phylogenetic tree visualisation, Sequence analysis, Genome visualisation, Sequence composition calculation, Sequencing quality control, Validation, Sequence contamination filtering, Statistical calculation, Sequence alignment, Global alignment, Variant calling, Phylogenetic tree generation, Antimicrobial resistance prediction, Sequence alignment analysis, Local alignment 2020-07-25 2026-01-06 32 True False True True tp_sed_tool, fastqc, multiqc, EMBOSS: seqret84, upload1, jbrowse, samtools_stats, __FLATTEN__, EMBOSS:%20seqret84, fastp, snippy, tb_variant_filter, jvarkit_wgscoverageplotter, tp_awk_tool, kraken2, mosdepth, tbvcfreport, qualimap_bamqc, tb_profiler_profile, bcftools_consensus 0 8191 12417 7.666667 0
Variant Analysis Pox virus genome analysis from tiled-amplicon sequencing data https://training.galaxyproject.org//topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html Read mapping, Generation, Sequence analysis, Genome indexing, Sequencing quality control, Sequence contamination filtering, Sequence alignment, Global alignment, Primer removal, Sequence alignment analysis, Local alignment, Multiple sequence alignment 2023-05-15 2024-03-20 4 True False False True fasta_regex_finder, bwa_mem, upload1, samtools_view, Cut1, mimodd_info, fastp, datamash_ops, fasta_compute_length, param_value_from_file, EMBOSS: maskseq51, compose_text_param, samtools_merge, ivar_trim, rbc_mafft, Add_a_column1, ivar_consensus, __ZIP_COLLECTION__, qualimap_bamqc, __APPLY_RULES__, fatovcf, Grep1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org (Main) 0 1164 1372 8.333333 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 Read mapping, Generation, Sequence analysis, Data retrieval, Genome indexing, Phylogenetic analysis, Sequencing quality control, De-novo assembly, Sequence contamination filtering, Sequence alignment, Sequence file editing, Primer removal, Multiple sequence alignment, Sequence alignment analysis, Data handling 2022-11-21 2024-10-04 10 True False False False qualimap_bamqc, Show beginning1, bamtools_split_ref, tp_find_and_replace, __RELABEL_FROM_FILE__, samtools_view, fastp, bwa_mem, upload1, iqtree, seqtk_subseq, rbc_mafft, ivar_consensus, collapse_dataset, Grep1, vapor UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 2246 3203 7.883333 0
Transcriptomics Whole transcriptome analysis of Arabidopsis thaliana https://training.galaxyproject.org//topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html Read mapping, RNA-Seq analysis, Read pre-processing, Visualisation, Sequencing quality control, Validation, Sequence composition calculation, Primer removal, Differential gene expression analysis, Gene expression analysis, RNA-Seq quantification, Sequence trimming 2021-04-08 2025-08-10 18 True True True True filter_by_fasta_ids, multiqc, sort1, falco, rbc_mirdeep2_mapper, rbc_mirdeep2_quantifier, cat1, trim_galore, Cut1, sample_seqs, Filter1, deseq2, __MERGE_COLLECTION__, targetfinder, salmon UseGalaxy.cz 0 3442450 8140369 8.616667 0
Sequence analysis Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants https://training.galaxyproject.org//topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html Sequence analysis, Phylogenetic tree editing, Phylogenetic inference (from molecular sequences), Phylogenetic analysis, Multiple sequence alignment 2025-03-26 2025-04-27 2 True False True True filter_by_fasta_ids, Remove beginning1, Cut1, quicktree, Filter1, trimal, iqtree, rbc_mafft, ete_treeviewer, tapscan_classify UseGalaxy.eu 0 367 479 10.166667 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_blastp_wrapper, bg_diamond, ncbi_blastx_wrapper Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@Pasteur, UseGalaxy.no 0 1876 2385 10.066667 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, Differential gene expression analysis, Principal component visualisation 2021-04-08 2025-02-13 7 True False True True scanpy_filter, anndata_import, anndata_manipulate, scanpy_normalize, scanpy_plot, scanpy_inspect, scanpy_cluster_reduce_dimension, scanpy_remove_confounders UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2992 3725 5.866667 0
Proteomics Statistical analysis of DIA data https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.html Spectrum calculation, Differential protein expression profiling, Tag-based peptide identification 2020-12-02 2023-11-09 9 True False False True histogram_rpy, Grep1, msstats, Filter1 UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz 0 1409 1949 8.200000 0
Proteomics Neoantigen 2: Database merge and FragPipe discovery https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.html 2025-01-14 2025-12-03 4 True False False False fragpipe, validate_fasta_database, Remove beginning1, query_tabular, fragpipe_manifest_generator, Grep1, collapse_dataset, fasta_merge_files_and_filter_unique_sequences UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) 0 305 345 2.900000 0
Proteomics Mass spectrometry imaging: Loading and exploring MSI data https://training.galaxyproject.org//topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.html Proteomics 2018-11-27 2025-04-08 18 True False False True cardinal_quality_report, cardinal_data_exporter, Grep1, tp_sort_header_tool UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2936 4447 5.466667 0
Proteomics Detection and quantitation of N-termini (degradomics) via N-TAILS https://training.galaxyproject.org//topics/proteomics/tutorials/ntails/tutorial.html Proteomics 2017-02-14 2025-04-08 16 True False False True FeatureFinderMultiplex, HighResPrecursorMassCorrector, MSGFPlusAdapter, FileMerger, IDFilter, MzTabExporter, FalseDiscoveryRate, IDConflictResolver, IDMapper, FileFilter, ConsensusID, PeptideIndexer, IDMerger 0 924 1251 5.783333 0
Proteomics Secretome Prediction https://training.galaxyproject.org//topics/proteomics/tutorials/secretome-prediction/tutorial.html 2017-04-13 2025-04-08 15 True False False True term_id_vs_term_name, uniprot, bg_uniq, Convert characters1, comp1, wolf_psort, Filter1, tp_easyjoin_tool, tp_cut_tool, tp_sorted_uniq, get_subontology_from, Grep1 0 676 995 8.433333 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, IDconverter, retrieve_from_hpa, Jvenn, rna_abbased_data, cluter_profiler, MQoutputfilter UseGalaxy.be UseGalaxy.fr 0 3177 4579 7.916667 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_tsvtofasta, pdaug_peptide_sequence_analysis, pdaug_fishers_plot, pdaug_addclasslabel, pdaug_sequence_property_based_descriptors, pdaug_peptide_data_access, pdaug_merge_dataframes, pdaug_basic_plots UseGalaxy.be 0 784 1049 9.616667 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 tp_awk_tool, seq2hla, optitype, query_tabular UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 115 123 4.150000 0
Proteomics Library Generation for DIA Analysis https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html Visualisation, Heat map generation, Statistical calculation, Protein quantification, Imputation, Standardisation and normalisation, Clustering, Principal component plotting 2020-12-02 2025-06-02 12 True False False True OpenSwathDecoyGenerator, TargetedFileConverter, Filter1, OpenSwathAssayGenerator, diapysef, maxquant UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no 0 4766 6199 4.250000 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, CONVERTER_gz_to_uncompressed, arriba, query_tabular, arriba_get_filters, rna_star, tab2fasta, regex1 UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 261 314 3.266667 0
Proteomics EncyclopeDIA https://training.galaxyproject.org//topics/proteomics/tutorials/encyclopedia/tutorial.html Formatting, Filtering 2021-06-21 2025-05-19 12 True False True True msconvert, encyclopedia_quantify, encyclopedia_searchtolib UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 2063 2791 8.083333 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 IDconverter, retr_pepatlas1, retrieve_from_hpa, prot_features, Jvenn, tp_cut_tool, rna_abbased_data, MQoutputfilter UseGalaxy.be, UseGalaxy.fr 0 1830 2498 9.650000 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 Spectrum calculation, Visualisation, Heat map generation, Tag-based peptide identification, Statistical calculation, Protein quantification, Imputation, Standardisation and normalisation, Clustering, Differential protein expression profiling, Principal component plotting 2021-02-17 2025-09-22 19 True False True True fasta2tab, uniprot, Summary_Statistics1, Cut1, Filter1, tp_easyjoin_tool, datamash_ops, ggplot2_heatmap2, msstats, tp_replace_in_column, maxquant, Grep1 UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) 0 8791 14145 6.216667 0
Proteomics Metaproteomics tutorial https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Prediction and recognition, Visualisation 2017-06-28 2024-06-14 41 True False True True search_gui, sqlite_to_tabular, query_tabular, peptide_shaker, unipept UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz 0 3044 4795 9.550000 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, Statistical calculation, Protein quantification, Imputation, Standardisation and normalisation, Clustering, Principal component plotting 2021-08-13 2025-01-08 11 True False False True maxquant, msstatstmt UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org (Main) 0 4442 5929 3.833333 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_ml_models, pdaug_addclasslabel, pdaug_sequence_property_based_descriptors, pdaug_merge_dataframes, pdaug_basic_plots UseGalaxy.be 0 1078 1594 11.600000 0
Proteomics Peptide and Protein ID using OpenMS tools https://training.galaxyproject.org//topics/proteomics/tutorials/protein-id-oms/tutorial.html Formatting, Filtering 2017-10-16 2025-04-08 32 True False False True PeakPickerHiRes, XTandemAdapter, IDPosteriorErrorProbability, IDMerger, TextExporter, MSGFPlusAdapter, msconvert, IDFilter, IDScoreSwitcher, FalseDiscoveryRate, PeptideIndexer, ConsensusID, FileInfo, Grep1, FidoAdapter UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3669 6104 7.583333 0
Proteomics Clinical Metaproteomics 4: Quantitation https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.html Visualisation, Heat map generation, Statistical calculation, Protein quantification, Imputation, Standardisation and normalisation, Clustering, Principal component plotting 2024-02-06 2025-08-10 5 True False True True Grouping1, Cut1, maxquant, Grep1 UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 213 279 29.450000 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 fasta2tab, addValue, DecoyDatabase, tab2fasta, dbbuilder, fasta_merge_files_and_filter_unique_sequences UseGalaxy.org.au, UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 4945 7791 7.983333 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 table_compute, fasta_to_tabular, iedb_api, query_tabular, Filter1 0 116 123 4.266667 0
Proteomics Clinical Metaproteomics 5: Data Interpretation https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-5-data-interpretation/tutorial.html Prediction and recognition, Visualisation 2024-02-06 2025-08-10 4 True False True True unipept, msstatstmt, Grep1 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 328 418 20.716667 0
Proteomics DIA Analysis using OpenSwathWorkflow https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html Formatting, Filtering 2020-12-02 2025-05-20 12 True False False True pyprophet_protein, pyprophet_score, msconvert, pyprophet_merge, pyprophet_export, pyprophet_peptide, Grep1, OpenSwathWorkflow UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no 0 3358 4738 8.150000 0
Proteomics Clinical Metaproteomics 2: Discovery https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html Formatting, Visualisation, Heat map generation, Statistical calculation, Protein quantification, Imputation, Standardisation and normalisation, Clustering, Filtering, Principal component plotting 2024-02-06 2025-08-10 5 True False True True search_gui, ident_params, fasta2tab, maxquant, filter_tabular, msconvert, Grouping1, fasta_merge_files_and_filter_unique_sequences, Remove beginning1, Cut1, query_tabular, Filter1, tp_cat, peptide_shaker, dbbuilder, fasta_cli, Grep1 UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 385 500 22.416667 0
Proteomics Clinical Metaproteomics 1: Database-Generation https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.html Target-Decoy, Expression analysis, Protein identification, de Novo sequencing, Tag-based peptide identification 2024-02-06 2025-07-30 7 True False True True metanovo, dbbuilder, fasta_merge_files_and_filter_unique_sequences, uniprotxml_downloader UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu UseGalaxy.be, UseGalaxy.org (Main) 0 662 970 18.266667 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 FileConverter, PeakPickerHiRes, search_gui, peptide_shaker, Grep1 0 3327 5221 5.916667 0
Proteomics Proteogenomics 2: Database Search https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html Peptide database search, Conversion 2018-11-20 2025-05-08 24 True False True True search_gui, ident_params, query_tabular, tab2fasta, mz_to_sqlite, peptide_shaker UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 1659 2434 11.850000 0
Proteomics metaQuantome 2: Function https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics Query and retrieval, Indexing, Principal component visualisation, Visualisation, Quantification, Differential protein expression analysis, Statistical inference, Heat map generation, Filtering, Functional clustering 2020-10-29 2024-03-15 14 True False False True metaquantome_sample, metaquantome_viz, metaquantome_stat, metaquantome_expand, metaquantome_db, metaquantome_filter UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 443 615 15.016667 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, Grouping1, Remove beginning1, Cut1, query_tabular, Filter1, pepquery2, tp_cat, dbbuilder, collapse_dataset, fasta_merge_files_and_filter_unique_sequences UseGalaxy.cz, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.org (Main) 0 232 300 26.650000 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 FeatureFinderMultiplex, XTandemAdapter, IDPosteriorErrorProbability, tp_tail_tool, TextExporter, Summary_Statistics1, histogram_rpy, IDScoreSwitcher, MultiplexResolver, FalseDiscoveryRate, ProteinQuantifier, IDConflictResolver, IDMapper, PeptideIndexer, FileInfo, Grep1, FidoAdapter UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 1435 1976 8.950000 0
Proteomics metaQuantome 1: Data creation https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Formatting, Label-free quantification, Prediction and recognition, Filtering, Visualisation 2020-10-16 2024-03-14 20 True False False True search_gui, flashlfq, tp_replace_in_line, msconvert, Remove beginning1, Cut1, query_tabular, Filter1, peptide_shaker, tp_replace_in_column, unipept, regex1, Grep1 UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no 0 924 1541 9.083333 0
Proteomics Proteogenomics 1: Database Creation https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html Statistical calculation, Sequence annotation, Sequence alignment, RNA-Seq analysis, Variant calling, Transcriptome assembly 2018-11-20 2025-05-08 29 True False True True cat_multi_datasets, translate_bed, fasta2tab, filter_tabular, regexColumn1, fasta_merge_files_and_filter_unique_sequences, sqlite_to_tabular, gffcompare_to_bed, freebayes, query_tabular, stringtie, bed_to_protein_map, gffcompare, hisat2, tab2fasta, tp_replace_in_column, custom_pro_db UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main) UseGalaxy.cz 0 6212 10036 6.583333 0
Proteomics Neoantigen 3: PepQuery2 Verification https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-peptide-verification/tutorial.html Formatting, Filtering 2025-01-14 2025-12-03 4 True False False False ncbi_blastp_wrapper, msconvert, query_tabular, pepquery2, tab2fasta UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 119 130 8.250000 0
Proteomics Neoantigen 1b: Non-Reference-Database-Generation https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html Statistical calculation, Sequence annotation, Sequence alignment, RNA-Seq analysis, Variant calling, Transcriptome assembly 2025-01-14 2025-12-03 6 True False False False translate_bed, fasta2tab, regexColumn1, column_regex_find_and_replace, CONVERTER_gz_to_uncompressed, fasta_merge_files_and_filter_unique_sequences, sqlite_to_tabular, gffcompare_to_bed, freebayes, concatenate, stringtie, gffcompare, hisat2, tab2fasta, bed_to_protein_map, custom_pro_db 0 155 170 3.233333 0
Proteomics Multiomics data analysis using MultiGSEA https://training.galaxyproject.org//topics/proteomics/tutorials/multiGSEA-tutorial/tutorial.html Gene-set enrichment analysis, Pathway analysis, Aggregation 2025-03-10 2025-03-11 2 True False False True multigsea, tp_grep_tool, Filter1 UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz 0 439 486 5.266667 0
Proteomics Single Cell Proteomics data analysis with bioconductor-scp https://training.galaxyproject.org//topics/proteomics/tutorials/bioconductor-scp/tutorial.html Visualisation, Expression analysis 2025-02-07 2025-02-10 2 True False False False bioconductor_scp, Grouping1 UseGalaxy.org.au, UseGalaxy.eu 0 361 429 5.233333 0
Proteomics metaQuantome 3: Taxonomy https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy Query and retrieval, Indexing, Principal component visualisation, Visualisation, Quantification, Differential protein expression analysis, Statistical inference, Heat map generation, Filtering, Functional clustering 2020-10-29 2024-03-15 14 True False False True metaquantome_sample, metaquantome_viz, metaquantome_stat, metaquantome_expand, metaquantome_db, metaquantome_filter UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 472 612 14.383333 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 regexColumn1, column_regex_find_and_replace, Convert characters1, cut, select, query_tabular, pep_pointer, tab2fasta 0 134 151 6.683333 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, ncbi_blastp_wrapper, pep_pointer, query_tabular UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no 0 1825 2614 12.816667 0
Proteomics Label-free data analysis using MaxQuant https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-label-free/tutorial.html Spectrum calculation, Visualisation, Heat map generation, Tag-based peptide identification, Statistical calculation, Protein quantification, Imputation, Standardisation and normalisation, Clustering, Differential protein expression profiling, Principal component plotting 2020-04-29 2025-05-21 14 True False False True Cut1, histogram_rpy, tp_sort_header_tool, Filter1, msstats, Add_a_column1, maxquant, Grep1 UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz 0 20489 29812 3.683333 0
Proteomics Introduction to proteomics, protein identification, quantification and statistical modelling https://training.galaxyproject.org//topics/proteomics/tutorials/introduction/slides.html 2017-12-01 2024-08-08 3 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3581127 8642637 2.150000 0
Proteomics Label-free versus Labelled - How to Choose Your Quantitation Method https://training.galaxyproject.org//topics/proteomics/tutorials/labelfree-vs-labelled/tutorial.html 2017-03-17 2025-05-27 18 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 7784 12505 2.533333 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.cz 0 2116 2848 3.833333 0
Sequence analysis Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes https://training.galaxyproject.org//topics/sequence-analysis/tutorials/viral_primer_design/tutorial.html Sequence alignment, Global alignment, PCR primer design, Sequence analysis, Sequence alignment analysis, Local alignment, Multiple sequence alignment 2025-03-20 2025-11-20 3 True False False True EMBOSS: degapseq20, split_file_to_collection, ncbi_makeblastdb, rbc_mafft, fasta_compute_length, varvamp UseGalaxy.be, UseGalaxy.eu 0 919 1107 3.083333 0
Sequence analysis Quality Control https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-control/tutorial.html Sequence composition calculation, Sequencing quality control, Validation, Read pre-processing, Statistical calculation, Primer removal, Box-Whisker plot plotting, Scatter plot plotting, Sequence trimming 2016-10-04 2026-03-09 48 True True True True multiqc, fastqc, nanoplot, cutadapt, fastqe, pycoqc UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr 0 3693341 8844634 9.083333 0
Sequence analysis Clean and manage Sanger sequences from raw files to aligned consensus https://training.galaxyproject.org//topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html Taxonomic classification, Sequence clustering, Phylogenetic analysis, Visualisation, Sequencing quality control, DNA barcoding, Sequence read processing, Demultiplexing, Sequence file editing, Data handling 2024-01-08 2024-03-05 2 True False False True fastq_masker_by_quality, fastq_to_tabular, cshl_fastq_to_fasta, tab2fasta, ncbi_blastn_wrapper, cshl_fastx_reverse_complement, filter_by_fasta_ids, fastq_groomer, __SORTLIST__, qiime_align_seqs, seqtk_trimfq, mothur_merge_files, unzip, collection_element_identifiers, mothur_degap_seqs, regex1, aligned_to_consensus, ab1_fastq_converter, __FILTER_FROM_FILE__, seqtk_mergepe UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 3766 4700 6.466667 0
Sequence analysis Mapping https://training.galaxyproject.org//topics/sequence-analysis/tutorials/mapping/tutorial.html Mapping Read mapping, Genome visualisation, Sequence composition calculation, Sequencing quality control, Validation, Read pre-processing, Statistical calculation, Primer removal, Sequence alignment analysis, Sequence trimming, Data handling 2016-10-04 2026-03-09 45 True True True True samtools_stats, fastqc, multiqc, bamFilter, trim_galore, __FLATTEN__, bowtie2, jbrowse UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3649270 8755835 9.516667 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 Taxonomic classification, Read mapping, Visualisation, Sequencing quality control, Sequence contamination filtering, Statistical calculation, Cross-assembly, Expression analysis 2024-07-15 2025-12-18 5 True False True True est_abundance, falco, fastp, upload1, kraken2, recentrifuge GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 1934 2590 10.616667 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 Mapping, Enrichment analysis, Read mapping, Generation, Peak calling, Genome indexing, Visualisation, Sequence composition calculation, Sequencing quality control, Gene regulatory network analysis, Statistical calculation, Sequence alignment, Expression profile clustering, Imputation, Differential gene expression analysis, Principal component visualisation 2023-04-24 2025-10-16 10 True False False True anndata_inspect, fastqc, bedtools_sortbed, falco, episcanpy_preprocess, sinto_barcode, bwa_mem, macs2_callpeak, scanpy_plot, episcanpy_build_matrix, tp_sorted_uniq, sinto_fragments UseGalaxy.org.au, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz 0 6384 7495 2.333333 0
Single Cell Pre-processing of Single-Cell RNA Data https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing/tutorial.html Sequence alignment, Sequence alignment analysis, RNA-Seq quantification, Read summarisation, Sequencing quality control, Validation, Data handling 2019-02-22 2025-04-08 5 True True False True umi_tools_extract, tp_sed_tool, samtools_stats, featurecounts, bamFilter, multiqc, __FLATTEN__, umi_tools_count, rna_star, collection_column_join UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 3587831 8651328 8.550000 0
Single Cell Pseudobulk Analysis with Decoupler and EdgeR https://training.galaxyproject.org//topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html Expression profile clustering, Differential gene expression analysis, Principal component visualisation 2025-02-12 2025-05-09 8 True False True True anndata_inspect, scanpy_filter, column_remove_by_header, tp_replace_in_line, anndata_manipulate, tp_awk_tool, volcanoplot, __EXTRACT_DATASET__, edger, tp_replace_in_column, decoupler_pseudobulk UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz 0 2048 2334 2.316667 0
Single Cell Converting between common single cell data formats https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-data-ingest/tutorial.html Loading, Community profiling 2024-02-13 2025-03-11 4 True False False True fastq_to_tabular, anndata_inspect, tp_tail_tool, monocle3_create, datamash_transpose, regexColumn1, anndata_ops, Cut1, seurat_read10x, Filter1, tabular_to_fastq, scanpy_filter_cells, dropletutils, join1, tp_cut_tool, sceasy_convert, dropletutils_read_10x UseGalaxy.org (Main) 0 2907 3420 3.783333 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_filter, scater_plot_pca, scater_plot_dist_scatter, scater_create_qcmetric_ready_sce UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no UseGalaxy.cz 0 740 832 5.700000 0
Single Cell Bulk RNA Deconvolution with MuSiC https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music/tutorial.html 2022-02-11 2025-02-14 10 True False True True music_construct_eset, music_inspect_eset, music_deconvolution UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 4262 5339 3.900000 0
Single Cell GO Enrichment Analysis on Single-Cell RNA-Seq Data https://training.galaxyproject.org//topics/single-cell/tutorials/GO-enrichment/tutorial.html Gene-set enrichment analysis 2024-09-17 2025-04-08 8 True True False True goenrichment, tp_split_on_column, Cut1, gprofiler_gost UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) 0 1481671 2816846 5.433333 0
Single Cell Pre-processing of 10X Single-Cell RNA Datasets https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html Sequence alignment, Community profiling, Loading, Sequencing quality control, Validation 2019-09-11 2025-04-29 13 True False True True rna_starsolo, multiqc, dropletutils UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.fr, UseGalaxy.no 0 13412 17316 5.733333 0
Single Cell Generating a single cell matrix using Alevin https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin/tutorial.html Gene expression analysis, Sequence composition calculation, RNA-Seq quantification 2021-03-03 2025-11-18 25 True False True True anndata_inspect, _salmon_kallisto_mtx_to_10x, anndata_manipulate, _ensembl_gtf2gene_list, alevin, Cut1, dropletutils_empty_drops, _dropletBarcodePlot, join1, sceasy_convert, dropletutils_read_10x UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 3687 5587 10.650000 0
Single Cell An introduction to scRNA-seq data analysis https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-intro/slides.html 2021-01-29 2025-02-13 8 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3548679 8528595 2.133333 0
Single Cell Generating a single cell matrix using Alevin and combining datasets (bash + R) https://training.galaxyproject.org//topics/single-cell/tutorials/alevin-commandline/tutorial.html 2023-12-08 2025-04-22 5 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 720 968 9.550000 0
Single Cell Understanding Barcodes https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-umis/tutorial.html Statistical calculation, Sequence composition calculation, Sequencing quality control 2019-02-20 2025-02-14 11 True False True True umi_tools_extract, fastqc, seq_filter_by_id UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, UseGalaxy.no 0 6697 8320 4.966667 0
Single Cell Importing files from public atlases https://training.galaxyproject.org//topics/single-cell/tutorials/EBI-retrieval/tutorial.html 2023-11-14 2025-03-11 8 True False True True retrieve_scxa, tp_grep_tool, regexColumn1, tp_find_and_replace, anndata_ops, seurat_read10x, hca_matrix_downloader, scanpy_read_10x, sceasy_convert 0 642 835 11.683333 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 Essential dynamics, Read mapping, Gene expression profiling, Generation, Dimensionality reduction, Principal component visualisation, Genome indexing, Sequence alignment, Expression profile clustering, Differential gene expression analysis 2024-07-11 2025-07-02 5 True False False True anndata_inspect, scanpy_filter, replace_column_with_key_value_file, anndata_manipulate, anndata_ops, Cut1, snapatac2_peaks_and_motif, bwa_mem, scanpy_normalize, scanpy_plot, snapatac2_plotting, scanpy_inspect, snapatac2_clustering, fasta_compute_length, snapatac2_preprocessing 0 1954 2314 2.750000 0
Single Cell Downstream Single-cell RNA analysis with RaceID https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-raceid/tutorial.html Expression profile clustering, Molecular dynamics, Expression analysis 2019-03-25 2025-02-14 7 True False False True tp_sed_tool, datamash_transpose, raceid_inspectclusters, tp_head_tool, raceid_inspecttrajectory, raceid_filtnormconf, raceid_clustering, datamash_ops, raceid_trajectory UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz 0 1135 1336 7.533333 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, Differential gene expression analysis, Principal component visualisation 2023-01-25 2025-03-11 14 True False False True anndata_inspect, table_compute, scanpy_regress_variable, sort1, addValue, cat1, anndata_manipulate, tp_easyjoin_tool, scanpy_plot, scanpy_inspect, scanpy_cluster_reduce_dimension 0 2277 2678 2.966667 0
Single Cell Combining single cell datasets after pre-processing https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html 2022-09-08 2025-11-18 23 True False True True anndata_inspect, anndata_manipulate, anndata_ops, Cut1, Paste1, tp_replace_in_column UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org (Main) 0 2664 3732 10.483333 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 0 3621 4109 3.116667 0
Single Cell Comparing inferred cell compositions using MuSiC deconvolution https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music-4-compare/tutorial.html 2023-01-20 2025-02-13 10 True False False True music_compare UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 330 476 11.666667 0
Single Cell Clustering 3K PBMCs with Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html Expression profile clustering, Differential gene expression analysis, Principal component visualisation 2019-12-19 2025-04-29 16 True True True True anndata_inspect, scanpy_filter, anndata_import, anndata_manipulate, datamash_ops, scanpy_normalize, scanpy_plot, scanpy_inspect, scanpy_cluster_reduce_dimension, scanpy_remove_confounders UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.fr, UseGalaxy.no 0 3589679 8654740 8.016667 0
Single Cell Filter, plot and explore single-cell RNA-seq data with Scanpy (Python) https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case-jupyter_basic-pipeline/tutorial.html 2023-08-25 2025-03-11 13 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3623 4280 4.033333 0
Single Cell Evaluating Reference Data for Bulk RNA Deconvolution https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html Annotation, Visualisation 2025-02-02 2025-03-11 3 True False False True bg_column_arrange_by_header, tp_sed_tool, __DUPLICATE_FILE_TO_COLLECTION__, ggplot2_violin, Count1, Cut1, tp_cut_tool, Paste1, collection_column_join, table_compute, music_deconvolution, datamash_transpose, tp_awk_tool, tp_multijoin_tool, join1, music_construct_eset, Add_a_column1, Remove beginning1, tp_easyjoin_tool, ggplot2_point, annotatemyids, collapse_dataset UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 149 172 9.616667 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, Differential gene expression analysis, Principal component visualisation 2021-03-24 2025-04-23 24 True False True True retrieve_scxa, scanpy_normalise_data, anndata_manipulate, anndata_ops, scanpy_find_variable_genes, scanpy_plot_embed, scanpy_plot, scanpy_cluster_reduce_dimension, scanpy_filter_cells, scanpy_scale_data, scanpy_find_markers, Cut1, scanpy_run_tsne, anndata_inspect, scanpy_filter, scanpy_run_pca, join1, interactive_tool_cellxgene_vip, scanpy_find_cluster, scanpy_run_umap, scanpy_compute_graph, scanpy_normalize, scanpy_inspect, scanpy_filter_genes 0 5777 9030 7.700000 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_create, seurat_reduce_dimension, Cut1, seurat_plot, Filter1, seurat_preprocessing, csv_to_tabular, seurat_clustering MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 1947 2409 5.100000 0
Single Cell Scanpy Parameter Iterator https://training.galaxyproject.org//topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.html 2023-07-19 2025-02-13 8 True False False True scanpy_find_cluster, scanpy_run_umap, scanpy_compute_graph, scanpy_plot_embed, scanpy_run_tsne, scanpy_parameter_iterator UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main) 0 333 368 6.466667 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, retrieve_scxa, seurat_normalise_data, seurat_find_variable_genes, seurat_find_markers, seurat_find_clusters, seurat_plot, seurat_read10x, seurat_scale_data, seurat_run_umap, seurat_run_pca, seurat_find_neighbours UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 2426 2911 5.933333 0
Single Cell Multi-sample batch correction with Harmony and SnapATAC2 https://training.galaxyproject.org//topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html Essential dynamics, Gene expression profiling, Dimensionality reduction 2025-02-28 2025-07-02 2 True False False True anndata_inspect, Show beginning1, anndata_manipulate, snapatac2_peaks_and_motif, collection_element_identifiers, __EXTRACT_DATASET__, __FILTER_FROM_FILE__, snapatac2_plotting, snapatac2_clustering, fasta_compute_length, snapatac2_preprocessing UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.org (Main) 0 658 724 2.050000 0
Single Cell Converting NCBI Data to the AnnData Format https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html 2023-12-13 2025-03-11 7 True False True True anndata_inspect, anndata_import, anndata_manipulate, anndata_ops, unzip, Cut1, Paste1, tp_replace_in_column, scanpy_filter_cells UseGalaxy.org.au, UseGalaxy.be UseGalaxy.cz 0 529 623 10.566667 0
Single Cell Plates, Batches, and Barcodes https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-plates-batches-barcodes/slides.html 2019-02-16 2025-02-13 4 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3581127 8642638 2.150000 0
Single Cell Inferring single cell trajectories with Scanpy (Python) https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_JUPYTER-trajectories/tutorial.html 2021-04-07 2025-03-11 20 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 4880 5727 3.483333 0
Single Cell Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html Annotation 2023-01-20 2024-02-13 8 True False False True anndata_inspect, table_compute, tp_sed_tool, retrieve_scxa, sort1, add_line_to_file, datamash_transpose, tp_awk_tool, Cut1, music_manipulate_eset, tp_easyjoin_tool, join1, music_construct_eset, tp_cut_tool, annotatemyids, scanpy_read_10x, regex1 UseGalaxy.cz 0 795 1301 7.633333 0
Single Cell Inferring single cell trajectories with Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_trajectories/tutorial.html 2023-12-08 2025-03-11 13 True False False True scanpy_find_cluster, scanpy_compute_graph, anndata_manipulate, scanpy_run_dpt, scanpy_plot_embed, scanpy_run_paga, scanpy_run_fdg, scanpy_run_diffmap, scanpy_plot_trajectory UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.org (Main) 0 1453 1814 7.133333 0
Single Cell Single-cell Formats and Resources https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-data-formats/slides.html 2024-07-26 2025-02-13 4 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1551450 2987409 1.633333 0
Single Cell Inferring single cell trajectories with Monocle3 (R) https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_monocle3-rstudio/tutorial.html 2023-04-12 2025-03-11 13 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 6957 7866 1.566667 0
Single Cell Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.html Annotation 2023-01-20 2024-02-13 8 True False False True table_compute, tp_sed_tool, sort1, column_remove_by_header, tp_awk_tool, music_manipulate_eset, tp_easyjoin_tool, music_construct_eset, tp_cut_tool, annotatemyids, regex1 UseGalaxy.cz 0 797 1216 7.500000 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 anndata_inspect, monocle3_create, monocle3_preprocess, monocle3_topmarkers, datamash_transpose, regexColumn1, monocle3_partition, Cut1, monocle3_reduceDim, Filter1, join1, tp_cut_tool, monocle3_learnGraph, monocle3_orderCells, monocle3_plotCells, monocle3_diffExp UseGalaxy.eu, UseGalaxy.org (Main) 0 4128 5105 3.950000 0
Single Cell Trajectory analysis https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-trajectories/slides.html 2022-09-30 2025-02-13 4 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 2625935 5556323 1.933333 0
Single Cell Automated Cell Annotation https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html 2023-09-04 2025-02-27 7 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 2026976 4108315 1.833333 0
Statistics and machine learning Machine learning: classification and regression https://training.galaxyproject.org//topics/statistics/tutorials/classification_regression/tutorial.html 2019-03-07 2025-04-08 13 True False False True sklearn_svm_classifier, sklearn_ensemble, plotly_regression_performance_plots, plotly_ml_performance_plots UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) 0 5803 10361 2.433333 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 ggplot2_point, sklearn_numeric_clustering, csv_to_tabular UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.fr 0 8660 14249 2.450000 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_map_mutation_class, pancancer_compare_within_models, pancancer_pathway_count_heatmaps, pancancer_visualize_decisions, pancancer_within_disease_analysis, pancancer_classifier, pancancer_alternative_genes_pathwaymapper, pancancer_external_sample_status_prediction, pancancer_targene_summary_figures, pancancer_targene_cell_line_predictions, pancancer_targene_pharmacology, pancancer_apply_weights 0 856 1305 10.516667 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 1277 1601 8.333333 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 ml_visualization_ex, keras_model_builder, model_prediction, keras_train_and_eval, keras_model_config UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.no 0 3514324 8392471 5.083333 0
Statistics and machine learning Identifing Survival Markers of Brain tumor with Flexynesis https://training.galaxyproject.org//topics/statistics/tutorials/flexynesis_survival/tutorial.html 2025-08-13 2025-08-13 2 True False False True flexynesis, flexynesis_plot, __EXTRACT_DATASET__, datamash_ops, Add_a_column1, tp_replace_in_column UseGalaxy.be, UseGalaxy.eu 0 109 128 6.133333 0
Statistics and machine learning Unsupervised Analysis of Bone Marrow Cells with Flexynesis https://training.galaxyproject.org//topics/statistics/tutorials/flexynesis_unsupervised/tutorial.html 2025-08-10 2025-08-13 2 True False False True flexynesis_plot, __EXTRACT_DATASET__, flexynesis, flexynesis_utils UseGalaxy.be, UseGalaxy.eu 0 63 69 6.966667 0
Statistics and machine learning Regression in Machine Learning https://training.galaxyproject.org//topics/statistics/tutorials/regression_machinelearning/tutorial.html 2020-01-25 2025-05-14 19 True True True True sklearn_build_pipeline, sklearn_searchcv, Remove beginning1, plotly_regression_performance_plots, sklearn_ensemble, sklearn_generalized_linear UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.no 0 3584495 8646907 7.416667 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_nn_classifier, sklearn_build_pipeline, sklearn_svm_classifier, sklearn_searchcv, Remove beginning1, plotly_ml_performance_plots, sklearn_ensemble, sklearn_generalized_linear UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.no 0 3584058 8646876 10.650000 0
Statistics and machine learning Basics of machine learning https://training.galaxyproject.org//topics/statistics/tutorials/machinelearning/tutorial.html 2018-11-05 2025-05-13 15 True True True True sklearn_svm_classifier UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.fr, UseGalaxy.no 0 3584021 8646519 12.533333 0
Statistics and machine learning Deep Learning (Part 3) - Convolutional neural networks (CNN) https://training.galaxyproject.org//topics/statistics/tutorials/CNN/tutorial.html 2021-04-19 2025-05-09 19 True True True True ml_visualization_ex, keras_model_builder, sklearn_to_categorical, model_prediction, keras_train_and_eval, keras_model_config UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 3439554 8111328 3.950000 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 table_compute, flexynesis_cbioportal_import, tp_sort_header_tool, __EXTRACT_DATASET__, tp_cut_tool, flexynesis_utils UseGalaxy.eu UseGalaxy.be 0 83 88 3.966667 0
Statistics and machine learning Age prediction using machine learning https://training.galaxyproject.org//topics/statistics/tutorials/age-prediction-with-ml/tutorial.html 2019-01-25 2025-04-08 12 True False False True sklearn_build_pipeline, plotly_parallel_coordinates_plot, sklearn_searchcv, plotly_regression_performance_plots, sklearn_ensemble UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.no 0 13362 21490 2.066667 0
Statistics and machine learning Text-mining with the SimText toolset https://training.galaxyproject.org//topics/statistics/tutorials/text-mining_simtext/tutorial.html 2021-04-05 2025-05-07 8 True False False True interactive_tool_simtext_app, pmids_to_pubtator_matrix, pubmed_by_queries UseGalaxy.eu 0 554 751 9.700000 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 2026-01-28 1 True True False True image_learner UseGalaxy.org (Main) 0 306488 425951 4.650000 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 2026-01-16 4 True False False True table_compute, pick_value, flexynesis, datamash_transpose, Show beginning1, tabpfn, tp_sort_header_tool, flexynesis_plot, tp_easyjoin_tool, __EXTRACT_DATASET__, join1, tp_cut_tool UseGalaxy.eu 0 142 188 9.650000 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 0 264 329 6.516667 0
Statistics and machine learning Deep Learning (Part 1) - Feedforward neural networks (FNN) https://training.galaxyproject.org//topics/statistics/tutorials/FNN/tutorial.html 2021-04-28 2024-06-14 12 True True True True keras_model_builder, plotly_regression_performance_plots, model_prediction, keras_train_and_eval, keras_model_config UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.no 0 3444192 8100488 3.366667 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 ml_visualization_ex, keras_model_builder, model_prediction, keras_train_and_eval, keras_model_config UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) 0 2566 3259 6.983333 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 2026-01-10 3 True True True True PyCaret_Model_Comparison, tabular_learner 0 1337692 2447019 9.416667 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 ml_visualization_ex, keras_model_builder, sklearn_to_categorical, tp_cut_tool, model_prediction, keras_train_and_eval, keras_model_config UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 3100044 7013942 5.200000 0
Statistics and machine learning Interval-Wise Testing for omics data https://training.galaxyproject.org//topics/statistics/tutorials/iwtomics/tutorial.html Genome annotation, Differentially-methylated region identification, Peak calling, Comparison, Differential gene expression analysis 2018-06-14 2023-11-09 17 True False False True iwtomics_plotwithscale, iwtomics_loadandplot, iwtomics_testandplot UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) 0 389 511 14.600000 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 1610179 3129546 6.816667 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.org.au, UseGalaxy.eu 0 4521 6931 4.916667 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 0 478 585 4.466667 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 rpscore, rpfba, rpranker, rpthermo UseGalaxy.be 0 686 1001 9.500000 0
Synthetic Biology Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools https://training.galaxyproject.org//topics/synthetic-biology/tutorials/retrosynthesis_analysis/tutorial.html 2022-06-23 2024-06-14 8 True False True True retropath2, rrparser, get_sbml_model, rp2paths, rpextractsink, rpcompletion UseGalaxy.be 0 634 902 9.350000 0
Synthetic Biology Designing plasmids encoding predicted pathways by using the BASIC assembly method https://training.galaxyproject.org//topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.html 2022-05-12 2024-06-14 8 True False True True dnabot, selenzy-wrapper, rpbasicdesign UseGalaxy.be UseGalaxy.fr 0 1100 1678 10.200000 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 3581127 8642643 2.150000 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 2636496 5583359 1.933333 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 0 178 194 14.200000 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 36 38 2.516667 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 0 308 336 12.116667 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 0 181 208 15.016667 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 0 334 570 14.366667 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 18 18 16.816667 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 0 273 467 15.233333 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 32 32 0.366667 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 0 214 345 15.633333 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 0 373 424 9.916667 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 0 102 106 2.316667 0
Transcriptomics 1: RNA-Seq reads to counts https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html Formatting, Read summarisation, Sequence composition calculation, Sequencing quality control, Validation, Read pre-processing, Statistical calculation, Sequence alignment, Primer removal, Sequence trimming, RNA-Seq quantification, Data handling 2018-09-23 2024-08-09 33 True False False True multiqc, fastqc, featurecounts, rseqc_geneBody_coverage, rseqc_read_distribution, cutadapt, samtools_idxstats, picard_MarkDuplicates, hisat2, collection_column_join, rseqc_infer_experiment UseGalaxy.eu MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 81826 147111 5.283333 0
Transcriptomics De novo transcriptome assembly, annotation, and differential expression analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/full-de-novo/tutorial.html Gene functional annotation, de Novo sequencing, De-novo assembly, Sequence composition calculation, Sequencing quality control, Validation, Statistical calculation, Coding region prediction, Transcriptome assembly 2020-02-13 2023-11-09 8 True False False True multiqc, fastqc, trinity_abundance_estimates_to_matrix, trinity, trinity_align_and_estimate_abundance, describe_samples, trimmomatic, trinity_define_clusters_by_cutting_tree, trinity_filter_low_expr_transcripts, trinity_samples_qccheck, transdecoder, trinotate, trinity_analyze_diff_expr, trinity_run_de_analysis, trinity_contig_exn50_statistic UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no 0 15288 27273 4.083333 0
Transcriptomics Small Non-coding RNA Clustering using BlockClust https://training.galaxyproject.org//topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.html 2018-12-14 2023-11-09 8 True False False True blockbuster, blockclust, samtools_sort, tp_sort_header_tool UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no 0 1079 1455 13.116667 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 158285 257054 2.083333 0
Transcriptomics 3: RNA-seq genes to pathways https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html Gene functional annotation, Gene-set enrichment analysis, Gene set testing 2018-12-31 2023-11-09 13 True False False True goseq, Cut1, tp_sort_header_tool, join1, tp_cut_tool, Add_a_column1, egsea, fgsea UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz 0 27453 43647 5.883333 0
Transcriptomics RNA-Seq data analysis, clustering and visualisation tutorial https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html Gene functional annotation, Differential gene expression analysis, RNA-Seq analysis 2025-05-28 2025-06-16 5 True False False True table_compute, Show beginning1, cat1, Grouping1, Multivariate, goseq, Cut1, length_and_gc_content, Filter1, tp_easyjoin_tool, tp_sort_header_tool, volcanoplot, deseq2, ggplot2_heatmap2, Add_a_column1, deg_annotate UseGalaxy.eu, UseGalaxy.fr UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 1865 2304 3.816667 0
Transcriptomics Network analysis with Heinz https://training.galaxyproject.org//topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html Pathway or network analysis, Differential gene expression analysis, RNA-Seq analysis 2018-10-11 2024-01-15 16 True True False True heinz_bum, heinz, Cut1, heinz_scoring, deseq2, heinz_visualization UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 3583232 8645885 11.600000 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 goslimmer, goenrichment, Filter1 Galaxy@AuBi, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 23691 38195 3.333333 0
Transcriptomics Genome-wide alternative splicing analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html Formatting, Sequence analysis, RNA-Seq analysis, Protein sequence analysis, De-novo assembly, Sequence composition calculation, Sequencing quality control, Validation, Sequence contamination filtering, Statistical calculation, Sequence annotation, Visualisation, Sequence comparison, Sequence assembly validation, Sequence alignment, Transcriptome assembly, Data handling 2023-05-17 2025-12-17 12 True True False True stringtie_merge, multiqc, fastqc, rseqc_geneBody_coverage, cpat, stringtie, rseqc_junction_annotation, addValue, gffread, Cut1, __FLATTEN__, tp_uniq_tool, fastp, pygenomeTracks, gffcompare, rseqc_infer_experiment, gtftobed12, sort1, tp_grep_tool, cat1, tp_awk_tool, collection_element_identifiers, Add_a_column1, regex1, isoformswitchanalyzer, gene2exon1, pfamscan, rseqc_junction_saturation, rseqc_read_distribution, Remove beginning1, Filter1, rna_quast, tp_cat, __FILTER_FROM_FILE__, rna_star, rseqc_inner_distance UseGalaxy.cz, UseGalaxy.fr 0 2225395 4549817 6.950000 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_replace_in_line, mergeCols1, tp_cut_tool, annotatemyids, limma_voom UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.fr 0 46076 77135 6.083333 0
Transcriptomics RNA-RNA interactome data analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-interactome/tutorial.html Statistical calculation, Primer removal, Read pre-processing, Sequence composition calculation, Sequencing quality control, Sequence trimming 2020-03-23 2023-11-09 12 True False False True fastqc, chira_map, query_tabular, cutadapt, chira_extract, chira_collapse, chira_merge, chira_quantify UseGalaxy.be, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu 0 1549 2309 10.916667 0
Transcriptomics CLIP-Seq data analysis from pre-processing to motif detection https://training.galaxyproject.org//topics/transcriptomics/tutorials/clipseq/tutorial.html Statistical calculation, Mapping, Primer removal, Read pre-processing, Sequence alignment, Sequence composition calculation, Sequencing quality control, Sequence trimming 2018-08-17 2023-11-09 23 True False False True bedtools_slopbed, bedtools_genomecoveragebed_bedgraph, fastqc, wig_to_bigWig, __SORTLIST__, umi_tools_dedup, __MERGE_COLLECTION__, umi_tools_extract, sort1, deeptools_plot_fingerprint, tp_awk_tool, deeptools_plot_correlation, bctools_extract_alignment_ends, deeptools_multi_bam_summary, peakachu, rcas, cutadapt, meme_chip, rna_star, Extract genomic DNA 1 0 8684 16761 3.383333 0
Transcriptomics Differential abundance testing of small RNAs https://training.galaxyproject.org//topics/transcriptomics/tutorials/srna/tutorial.html RNA-Seq analysis, Read pre-processing, Sequence composition calculation, Sequencing quality control, Statistical calculation, Sequence alignment, Primer removal, Differential gene expression analysis, Gene expression analysis, RNA-Seq quantification, Sequence trimming 2017-06-29 2023-11-09 26 True False False True fastqc, samtool_filter2, bedtools_bamtofastq, trim_galore, Filter1, deseq2, hisat2, salmon, fastq_manipulation UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 7204 12471 4.950000 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 2025-11-24 14 True False False True datamash_transpose, Show beginning1, cat1, Show tail1, Cut1, Filter1, tp_sort_header_tool, join1, ggplot2_heatmap2 GalaxyTrakr, UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.no 0 79246 129635 2.633333 0
Transcriptomics RNA-Seq analysis with AskOmics Interactive Tool https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-analysis-with-askomics-it/tutorial.html 2020-07-09 2023-11-09 13 True True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3582201 8644002 18.583333 0
Transcriptomics Introduction to Transcriptomics https://training.galaxyproject.org//topics/transcriptomics/tutorials/introduction/slides.html 2016-10-05 2025-04-08 3 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3581127 8642646 2.150000 0
Transcriptomics Visualization of RNA-Seq results with CummeRbund https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-cummerbund/tutorial.html 2017-10-16 2023-11-09 16 True True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3583769 8646591 11.133333 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.org.au, UseGalaxy.eu 0 4378 5606 10.783333 0
Transcriptomics RNA-seq Alignment with STAR https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.html 2023-05-15 2023-11-09 6 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 11687 14281 3.250000 0
Transcriptomics Visualization of RNA-Seq results with Volcano Plot in R https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot-r/tutorial.html 2021-06-14 2024-06-14 8 True False True False volcanoplot, interactive_tool_rstudio UseGalaxy.org.au, UseGalaxy.eu 0 31333 42695 3.700000 0
Transcriptomics Reference-based RNAseq data analysis (long) https://training.galaxyproject.org//topics/transcriptomics/tutorials/rb-rnaseq/tutorial.html 2017-02-22 2023-02-17 12 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 22541 35109 4.150000 0
Transcriptomics Reference-based RNA-Seq data analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/ref-based/tutorial.html Formatting, Enrichment analysis, Read mapping, Visualisation, Sequence alignment, Primer removal, Differential gene expression analysis, Exonic splicing enhancer prediction, Gene functional annotation, Structure visualisation, RNA-Seq analysis, Read summarisation, Genome visualisation, Pathway visualisation, Sequencing quality control, Validation, Read pre-processing, Sequence trimming, Pathway or network analysis, RNA-Seq quantification, Pathway or network visualisation, Data handling 2016-10-05 2026-03-09 107 True False True True multiqc, featurecounts, rseqc_geneBody_coverage, tp_sort_header_tool, pathview, falco, tp_replace_in_line, Grouping1, goseq, samtools_view, Cut1, __FLATTEN__, pygenomeTracks, __EXTRACT_DATASET__, __MERGE_COLLECTION__, dexseq_count, rseqc_infer_experiment, gtftobed12, __TAG_FROM_FILE__, dexseq, table_compute, tp_grep_tool, cat1, collection_element_identifiers, join1, picard_MarkDuplicates, samtools_idxstats, Add_a_column1, deg_annotate, ChangeCase, length_and_gc_content, rseqc_read_distribution, jbrowse2, Remove beginning1, Filter1, cutadapt, deseq2, tp_cat, __FILTER_FROM_FILE__, ggplot2_heatmap2, rna_star UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.org.au 0 198763 366636 4.483333 0
Transcriptomics Pathway analysis with the MINERVA Platform https://training.galaxyproject.org//topics/transcriptomics/tutorials/minerva-pathways/tutorial.html Gene functional annotation, RNA-Seq analysis, Read summarisation, Sequence composition calculation, Sequencing quality control, Validation, Read pre-processing, Statistical calculation, Sequence alignment, Primer removal, Sequence trimming, Annotation, RNA-Seq quantification, Data handling 2024-03-28 2024-07-26 3 True False False True multiqc, fastqc, featurecounts, rseqc_geneBody_coverage, tp_sort_header_tool, tp_replace_in_line, goseq, Cut1, __EXTRACT_DATASET__, collection_column_join, fasterq_dump, join1, hisat2, Add_a_column1, limma_voom, rseqc_read_distribution, cutadapt, annotatemyids, tp_sorted_uniq, Grep1 UseGalaxy.org.au, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 727 850 13.750000 0
Transcriptomics De novo transcriptome reconstruction with RNA-Seq https://training.galaxyproject.org//topics/transcriptomics/tutorials/de-novo/tutorial.html RNA-Seq analysis, Read summarisation, Sequence composition calculation, Sequencing quality control, Statistical calculation, Sequence annotation, Sequence alignment, Transcriptome assembly, Differential gene expression analysis, RNA-Seq quantification 2017-02-19 2024-06-14 36 True False True True stringtie_merge, fastqc, featurecounts, trimmomatic, stringtie, Filter1, deseq2, gffcompare, deeptools_bam_coverage, hisat2 Galaxy@AuBi, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 17382 29608 6.666667 0
Variant Analysis Introduction to Variant analysis https://training.galaxyproject.org//topics/variant-analysis/tutorials/introduction/slides.html 2016-08-19 2023-03-05 2 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3581127 8642647 2.150000 0
Variant Analysis Calling very rare variants https://training.galaxyproject.org//topics/variant-analysis/tutorials/dunovo/tutorial.html Statistical calculation, Sequence alignment, Variant calling, Read mapping, Generation, Genome indexing, Sequence composition calculation, Sequencing quality control 2017-02-22 2024-12-09 21 True False False True fastqc, naive_variant_caller, bamleftalign, Filter1, bwa_mem, allele_counts_1, make_families, align_families, sequence_content_trimmer, correct_barcodes, dunovo UseGalaxy.org (Main) 0 2377 3515 4.966667 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, Read mapping, Generation, Genome indexing, Sequence composition calculation, Sequencing quality control, Statistical calculation, Sequence alignment, Sequence alignment analysis, Variant calling, Data handling 2017-02-16 2024-03-15 23 True False False True fastqc, bamFilter, bamleftalign, picard_MergeSamFiles, vcf2tsv, Cut1, freebayes, bwa_mem, picard_MarkDuplicates, vcffilter2 UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no 0 9674 16666 5.516667 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 bcftools_merge, tp_grep_tool, regexColumn1, CONVERTER_gz_to_uncompressed, CONVERTER_uncompressed_to_gz, gemini_inheritance, Filter1, gemini_load, snpEff, gene_iobio_display_generation_iframe, pyega3, bcftools_norm UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz 0 2132 3681 9.533333 0
Variant Analysis Identification of somatic and germline variants from tumor and normal sample pairs https://training.galaxyproject.org//topics/variant-analysis/tutorials/somatic-variants/tutorial.html Read mapping, Generation, Genome indexing, Sequence composition calculation, Sequencing quality control, Visualisation, Validation, Statistical calculation, Sequence alignment, Sequence alignment analysis, Variant calling, Data handling 2019-03-13 2025-03-20 16 True False False True samtools_rmdup, bg_column_arrange_by_header, gemini_annotate, fastqc, gemini_query, bamFilter, bamleftalign, falco, multiqc, trimmomatic, samtools_calmd, tp_easyjoin_tool, bwa_mem, gemini_load, varscan_somatic, snpEff UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.fr 0 15326 27241 5.650000 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 Read mapping, Generation, Genome indexing, Read pre-processing, Visualisation, Sequence alignment, Primer removal, Sequence trimming, Data handling 2025-02-24 2025-02-24 1 True False False True tp_replace_in_line, tp_awk_tool, trim_galore, vcf2tsv, fastq_dump, Filter1, bwa_mem, ggplot2_point, ncbi_acc_download, tp_replace_in_column, collapse_dataset, bcftools_call, bcftools_mpileup UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz 0 428 529 3.683333 0
Variant Analysis Exome sequencing data analysis for diagnosing a genetic disease https://training.galaxyproject.org//topics/variant-analysis/tutorials/exome-seq/tutorial.html Read mapping, Sequence analysis, Generation, Genome indexing, Visualisation, Sequence composition calculation, Sequencing quality control, Validation, Statistical calculation, Sequence alignment, Genetic variation analysis, Variant calling 2016-08-19 2026-03-09 30 True False True True samtools_rmdup, multiqc, fastqc, falco, trimmomatic, samtools_view, gemini_inheritance, freebayes, bwa_mem, gemini_load, snpEff, snpEff_download, bcftools_norm UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.org.au, UseGalaxy.fr 0 38036 67880 5.283333 0
Variant Analysis Calling variants in diploid systems https://training.galaxyproject.org//topics/variant-analysis/tutorials/dip/tutorial.html Genetic variation analysis, Variant calling, Statistical calculation, Sequence analysis 2017-02-20 2025-04-28 17 True False False True gemini_query, gemini_load, gemini_db_info, freebayes, snpEff, vcfallelicprimitives UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.org.au, UseGalaxy.no 0 16626 28202 8.683333 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 Read mapping, Generation, Copy number estimation, Genome alignment, Sequence composition calculation, Sequencing quality control, Validation, Visualisation, Statistical calculation, Sequence alignment, Genome indexing, Sequence visualisation, Variant calling 2022-10-05 2025-03-20 14 True False False True samtools_rmdup, multiqc, fastqc, control_freec, bamleftalign, tp_replace_in_line, falco, circos, __RELABEL_FROM_FILE__, samtools_view, trimmomatic, __BUILD_LIST__, bwa_mem, samtools_calmd, __EXTRACT_DATASET__, tp_text_file_with_recurring_lines, Grep1 UseGalaxy.org.au, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 2000 2545 7.633333 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, mimodd_varreport, mimodd_vcf_filter, tp_find_and_replace, mimodd_varcall, snpEff, snpEff_download, mimodd_map UseGalaxy.be, UseGalaxy.eu UseGalaxy.org.au, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 4627 6704 10.266667 0
Variant Analysis Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs) https://training.galaxyproject.org//topics/variant-analysis/tutorials/beacon_cnv_query/tutorial.html Genetic variation analysis, Service discovery, Database search 2024-08-06 2024-09-27 3 True False False False beacon2_cnv UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.fr 0 234 272 8.150000 0
Variant Analysis Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons https://training.galaxyproject.org//topics/variant-analysis/tutorials/beaconise_1000hg/tutorial.html Database search, Genetic variation analysis, Service discovery 2024-08-06 2026-01-12 4 True False False False beacon2_import, cnv_phenopacket, beacon2_cnv, cnv_vcf2json UseGalaxy.eu 0 390 431 3.483333 0
Visualisation Visualisation with Circos https://training.galaxyproject.org//topics/visualisation/tutorials/circos/tutorial.html Sequence visualisation 2020-01-10 2024-10-15 22 True True True True random_lines1, circos, Remove beginning1, Cut1, upload1, Grep1 Galaxy@AuBi, Galaxy@Pasteur, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.no 0 3612319 8692067 4.783333 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_gc_skew, circos_wiggle_to_scatter, circos, Cut1, gff2bed1, circos_interval_to_tile, circos_interval_to_text, deeptools_bam_coverage UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr Galaxy@AuBi, MISSISSIPPI, UseGalaxy.org.au, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) 0 1663 2077 8.000000 0
Visualisation Visualisations in Galaxy https://training.galaxyproject.org//topics/visualisation/tutorials/introduction/slides.html 2020-01-10 2023-01-12 1 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3581127 8642651 2.150000 0
Visualisation Friends Don't Let Friends Make Bad Graphs https://training.galaxyproject.org//topics/visualisation/tutorials/bad-graphs/slides.html 2023-11-20 2023-11-20 2 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1942787 3924349 1.800000 0