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 2743129 7359672 2.516667 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 2744885 7362189 5.966667 0
Galaxy Server administration Galaxy Installation with Ansible https://training.galaxyproject.org//topics/admin/tutorials/ansible-galaxy/tutorial.html Database management, Informatics, Data management 2019-01-28 2025-04-08 102 True True True False 0 2768373 7406804 4.250000 0
Galaxy Server administration Connecting Galaxy to a compute cluster https://training.galaxyproject.org//topics/admin/tutorials/connect-to-compute-cluster/tutorial.html 2018-01-07 2025-04-08 59 True True True False 0 2747116 7366580 5.783333 0
Galaxy Server administration Galaxy Monitoring with gxadmin https://training.galaxyproject.org//topics/admin/tutorials/gxadmin/tutorial.html 2019-01-28 2024-08-08 27 True True True False 0 2743991 7361028 5.233333 0
Galaxy Server administration Reference Data with CVMFS https://training.galaxyproject.org//topics/admin/tutorials/cvmfs/tutorial.html 2019-01-27 2025-04-03 50 True True True False 0 2745198 7362747 5.683333 0
Galaxy Server administration Galaxy Monitoring with Telegraf and Grafana https://training.galaxyproject.org//topics/admin/tutorials/monitoring/tutorial.html 2019-01-31 2024-12-18 47 True True True False 0 2745973 7364964 3.383333 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 2743129 7359672 2.516667 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 2744466 7361773 4.066667 0
Galaxy Server administration Galaxy Interactive Tools https://training.galaxyproject.org//topics/admin/tutorials/interactive-tools/tutorial.html 2020-02-27 2025-04-08 27 True True True False 0 2745371 7363060 5.250000 0
Galaxy Server administration Gearing towards production https://training.galaxyproject.org//topics/admin/tutorials/production/slides.html 2019-01-28 2025-04-08 10 False True True False 0 2743129 7359672 2.516667 0
Galaxy Server administration Data Libraries https://training.galaxyproject.org//topics/admin/tutorials/data-library/tutorial.html 2021-01-14 2024-06-14 32 True True True False 0 2726519 7296135 4.566667 0
Galaxy Server administration Server Maintenance: Cleanup, Backup, and Restoration https://training.galaxyproject.org//topics/admin/tutorials/backup-cleanup/tutorial.html Database management, Informatics, Data management 2019-01-31 2024-08-09 5 True True True False 0 2743672 7360399 11.500000 0
Galaxy Server administration Running Jobs on Remote Resources with Pulsar https://training.galaxyproject.org//topics/admin/tutorials/pulsar/tutorial.html 2019-01-28 2025-04-08 49 True True True False 0 2745619 7363787 5.350000 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 2749471 7371045 4.166667 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 2743129 7359673 2.516667 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 2743129 7359673 2.516667 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 2743129 7359673 2.516667 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 2743129 7359673 2.516667 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 2743820 7360767 3.333333 0
Galaxy Server administration Galactic Database https://training.galaxyproject.org//topics/admin/tutorials/database/slides.html 2019-01-28 2022-06-16 5 False True True False 0 2743129 7359674 2.516667 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 2743129 7359674 2.516667 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 2743129 7359674 2.516667 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 731223 1763759 2.466667 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 2743129 7359674 2.516667 0
Galaxy Server administration Reference Data with Data Managers https://training.galaxyproject.org//topics/admin/tutorials/reference-genomes/tutorial.html Genome indexing, Sequence alignment, Generation, Read mapping 2019-01-28 2023-04-21 7 True True False False bwa, data_manager_fetch_genome_all_fasta_dbkey, bwa_mem_index_builder_data_manager 0 2743669 7360380 7.050000 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 2743129 7359675 2.516667 0
Galaxy Server administration Setting up Celery Workers for Galaxy https://training.galaxyproject.org//topics/admin/tutorials/celery/tutorial.html 2022-07-16 2025-04-08 12 True True False False 0 1887678 4539111 4.000000 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 2743129 7359675 2.516667 0
Galaxy Server administration Deploying a Beacon v1 in Galaxy https://training.galaxyproject.org//topics/admin/tutorials/beacon/tutorial.html 2023-04-16 2024-12-18 5 True False False False 0 138 156 2.166667 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 33 38 5.650000 0
Galaxy Server administration Enable upload via FTP https://training.galaxyproject.org//topics/admin/tutorials/ftp/tutorial.html 2021-06-18 2024-02-20 23 True False False False 0 1219 1680 1.683333 0
Galaxy Server administration Upgrading Galaxy https://training.galaxyproject.org//topics/admin/tutorials/upgrading/tutorial.html 2021-06-08 2024-11-25 10 True False True False 0 669 1037 2.966667 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 25 30 6.133333 0
Galaxy Server administration Performant Uploads with TUS https://training.galaxyproject.org//topics/admin/tutorials/tus/tutorial.html 2022-03-01 2024-06-14 17 True False True False 0 832 1224 5.266667 0
Galaxy Server administration Monitoring Galaxy and Pulsar with Sentry https://training.galaxyproject.org//topics/admin/tutorials/sentry/tutorial.html 2023-04-19 2024-03-18 6 True False False False 0 205 250 1.133333 0
Galaxy Server administration Galaxy Monitoring with Reports https://training.galaxyproject.org//topics/admin/tutorials/reports/tutorial.html 2019-01-31 2025-04-08 43 True False False False 0 489 655 2.800000 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 0 667 769 0.633333 0
Galaxy Server administration Training Infrastructure as a Service (TIaaS) https://training.galaxyproject.org//topics/admin/tutorials/tiaas/tutorial.html 2020-02-12 2024-12-18 38 True False True False 0 529 710 3.450000 0
Galaxy Server administration Mapping Jobs to Destinations using TPV https://training.galaxyproject.org//topics/admin/tutorials/job-destinations/tutorial.html 2021-01-17 2024-06-14 36 True False True False 0 1627 2558 3.150000 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 0 188 226 2.233333 0
Galaxy Server administration Customizing the look of Galaxy https://training.galaxyproject.org//topics/admin/tutorials/customization/tutorial.html 2023-04-16 2025-04-08 5 True False False False 0 557 685 4.700000 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 53 59 3.866667 0
Galaxy Server administration Use Apptainer containers for running Galaxy jobs https://training.galaxyproject.org//topics/admin/tutorials/apptainer/tutorial.html 2021-01-08 2025-04-08 13 True False True False 0 1020 1296 2.433333 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 3007 4932 1.066667 0
Galaxy Server administration Adding file-sources to Galaxy https://training.galaxyproject.org//topics/admin/tutorials/file_sources/tutorial.html 2025-01-20 2025-01-20 1 True False False False 0 44 61 3.583333 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 8211 16266 0.650000 0
Galaxy Server administration Reference Data with CVMFS without Ansible https://training.galaxyproject.org//topics/admin/tutorials/cvmfs-manual/tutorial.html 2020-06-17 2023-11-23 9 True False False False 0 379 514 2.566667 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 1590 2638 2.283333 0
Galaxy Server administration Managing Galaxy on Kubernetes https://training.galaxyproject.org//topics/admin/tutorials/k8s-managing-galaxy/tutorial.html 2019-07-02 2024-12-19 7 True False False False 0 653 963 2.183333 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 62 81 2.166667 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 46 54 0.583333 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 1092 1246 0.333333 0
Galaxy Server administration Deploying Tailscale/Headscale for private mesh networking https://training.galaxyproject.org//topics/admin/tutorials/wireguard-headscale/tutorial.html Data security, Software engineering 2022-09-21 2024-12-19 4 True False False False 0 2334 3017 0.450000 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 2758944 7389436 3.433333 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 1380027 3251527 2.433333 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 1394291 3283903 2.433333 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 1441212 3387299 2.433333 0
Assembly An Introduction to Genome Assembly https://training.galaxyproject.org//topics/assembly/tutorials/general-introduction/tutorial.html Visualisation, Sequence assembly validation, De-novo assembly, Statistical calculation, Sequence composition calculation, Formatting, Sequencing quality control, Validation 2017-05-23 2024-09-12 29 True True True True fastq_paired_end_interlacer, velveth, velvetg, quast, multiqc, fastqc Galaxy@AuBi, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 2777812 7416792 5.350000 0
Assembly Genome Assembly Quality Control https://training.galaxyproject.org//topics/assembly/tutorials/assembly-quality-control/tutorial.html Biodiversity, Sequence assembly, Data quality management Genome assembly, Visualisation, Sequence assembly validation, De-novo assembly, Phasing, k-mer counting, Scaffolding 2022-08-26 2025-06-04 6 True True False True meryl, busco, quast, chromeister, merqury UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au UseGalaxy.cz 0 1840210 4405458 4.583333 0
Assembly Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial resistance Sequence assembly visualisation, Visualisation, Sequence assembly validation, Cross-assembly, De-novo assembly, Box-Whisker plot plotting, Statistical calculation, Sequence composition calculation, Filtering, Mapping assembly, Genome assembly, Scatter plot plotting, Sequence alignment, Sequencing quality control, Sequencing error detection, Sequence contamination filtering, Read mapping 2021-03-24 2024-11-29 15 True False False True bwa_mem2, porechop, fastp, polypolish, CONVERTER_bz2_to_uncompressed, flye, bandage_image, filtlong, nanoplot, upload1, quast, fastqc UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr 0 10067 15121 3.450000 0
Assembly Large genome assembly and polishing https://training.galaxyproject.org//topics/assembly/tutorials/largegenome/tutorial.html Genomics, Sequence assembly, Biodiversity Sequence assembly visualisation, Visualisation, Sequence assembly validation, Cross-assembly, Sequence composition calculation, Mapping assembly, Scatter plot plotting, Validation, Variant calling, Sequence contamination filtering, De-novo assembly, Box-Whisker plot plotting, Base-calling, Statistical calculation, Genome assembly, Sequencing quality control, Pairwise sequence alignment, Sequence assembly 2023-03-06 2025-06-04 14 True False True True medaka_consensus_pipeline, fastp, meryl, flye, bandage_image, fasta-stats, nanoplot, minimap2, racon, busco, quast, multiqc, genomescope, barchart_gnuplot, fastqc UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 6922 9015 2.050000 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, Visualisation, Sequence assembly validation, De-novo assembly, Phasing, k-mer counting, Scaffolding, Data handling, Sequence alignment analysis, Genotyping, Genome assembly, Sequence alignment, Data parsing, Sequence trimming, Pairwise sequence alignment, Data deposition 2023-06-23 2025-06-04 8 True False True True bwa_mem2, pretext_snapshot, pretext_map, bandage_image, interactive_tool_blobtoolkit, CONVERTER_gz_to_uncompressed, collapse_dataset, meryl, merqury, tp_find_and_replace, blobtoolkit, minimap2, gfastats, genomescope, bg_diamond, smudgeplot, bellerophon, busco, samtools_stats, __EXTRACT_DATASET__ UseGalaxy.eu UseGalaxy.org.au 0 1814 2326 2.033333 0
Assembly Chloroplast genome assembly https://training.galaxyproject.org//topics/assembly/tutorials/chloroplast-assembly/tutorial.html Sequence assembly visualisation, Cross-assembly, De-novo assembly, Box-Whisker plot plotting, Genome indexing, Read alignment, Sequence assembly, Analysis, Mapping assembly, Genome assembly, Scatter plot plotting, Sequence alignment, Genome visualisation, Gene prediction, Genome annotation, Coding region prediction, Generation, Read mapping 2020-12-04 2025-05-15 21 True False True True prokka, bwa_mem, flye, bandage_image, bandage_info, fasta-stats, nanoplot, pilon, upload1, jbrowse UseGalaxy.eu GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 7722 11974 2.783333 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 compress_file, mitohifi UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 775 957 2.083333 0
Assembly Decontamination of a genome assembly https://training.galaxyproject.org//topics/assembly/tutorials/assembly-decontamination/tutorial.html Genomics, Sequence assembly, Biodiversity Data handling, Taxonomic classification 2024-09-04 2025-06-04 5 True False True True tp_sed_tool, Filter1, ncbi_blastn_wrapper, ncbi_dustmasker_wrapper, kraken2, tp_cat, Cut1, gfastats, parse_mito_blast UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 1462 1820 2.516667 0
Assembly Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology Sequence assembly visualisation, Visualisation, Sequence assembly validation, Statistical calculation, Sequence composition calculation, Genome assembly, Sequencing quality control, Sequence contamination filtering, Read mapping 2021-03-24 2025-03-20 16 True False True True fastp, bandage_image, bandage_info, upload1, quast, shovill, falco, fastqc UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 9706 15037 3.633333 0
Assembly Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Sequence assembly visualisation, Visualisation, Sequence assembly validation, Data handling, Local alignment, Sequence composition calculation, Formatting, Read pre-processing, Variant calling, Sequence contamination filtering, Primer removal, Sequence alignment analysis, Statistical calculation, Sequence file editing, Genome assembly, Sequence trimming, Sequencing quality control, Read mapping 2025-09-28 2025-09-28 0 True False True True megahit_contig2fastg, coverm_contig, megahit, seqtk_subseq, metaspades, bowtie2, bg_uniq, filter_tabular, quast, bandage_image, bandage_info, cutadapt, tp_cat, ngsutils_bam_filter, collection_column_join, random_lines1, fastqc, bamtools UseGalaxy.cz, UseGalaxy.eu 0 1 1 0.000000 0
Assembly De Bruijn Graph Assembly https://training.galaxyproject.org//topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html Genome assembly, Sequence assembly, Optimisation and refinement 2017-05-24 2024-02-01 25 True True False True spades, velvetoptimiser, fasta-stats Galaxy@AuBi, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz 0 2749440 7369687 5.116667 0
Assembly Unicycler Assembly https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html Sequence assembly, Genomics, Microbiology Visualisation, Sequence assembly validation, Statistical calculation, Sequence composition calculation, Genome assembly, Sequencing quality control, Gene prediction, Aggregation, Validation, Coding region prediction, Genome annotation 2017-10-11 2025-05-15 24 True True False True prokka, quast, multiqc, unicycler, fastqc UseGalaxy.eu, UseGalaxy.org.au Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2755933 7381639 4.583333 0
Assembly Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads https://training.galaxyproject.org//topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html Sequence assembly visualisation, Validation, Box-Whisker plot plotting, Data handling, Sequence file editing, Scatter plot plotting, Genome assembly, Sequencing quality control, Aggregation, Pairwise sequence alignment, Sequence contamination filtering, Read mapping 2020-04-21 2025-05-15 14 True True True True collapse_dataset, fasta_filter_by_length, fastp, bowtie2, __ZIP_COLLECTION__, bandage_image, bandage_info, nanoplot, fasterq_dump, samtools_fastx, minimap2, samtools_view, seqtk_sample, multiqc, unicycler, samtools_stats UseGalaxy.eu, UseGalaxy.org.au Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2748831 7369249 5.833333 0
Assembly Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step https://training.galaxyproject.org//topics/assembly/tutorials/vgp_genome_assembly/tutorial.html Genomics, Sequence assembly, Biodiversity Visualisation, Sequence assembly validation, De-novo assembly, Phasing, k-mer counting, Scaffolding, Data handling, Read pre-processing, Primer removal, Read binning, Genome assembly, Sequence alignment, Sequence trimming, Pairwise sequence alignment, Mapping 2021-06-04 2025-06-04 57 True False True True sort1, bwa_mem2, yahs, pretext_snapshot, hifiasm, pretext_map, salsa, collapse_dataset, meryl, Add_a_column1, bionano_scaffold, Convert characters1, collection_column_join, quast, merqury, bedtools_bamtobed, tp_find_and_replace, gfa_to_fa, minimap2, gfastats, genomescope, cat1, tp_grep_tool, tp_cut_tool, cutadapt, bellerophon, busco, purge_dups UseGalaxy.cz 0 15375 23337 2.000000 0
Assembly Genome assembly using PacBio data https://training.galaxyproject.org//topics/assembly/tutorials/hifi-assembly/tutorial.html Genomics, Sequence assembly, Biodiversity Genome assembly, Visualisation, Sequence assembly validation, Cross-assembly, De-novo assembly, Mapping assembly 2021-11-29 2025-06-04 2 True False False True hifiasm, gfa_to_fa, flye, fasta-stats, busco, quast UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au GalaxyTrakr, UseGalaxy.cz 0 604 711 1.400000 0
Assembly Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data https://training.galaxyproject.org//topics/assembly/tutorials/vgp_workflow_training/tutorial.html Sequence assembly, Chromosome conformation capture Visualisation, Sequence assembly validation 2022-04-06 2025-09-09 26 True False True False quast Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 3368 4691 2.733333 0
Assembly Making sense of a newly assembled genome https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html Sequence assembly, Genomics, Microbiology Sequence visualisation, Sequence alignment, Genome visualisation, Mapping, Read mapping 2018-06-14 2024-06-24 29 True False False True tp_sort_header_tool, circos_aln_to_links, Cut1, addValue, tp_replace_in_column, Grep1, collapse_dataset, tp_sed_tool, join1, datamash_ops, jbrowse, circos, tp_replace_in_line, circos_interval_to_tiles, fasta_compute_length, Filter1, bedtools_sortbed, fasta_filter_by_length, mergeCols1, cat1, tp_grep_tool, lastz_wrapper_2, bedtools_complementbed, bedtools_intersectbed, tp_cat, upload1, random_lines1 0 6674 12921 2.950000 0
Assembly Genome assembly and assembly QC - Introduction short version https://training.galaxyproject.org//topics/assembly/tutorials/assembly_and_qc_short/slides.html 2025-04-22 2025-04-23 2 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 283100 650696 2.233333 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 2722393 7291140 2.516667 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 2261589 5734622 2.483333 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_notebook, interactive_tool_copernicus, interactive_tool_panoply 0 286 332 0.533333 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 2136500 5335228 4.500000 0
Climate Analyse Argo data https://training.galaxyproject.org//topics/climate/tutorials/argo_pangeo/tutorial.html 2024-03-24 2025-05-10 2 True False False True interactive_tool_odv, xarray_metadata_info, xarray_coords_info, timeseries_extraction, argo_getdata UseGalaxy.eu 0 280 341 1.250000 0
Climate Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools https://training.galaxyproject.org//topics/climate/tutorials/pangeo/tutorial.html Visualisation 2022-02-18 2025-05-10 6 True True True True __MERGE_COLLECTION__, xarray_metadata_info, xarray_coords_info, climate_stripes, ggplot2_point, graphicsmagick_image_montage, xarray_mapplot, xarray_netcdf2netcdf, xarray_select, regexColumn1, __EXTRACT_DATASET__ UseGalaxy.eu UseGalaxy.cz 0 2136294 5334739 5.383333 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, interactive_tool_odv, divand_full_analysis UseGalaxy.eu 0 200 240 2.000000 0
Climate Nitrate DMQC for autonomous platforms such as Argo floats https://training.galaxyproject.org//topics/climate/tutorials/ocean_qcv_analysis/tutorial.html 2025-08-08 2025-09-16 3 True False False True tool_biogeochemical_calibration, harmonize_insitu_to_netcdf, tool_odv_history, interactive_tool_odv, tool_odv UseGalaxy.eu 0 23 34 3.233333 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 tp_find_and_replace, interactive_tool_panoply, __EXTRACT_DATASET__, xarray_metadata_info, ggplot2_point, xarray_select, ctsm_fates UseGalaxy.eu 0 2744579 7361976 4.366667 0
Climate Getting your hands-on climate data https://training.galaxyproject.org//topics/climate/tutorials/climate-101/tutorial.html Visualisation 2020-04-30 2025-05-10 14 True False False True interactive_tool_panoply, tp_awk_tool, psy_maps, ggplot2_point, climate_stripes, cds_essential_variability, datamash_ops, Grep1 UseGalaxy.eu 0 1026 1432 1.300000 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 2743129 7359676 2.516667 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 0 376 455 1.200000 0
Climate Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab https://training.galaxyproject.org//topics/climate/tutorials/fates-jupyterlab/tutorial.html 2020-10-25 2025-05-10 16 True False False False interactive_tool_jupyter_notebook UseGalaxy.eu, UseGalaxy.org.au 0 541 948 1.833333 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 spocc_occ, c3s, obis_data, argo_getdata UseGalaxy.eu 0 87 121 2.916667 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 0 164 206 0.900000 0
Climate Visualize Climate data with Panoply netCDF viewer https://training.galaxyproject.org//topics/climate/tutorials/panoply/tutorial.html 2020-03-05 2025-05-10 18 True False False False interactive_tool_panoply UseGalaxy.eu 0 6244 10203 0.800000 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 37 50 0.116667 0
Galaxy Community Building Creation of resources listing Galaxy workflow for your community https://training.galaxyproject.org//topics/community/tutorials/community-workflow-table/tutorial.html 2025-09-17 2025-09-17 1 True False False False 0 5 6 0.000000 0
Galaxy Community Building 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 36 51 12.316667 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 2025-09-17 3 True False False False 0 69 91 3.383333 0
Galaxy Community Building Creation of a Galaxy tutorial table for your community https://training.galaxyproject.org//topics/community/tutorials/community-tutorial-table/tutorial.html 2025-09-17 2025-09-17 1 True False False False 0 4 5 0.000000 0
Galaxy Community Building What's a Special Interest Group? https://training.galaxyproject.org//topics/community/tutorials/sig_define/tutorial.html 2024-07-08 2024-12-20 3 True False False False 0 73 104 4.116667 0
Galaxy Community Building Creating a Special Interest Group https://training.galaxyproject.org//topics/community/tutorials/sig_create/tutorial.html 2024-07-08 2024-12-20 2 True False False False 0 92 101 1.950000 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 sort1, ctb_alignit, rdconf, tp_cat, openbabel_addh, split_file_to_collection UseGalaxy.cz 0 1192 1734 2.383333 0
Computational chemistry Data management in Medicinal Chemistry https://training.galaxyproject.org//topics/computational-chemistry/tutorials/med-chem-data/tutorial.html 2024-01-08 2024-09-13 4 True False True True chembl, md_converter, get_pdb, ctb_im_rxn_maker, openbabel_compound_convert, ctb_silicos_qed, openbabel_svg_depiction UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.no 0 422 509 1.766667 0
Computational chemistry Protein-ligand docking https://training.galaxyproject.org//topics/computational-chemistry/tutorials/cheminformatics/tutorial.html 2019-10-19 2023-11-09 16 True False False True chembl, prepare_box, openbabel_compound_convert, ctb_change_title, collapse_dataset, ctb_online_data_fetch, ctb_remIons, ctb_chemfp_nxn_clustering, get_pdb, ctb_filter, ctb_np-likeness-calculator, sdf_to_tab, tp_find_and_replace, ctb_remDuplicates, prepare_receptor, openbabel_svg_depiction, ctb_chemfp_mol2fps, ctb_chemfp_butina_clustering, tp_grep_tool, docking, fpocket, ctb_obgrep, ctb_compound_convert, tp_cat 0 18843 32261 1.533333 0
Computational chemistry Analysis of molecular dynamics simulations https://training.galaxyproject.org//topics/computational-chemistry/tutorials/analysis-md-simulations/tutorial.html 2019-06-03 2023-11-09 13 True False False True bio3d_rmsf, mdanalysis_cosine_analysis, bio3d_rmsd, mdanalysis_rdf, mdanalysis_distance, mdanalysis_ramachandran_plot, bio3d_pca, mdanalysis_dihedral UseGalaxy.eu Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 32166 57149 1.233333 0
Computational chemistry Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring https://training.galaxyproject.org//topics/computational-chemistry/tutorials/covid19-docking/tutorial.html 2020-03-27 2023-11-09 10 True False False True rdock_rbcavity, collapse_dataset, xchem_transfs_scoring, rxdock_rbdock, enumerate_charges, ctb_frankenstein_ligand, xchem_pose_scoring, sucos_max_score, openbabel_compound_convert, rxdock_rbcavity, split_file_to_collection, rdock_rbdock 0 3146 5194 3.050000 0
Computational chemistry Running molecular dynamics simulations using GROMACS https://training.galaxyproject.org//topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.html 2019-06-03 2023-11-09 15 True False False True gmx_editconf, tp_grep_tool, gmx_sim, gmx_setup, get_pdb, gmx_solvate, gmx_em UseGalaxy.eu, UseGalaxy.org.au Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 26210 47193 1.433333 0
Computational chemistry High Throughput Molecular Dynamics and Analysis https://training.galaxyproject.org//topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html 2020-05-20 2025-04-08 19 True False True True bio3d_rmsf, tp_grep_tool, gmx_merge_topology_files, mdanalysis_cosine_analysis, md_converter, gmx_energy, vmd_hbonds, ambertools_acpype, bio3d_rmsd, bio3d_pca_visualize, gmx_setup, get_pdb, gmx_sim, openbabel_compound_convert, gmx_solvate, gmx_em, gmx_editconf, bio3d_pca UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 10550 18638 2.450000 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 4167 7009 1.216667 0
Computational chemistry Setting up molecular systems https://training.galaxyproject.org//topics/computational-chemistry/tutorials/setting-up-molecular-systems/tutorial.html 2019-06-03 2023-11-09 14 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1762 2380 1.683333 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 2743210 7359771 3.683333 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 2743129 7359677 2.516667 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 5324 6352 0.783333 0
Contributing to the Galaxy Training Material Teaching Python https://training.galaxyproject.org//topics/contributing/tutorials/python/tutorial.html 2022-10-19 2023-11-23 4 True False False False 0 239 532 1.183333 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 0 260 340 4.000000 0
Contributing to the Galaxy Training Material Contributing with GitHub via its interface https://training.galaxyproject.org//topics/contributing/tutorials/github-interface-contribution/tutorial.html 2018-06-12 2023-11-09 17 True False False False 0 676 1027 2.366667 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 72 89 3.100000 0
Contributing to the Galaxy Training Material Preview the GTN website as you edit your training material https://training.galaxyproject.org//topics/contributing/tutorials/rendering_gtn/tutorial.html 2025-03-14 2025-07-02 3 True False True False 0 305 429 5.316667 0
Contributing to the Galaxy Training Material Creating Interactive Galaxy Tours https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-tours/tutorial.html 2017-06-25 2025-04-08 13 True False False False 0 289 447 2.500000 0
Contributing to the Galaxy Training Material GTN Metadata https://training.galaxyproject.org//topics/contributing/tutorials/schemas/tutorial.html 2022-06-02 2024-10-15 8 True False False False 0 258 344 2.950000 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 55 97 0.850000 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 0 547 738 1.666667 0
Contributing to the Galaxy Training Material Including a new topic https://training.galaxyproject.org//topics/contributing/tutorials/create-new-topic/tutorial.html 2018-06-04 2025-03-14 32 True False False False 0 1208 1666 0.566667 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 0 566 756 2.900000 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 30 35 0.816667 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 97 111 0.350000 0
Contributing to the Galaxy Training Material Creating a new tutorial https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial/tutorial.html Sequence trimming, Sequence file editing, Primer removal, Data handling, Read pre-processing, Read mapping 2018-06-20 2025-03-14 32 True False True True c3s, fastq_to_tabular, tp_sed_tool, seqtk_subseq, Filter1, bowtie2, tp_cut_tool, cutadapt, tp_cat, Cut1, tp_sorted_uniq, random_lines1, bam_to_sam 0 1749 2597 4.983333 0
Contributing to the Galaxy Training Material FAIR Galaxy Training Material https://training.galaxyproject.org//topics/contributing/tutorials/fair-gtn/tutorial.html 2025-09-28 2025-09-28 0 True False False False 0 0 0 0.000000 0
Contributing to the Galaxy Training Material Single Cell Publication - Data Analysis https://training.galaxyproject.org//topics/contributing/tutorials/meta-analysis-data/tutorial.html 2024-11-07 2024-11-07 1 True False False False 0 37 39 0.900000 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 35 35 0.000000 0
Contributing to the Galaxy Training Material Creating content in Markdown https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-content/tutorial.html Validation, Sequencing quality control 2017-06-25 2025-04-08 85 True False False False multiqc, upload1 0 3673 9671 2.100000 0
Contributing to the Galaxy Training Material Creating Slides https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-slides/slides.html 2018-06-13 2024-11-08 17 False True True False 0 2743129 7359677 2.516667 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 82 101 5.366667 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 Variant classification, Tree-based sequence alignment 2021-06-08 2025-04-08 9 True False True True collapse_dataset, snpSift_filter, compose_text_param, pangolin, bcftools_consensus UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org.au MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr 0 2814 3419 2.066667 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 2422250 6269103 3.883333 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, Variant classification, Tree-based sequence alignment, Variant calling 2021-06-30 2025-03-28 18 True False True False upload1, Filter1, nextclade, datamash_ops, fasta_regex_finder, pangolin UseGalaxy.cz, UseGalaxy.eu 0 7243 13014 3.450000 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 Genome indexing, Data handling, Formatting, Sequencing quality control, Sequence alignment, Validation, Sequence contamination filtering, SNP detection, Generation, Read mapping 2020-06-24 2024-06-14 16 True False True True lofreq_indelqual, fastp, Filter1, bwa_mem, snpeff_sars_cov_2, tp_cut_tool, lofreq_viterbi, picard_MarkDuplicates, fasterq_dump, lofreq_call, multiqc, samtools_stats, Grep1, snpSift_extractFields UseGalaxy.eu MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 13562 20447 2.883333 0
Sequence analysis Removal of human reads from SARS-CoV-2 sequencing data https://training.galaxyproject.org//topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html Read mapping, Sequence alignment, Data handling, Genome indexing, Generation, Sequence file editing 2021-08-04 2023-11-09 5 True False False True trimmomatic, __UNZIP_COLLECTION__, seqtk_subseq, bwa_mem, __ZIP_COLLECTION__, samtools_fastx, Grep1, tp_replace_in_line UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 3979 5519 2.216667 0
Using Galaxy and Managing your Data SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis https://training.galaxyproject.org//topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.html Data handling, SNP detection 2021-05-31 2024-06-14 12 True True True False snpeff_sars_cov_2, fasterq_dump, tp_cat, fastq_dump, jq, query_tabular, fastq_to_fasta_python UseGalaxy.be, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2523718 6605089 4.250000 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, Genome visualisation, Sequencing quality control, Genome indexing, Statistical calculation, Sequence composition calculation, Generation, Read mapping 2023-07-10 2024-02-29 2 True False False False bwa_mem, jbrowse, fastqc UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au Galaxy@AuBi, Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz 0 1197 1554 4.183333 0
Foundations of Data Science Data Manipulation Olympics https://training.galaxyproject.org//topics/data-science/tutorials/data-manipulation-olympics/tutorial.html 2025-09-28 2025-09-28 0 True False False True tp_sort_header_tool, {{version_split}}, Remove beginning1, Cut1, tp_sorted_uniq, {{version_cat}}, Add_a_column1, join1, {{version_wc}}, {{version_replace_text_line}}, datamash_ops, {{version_filter}}, {{version_join}}, {{version_replace_text_column}}, {{version_cut_columns}}, {{version_datamash}}, {{version_remove_beginning}}, tabular_to_csv, {{version_cut_advanced}}, Filter1, {{version_unique}}, {{version_count}}, {{version_compute}}, Count1, {{version_remove_columns_by_header}}, regexColumn1, {{version_sort}}, Show beginning1, cat1, Grouping1, {{version_paste}}, {{version_select_first}}, tp_split_on_column, tp_cat, upload1, wc_gnu 0 1 1 0.000000 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 1019999 2458643 3.566667 0
Foundations of Data Science Learning about one gene across biological resources and formats https://training.galaxyproject.org//topics/data-science/tutorials/online-resources-gene/tutorial.html 2023-09-07 2023-11-09 3 True True True False ncbi_blastp_wrapper Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, PepSimili, UseGalaxy.no 0 1177725 2808995 5.616667 0
Foundations of Data Science Version Control with Git https://training.galaxyproject.org//topics/data-science/tutorials/bash-git/tutorial.html 2022-07-06 2023-10-23 6 True False False False interactive_tool_rstudio UseGalaxy.eu, UseGalaxy.org.au 0 271 502 0.650000 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 97 113 0.633333 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 0 500 682 0.483333 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 0 663 717 0.383333 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 8634 11290 2.016667 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 0 928 1186 2.383333 0
Foundations of Data Science Introduction to SQL https://training.galaxyproject.org//topics/data-science/tutorials/sql-basic/tutorial.html 2021-10-11 2024-12-13 8 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 549 674 1.416667 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 1276 1667 1.900000 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 1120 1587 2.816667 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 2024-12-05 5 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 414 440 0.383333 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 0 914 1143 1.266667 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 3298 4273 0.916667 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 1985 2262 0.566667 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 0 130 375 0.366667 0
Foundations of Data Science R basics in Galaxy https://training.galaxyproject.org//topics/data-science/tutorials/r-basics/tutorial.html 2019-10-08 2024-06-14 11 True False True False interactive_tool_rstudio UseGalaxy.eu, UseGalaxy.org.au 0 2635 3563 2.150000 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 1410 1773 0.550000 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 0 594 755 0.533333 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 0 593 671 1.033333 0
Foundations of Data Science Advanced R in Galaxy https://training.galaxyproject.org//topics/data-science/tutorials/r-advanced/tutorial.html 2019-12-09 2024-10-15 11 True False True False interactive_tool_rstudio UseGalaxy.eu, UseGalaxy.org.au 0 1497 2351 2.633333 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 0 951 1119 0.750000 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 0 227 288 2.116667 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 0 508 686 1.366667 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 0 383 661 6.133333 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 0 105 111 0.566667 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 0 583 766 0.866667 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 0 550 672 1.600000 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 0 768 861 0.550000 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 0 312 356 0.816667 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 0 107 116 0.416667 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 2057 2436 0.533333 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 0 111 122 0.850000 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 0 256 307 0.850000 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 0 365 440 1.700000 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 39 45 1.266667 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 9 9 0.100000 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 0 528 617 0.666667 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 0 562 644 0.316667 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 0 223 265 1.700000 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 0 627 677 0.566667 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 1306 1421 0.400000 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 0 169 191 1.483333 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 0 607 643 0.183333 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 0 214 237 0.400000 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 0 512 554 0.416667 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 1143 1328 0.316667 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 0 173 186 0.583333 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 0 838 902 0.300000 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 2743129 7359679 2.516667 0
Development in Galaxy Galaxy Code Architecture https://training.galaxyproject.org//topics/dev/tutorials/architecture/slides.html 2017-06-20 2024-06-14 34 False True False False 0 2743129 7359679 2.516667 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 2743812 7360571 4.666667 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 2743818 7360502 3.466667 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 2743129 7359679 2.516667 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 2743129 7359679 2.516667 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 2743129 7359679 2.516667 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 2743458 7360159 4.550000 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 2531491 6630378 4.933333 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 2743313 7359926 3.866667 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 2743129 7359679 2.516667 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 2743132 7359683 2.516667 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 2743129 7359679 2.516667 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 0 395 479 1.666667 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 0 221 330 3.116667 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 1142 1527 2.850000 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 0 212 299 3.550000 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 2707 4384 2.583333 0
Development in Galaxy Debugging Galaxy https://training.galaxyproject.org//topics/dev/tutorials/debugging/tutorial.html 2021-06-15 2024-06-14 14 True False False False 0 578 1182 2.933333 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 0 235 280 2.750000 0
Development in Galaxy Contributing a New Feature to Galaxy Core https://training.galaxyproject.org//topics/dev/tutorials/core-contributing/tutorial.html 2021-06-08 2025-03-14 9 True False False False 0 696 1050 2.700000 0
Development in Galaxy Writing Automated Tests for Galaxy https://training.galaxyproject.org//topics/dev/tutorials/writing_tests/tutorial.html 2022-07-15 2024-06-25 5 True False False False 0 251 679 2.416667 0
Development in Galaxy Setting up a dev Onedata instance https://training.galaxyproject.org//topics/dev/tutorials/onedata-dev-instance/tutorial.html 2025-03-24 2025-04-08 2 True False False False 0 18 21 3.900000 0
Digital Humanities Introduction to Digital Humanities in Galaxy https://training.galaxyproject.org//topics/digital-humanities/tutorials/introduction_to_dh/tutorial.html 2025-09-11 2025-09-16 3 True False False True tp_find_and_replace, tp_grep_tool, wordcloud, Remove beginning1, diff, wc_gnu, tp_replace_in_line UseGalaxy.eu, UseGalaxy.org.au 0 30 37 3.116667 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, Filter1, wordcloud, Add_a_column1, Cut1, datamash_ops, diff, tp_replace_in_line 0 132 159 1.833333 0
Digital Humanities OpenRefine Tutorial for researching cultural data https://training.galaxyproject.org//topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html 2025-09-24 2025-09-24 1 True False False True tp_sort_header_tool, tp_grep_tool, wordcloud, Remove beginning1, filter_tabular, interactive_tool_openrefine, Cut1, datamash_ops, compose_text_param, param_value_from_file, regexColumn1, barchart_gnuplot, tp_head_tool UseGalaxy.eu 0 3 4 0.000000 0
Ecology Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities https://training.galaxyproject.org//topics/ecology/tutorials/MetaShARK_tutorial/tutorial.html 2024-03-04 2024-09-10 7 True False False False interactive_tool_metashark UseGalaxy.eu, UseGalaxy.fr 0 173 214 2.116667 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 60 85 0.933333 0
Ecology Sentinel 2 biodiversity https://training.galaxyproject.org//topics/ecology/tutorials/remote-sensing/tutorial.html 2023-04-13 2025-06-03 6 True False False True srs_process_data, srs_preprocess_s2, srs_diversity_maps, srs_global_indices, srs_pca, srs_spectral_indices UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 576 746 1.500000 0
Ecology Compute and analyze biodiversity metrics with PAMPA toolsuite https://training.galaxyproject.org//topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html 2020-11-19 2025-09-03 23 True False True True tp_sort_header_tool, mergeCols1, Filter1, datamash_transpose, tp_cut_tool, Count1, tp_easyjoin_tool, pampa_communitymetrics, tp_cat, pampa_glmcomm, pampa_glmsp, pampa_plotglm, regexColumn1, pampa_presabs, regex1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au 0 1075 1422 1.850000 0
Ecology RAD-Seq to construct genetic maps https://training.galaxyproject.org//topics/ecology/tutorials/genetic-map-rad-seq/tutorial.html Data handling 2017-02-14 2025-06-03 13 True False False True stacks_denovomap, stacks_genotypes UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 867 1222 1.300000 0
Ecology Champs blocs indicators https://training.galaxyproject.org//topics/ecology/tutorials/champs-blocs/tutorial.html 2023-01-04 2025-06-03 11 True False False True cb_div, cb_qecb, cb_ivr, cb_dissim, cb_eco 0 161 310 1.966667 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 spocc_occ, tp_find_and_replace, tabular_to_csv, Filter1, tp_cut_tool, interactive_tool_wallace UseGalaxy.eu, UseGalaxy.fr 0 3103 4714 1.166667 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 cdo_operations, xarray_metadata_info, xarray_coords_info, xarray_mapplot, graphicsmagick_image_montage UseGalaxy.eu UseGalaxy.cz 0 2323 2693 0.466667 0
Ecology RAD-Seq de-novo data analysis https://training.galaxyproject.org//topics/ecology/tutorials/de-novo-rad-seq/tutorial.html Data handling, Statistical calculation, Sequencing quality control, Sequence composition calculation 2017-02-14 2025-06-03 14 True False False True stacks_procrad, stacks_denovomap, stacks_populations, fastqc UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 2611 4190 2.083333 0
Ecology Regional GAM https://training.galaxyproject.org//topics/ecology/tutorials/regionalGAM/tutorial.html Ecology Visualisation 2019-07-04 2025-06-03 18 True False False True mergeCols1, flight-curve, Filter1, tp_awk_tool, regionalgam_autocor_acf, Remove beginning1, Count1, ggplot2_point, csv2tab_R, regionalgam_plot_trend, regionalgam_gls, regionalgam_ab_index, regionalgam_flight_curve, regionalgam_glmmpql, regexColumn1, Paste1, tab2csv_R 0 330 444 3.600000 0
Ecology Metabarcoding/eDNA through Obitools https://training.galaxyproject.org//topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html Sequence analysis, Sequencing quality control, Sequence composition calculation, Statistical calculation 2022-02-28 2025-06-03 12 True False True True obi_grep, obi_tab, obi_uniq, Filter1, ncbi_blastn_wrapper, obi_clean, join1, obi_ngsfilter, fastq_groomer, unzip, obi_stat, Cut1, obi_annotate, seq_filter_by_id, obi_illumina_pairend, wc_gnu, fastqc UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 4347 6052 1.950000 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 obisindicators, obis_data, tp_cut_tool UseGalaxy.eu 0 300 378 2.166667 0
Ecology Preparing genomic data for phylogeny reconstruction https://training.galaxyproject.org//topics/ecology/tutorials/phylogeny-data-prep/tutorial.html Sequence assembly validation, Multiple sequence alignment, Genetic variation analysis, Sequence analysis, Sequence clustering, Genome annotation 2022-10-21 2025-06-03 5 True False False True glimmer_gbk_to_orf, collapse_dataset, clustalw, phykit_alignment_based, Filter1, funannotate_predict, proteinortho, clipkit, regex1, proteinortho_grab_proteins, busco, repeatmasker_wrapper, tp_replace_in_line 0 2120 2908 2.733333 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, mergeCols1, ecoregion_GeoNearestNeighbor, tp_cut_tool, filter_tabular, unzip, ecoregion_brt_analysis, ecoregion_clara_cluster, ecoregion_cluster_estimate, ecoregion_eco_map, regexColumn1 UseGalaxy.eu 0 226 312 3.383333 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, ecoregion_GeoNearestNeighbor, Filter1, column_remove_by_header, tp_cut_tool, WormsMeasurements, unzip, ecoregion_brt_analysis, ClaraGuess, ecoregion_eco_map, regexColumn1 UseGalaxy.eu 0 23 25 4.766667 0
Ecology Checking expected species and contamination in bacterial isolate https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Statistical calculation, Expression analysis, Taxonomic classification, Cross-assembly 2024-03-04 2024-06-27 4 True False False True kraken2, upload1, recentrifuge, est_abundance UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz 0 773 1033 3.350000 0
Ecology RAD-Seq Reference-based data analysis https://training.galaxyproject.org//topics/ecology/tutorials/ref-based-rad-seq/tutorial.html Data handling, Genome indexing, Statistical calculation, Sequence composition calculation, Sequence alignment, Sequencing quality control, Validation, Generation, Read mapping 2017-02-14 2025-06-03 14 True False False True Summary_Statistics1, tp_sort_header_tool, stacks_populations, cat1, Filter1, Count1, stacks_refmap, bwa, stacks_procrad, Cut1, Convert characters1, bwa_wrapper, addValue, multiqc, regex_replace, Grep1, fastqc, tp_replace_in_line 0 2901 4577 1.750000 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 93 100 2.233333 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 ncbi_blastn_wrapper, cshl_fastq_to_fasta, Count1, fastp UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.no 0 349 443 0.833333 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 spocc_occ, Summary_Statistics1, Filter1, gdal_ogr2ogr, Count1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no 0 609 759 0.900000 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 0 177 215 1.216667 0
Ecology Marine Omics identifying biosynthetic gene clusters https://training.galaxyproject.org//topics/ecology/tutorials/marine_omics_bgc/tutorial.html Protein feature detection, Sequence motif recognition, Genome annotation 2024-08-19 2025-06-03 3 True False False True prodigal, SanntiS_marine, sanntis_marine, interproscan, regex1 0 152 178 2.666667 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, ecology_presence_abs_abund, tp_cut_tool, Remove beginning1, ecology_beta_diversity, ecology_link_between_var, ecology_stat_presence_abs, regexColumn1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr 0 1570 2206 2.766667 0
Ecology Data submission using ENA upload Tool https://training.galaxyproject.org//topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html Visualisation, Sequence trimming, Sequencing quality control, Primer removal, Validation, Read pre-processing, Read mapping 2024-12-13 2025-03-20 2 True False False False ab1_fastq_converter, fastq_filter, collection_element_identifiers, ncbi_blastn_wrapper, bg_uniq, cutadapt, fastq_groomer, __RELABEL_FROM_FILE__, regex1, __FILTER_EMPTY_DATASETS__, multiqc, Paste1, falco, fastq_to_fasta_python UseGalaxy.eu UseGalaxy.cz 0 173 179 0.366667 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 0 216 279 1.400000 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 0 128 155 0.933333 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 0 260 301 1.666667 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 0 355 422 1.100000 0
Statistics and machine learning Pretraining a Large Language Model (LLM) from Scratch on DNA Sequences https://training.galaxyproject.org//topics/statistics/tutorials/genomic-llm-pretraining/tutorial.html 2025-04-17 2025-05-22 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 623 727 1.766667 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 1872 2218 0.666667 0
Teaching and Hosting Galaxy training Train-the-Trainer: putting it all together https://training.galaxyproject.org//topics/teaching/tutorials/workshop-final-exercise/tutorial.html 2023-06-12 2025-03-11 3 True False False False 0 76 88 0.683333 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 1566 1849 0.750000 0
Teaching and Hosting Galaxy training Assessment and feedback in training and teachings https://training.galaxyproject.org//topics/teaching/tutorials/assessment/tutorial.html 2022-09-23 2025-03-11 11 True False False False 0 1224 1420 0.750000 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 0 393 456 1.300000 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 362560 842782 2.300000 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 97 100 2.700000 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 362561 842787 2.416667 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 90 101 0.950000 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 16 18 0.050000 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 362587 842825 4.116667 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 Primer removal, Statistical calculation, Peak calling, Sequence composition calculation, Gene regulatory network analysis, Structure visualisation, Read mapping, Sequence trimming, Genome visualisation, Sequencing quality control, Enrichment analysis, Read pre-processing, Mapping, Pathway visualisation 2018-09-17 2025-04-08 14 True True False True cat1, Filter1, deeptools_plot_fingerprint, bowtie2, bedtools_sortbed, trim_galore, bbgtobigwig, jbrowse2, samtools_idxstats, deeptools_multi_bam_summary, macs2_callpeak, bedtools_mergebed, deeptools_plot_correlation, deeptools_bam_compare, deeptools_compute_matrix, deeptools_bam_coverage, deeptools_plot_heatmap, fastqc UseGalaxy.eu 0 2748998 7371342 6.200000 0
Epigenetics CUT&RUN data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/cut_and_run/tutorial.html Visualisation, Primer removal, Read pre-processing, Data handling, Sequence alignment analysis, Peak calling, Gene regulatory network analysis, Formatting, Sequence trimming, Sequencing quality control, Enrichment analysis, Validation, Mapping, Read mapping 2024-03-06 2025-03-19 5 True False False True wig_to_bigWig, bamFilter, datamash_transpose, deeptools_plot_fingerprint, trim_galore, multiqc, Grep1, bowtie2, idr, bedtools_bamtobed, picard_MarkDuplicates, __FLATTEN__, meme_chip, deeptools_compute_matrix, pe_histogram, __EXTRACT_DATASET__, bedtools_intersectbed, macs2_callpeak, Extract genomic DNA 1, deeptools_plot_heatmap, falco 0 5520 7032 1.383333 0
Epigenetics ATAC-Seq data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/atac-seq/tutorial.html Visualisation, Primer removal, Data handling, Sequence alignment analysis, Statistical calculation, Peak calling, Sequence composition calculation, Gene regulatory network analysis, Formatting, Sequence trimming, Sequencing quality control, Enrichment analysis, Read pre-processing, Mapping, Read mapping 2019-09-02 2024-08-08 23 True True True True wig_to_bigWig, pe_histogram, tp_sort_header_tool, bamFilter, Filter1, bowtie2, cutadapt, pygenomeTracks, picard_MarkDuplicates, bedtools_intersectbed, samtools_idxstats, Cut1, macs2_callpeak, bedtools_bamtobed, deeptools_compute_matrix, Grep1, deeptools_plot_heatmap, fastqc 0 2805812 7473075 4.316667 0
Epigenetics Hi-C analysis of Drosophila melanogaster cells using HiCExplorer https://training.galaxyproject.org//topics/epigenetics/tutorials/hicexplorer/tutorial.html Formatting, Visualisation, Read mapping 2018-02-23 2025-08-11 30 True False False True hicexplorer_hiccorrectmatrix, hicexplorer_hicfindtads, hicexplorer_hicplotmatrix, bowtie2, hicexplorer_hicfindrestrictionsites, hicexplorer_hicinfo, hicexplorer_hicbuildmatrix, hicexplorer_hicmergematrixbins, pygenomeTracks, hicexplorer_hicpca, hicexplorer_hicdetectloops UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no 0 7267 12306 1.516667 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 Primer removal, Read pre-processing, Statistical calculation, Peak calling, Sequence composition calculation, Gene regulatory network analysis, Sequence trimming, Sequencing quality control, Enrichment analysis, Read mapping 2017-09-18 2025-04-08 10 True False False True deeptools_compute_matrix, deeptools_plot_fingerprint, bowtie2, trim_galore, samtools_idxstats, deeptools_multi_bam_summary, macs2_callpeak, deeptools_plot_correlation, deeptools_bam_compare, deeptools_compute_gc_bias, deeptools_bam_coverage, deeptools_plot_heatmap, fastqc, bam_to_sam UseGalaxy.be Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 1889 2800 2.800000 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 Genome indexing, Statistical calculation, Peak calling, Sequence composition calculation, Gene regulatory network analysis, Sequence alignment, Sequencing quality control, Enrichment analysis, Mapping, Generation, Read mapping 2016-12-20 2025-04-08 11 True False False True trimmomatic, deeptools_compute_matrix, deeptools_plot_fingerprint, deeptools_correct_gc_bias, bedtools_intersectbed, bwa, deeptools_multi_bam_summary, macs2_callpeak, deeptools_plot_correlation, deeptools_bam_compare, deeptools_compute_gc_bias, samtools_idxstats, deeptools_plot_heatmap, fastqc UseGalaxy.be, UseGalaxy.fr Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 7066 12984 3.300000 0
Epigenetics Infinium Human Methylation BeadChip https://training.galaxyproject.org//topics/epigenetics/tutorials/ewas-suite/tutorial.html 2018-08-27 2024-10-15 21 True True False True chipeakanno_annopeaks, clusterprofiler_go, Remove beginning1, clusterprofiler_bitr, Cut1, minfi_analysis UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2745158 7362882 4.416667 0
Epigenetics DNA Methylation data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/methylation-seq/tutorial.html Epigenomics Visualisation, Sequencing quality control, Statistical calculation, Sequence composition calculation, Read mapping 2017-02-16 2025-04-03 24 True False False True wig_to_bigWig, pileometh, tp_awk_tool, bwameth, tp_tail_tool, falco, deeptools_plot_profile, metilene, deeptools_compute_matrix, replace_column_with_key_value_file, fastqc 0 14598 24441 2.050000 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 2743129 7359682 2.516667 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 2743129 7359682 2.516667 0
Evolution Phylogenetics - Back to basics https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo/tutorial.html Phylogenetic tree analysis, Phylogenetic tree reconstruction, Sequence analysis, Phylogenetic analysis, Multiple sequence alignment, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation 2024-05-10 2024-05-10 1 True False False True fasttree, rbc_mafft, newick_display, iqtree UseGalaxy.eu, UseGalaxy.org.au GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 4329 5583 1.966667 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 Variant calling, Phylogenetic tree visualisation, Antimicrobial resistance prediction, Phylogenetic tree generation 2022-03-16 2025-05-26 13 True False False True snp_sites, Grep1, collapse_dataset, tp_sed_tool, tp_easyjoin_tool, tb_profiler_profile, tp_replace_in_line, trimmomatic, tb_variant_filter, bcftools_consensus, tp_grep_tool, __MERGE_COLLECTION__, samtools_view, tp_cat, snp_dists, upload1, clustering_from_distmat, addName, snippy UseGalaxy.eu 0 2582 3721 2.866667 0
Evolution Tree thinking for tuberculosis evolution and epidemiology https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html Genomics, Microbiology, Phylogeny, Infectious disease Sequence analysis, Phylogenetic tree analysis 2022-03-16 2025-06-04 12 True False False True raxml, upload1, interactive_tool_rstudio UseGalaxy.eu 0 2136 3089 2.283333 0
Evolution Phylogenetics - Back to Basics - Introduction https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo-intro/slides.html 2024-05-10 2024-05-10 1 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 818414 1980985 2.483333 0
Evolution Phylogenetic analysis for bacterial comparative genomics https://training.galaxyproject.org//topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html Genomics, Microbiology, Phylogeny Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree generation (from molecular sequences) 2025-03-14 2025-03-14 1 True False False False fasttree, upload1 GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no Galaxy@AuBi 0 71 91 3.266667 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 818414 1980985 2.483333 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 818414 1980985 2.483333 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 818414 1980985 2.483333 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 818414 1980985 2.483333 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 818414 1980985 2.483333 0
FAIR Data, Workflows, and Research Data management in Medicinal Chemistry https://training.galaxyproject.org//topics/fair/tutorials/med-chem-data/tutorial.html 2025-09-28 2025-09-28 0 True False True True chembl, md_converter, get_pdb, ctb_im_rxn_maker, openbabel_compound_convert, ctb_silicos_qed, openbabel_svg_depiction UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.no 0 0 0 0.000000 0
FAIR Data, Workflows, and Research An earth-system RO-Crate https://training.galaxyproject.org//topics/fair/tutorials/earth_system_rocrate/slides.html 2024-12-02 2024-12-02 1 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 513044 1211288 2.366667 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 0 565 752 1.750000 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 0 794 1031 1.800000 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 0 483 569 0.966667 0
FAIR Data, Workflows, and Research Introduction to Data Management Plan (DMP) for Peatland Research and PeatDataHub https://training.galaxyproject.org//topics/fair/tutorials/data-management-peatlands/tutorial.html 2024-09-13 2024-09-13 1 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 80 109 2.600000 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 0 324 416 1.383333 0
FAIR Data, Workflows, and Research FAIR and its Origins https://training.galaxyproject.org//topics/fair/tutorials/fair-origin/tutorial.html 2024-03-26 2024-03-27 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 123 139 0.666667 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 0 284 372 1.783333 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 573493 1355589 4.733333 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 0 346 430 2.866667 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 0 226 252 1.416667 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 0 259 316 2.433333 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 0 158 193 1.416667 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 0 129 155 2.666667 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 67 71 1.683333 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 0 352 408 1.250000 0
FAIR Data, Workflows, and Research FAIR Bioimage Metadata https://training.galaxyproject.org//topics/fair/tutorials/bioimage-metadata/tutorial.html 2023-09-13 2024-10-15 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 264 317 2.350000 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 49 58 3.416667 0
FAIR Data, Workflows, and Research Submitting workflows to LifeMonitor https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-submitting-life-monitor/tutorial.html 2023-05-11 2024-09-26 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 43 51 4.750000 0
FAIR Data, Workflows, and Research REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data https://training.galaxyproject.org//topics/fair/tutorials/bioimage-REMBI/tutorial.html 2023-09-13 2024-10-15 6 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 259 293 2.350000 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 0 140 158 0.616667 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 0 226 279 1.450000 0
Using Galaxy and Managing your Data Workflow Reports https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-reports/tutorial.html Visualisation 2022-06-02 2024-06-14 9 True False True True csv_to_tabular, Grouping1, Remove beginning1, ggplot2_point, Cut1, datamash_ops, upload1, tp_sorted_uniq UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz 0 835 1163 2.933333 0
Using Galaxy and Managing your Data Creating, Editing and Importing Galaxy Workflows https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-editor/tutorial.html 2020-07-17 2023-11-09 12 True False False True Paste1, tp_tac, Show beginning1 Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au MISSISSIPPI 0 5769 7193 3.000000 0
Using Galaxy and Managing your Data InterMine integration with Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/intermine/tutorial.html 2020-12-09 2024-02-29 9 True False False True intermine, galaxy_intermine_exchange UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 172 229 3.300000 0
Using Galaxy and Managing your Data Using Workflow Parameters https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-parameters/tutorial.html 2019-06-27 2024-06-14 15 True False True True tp_head_tool Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au MISSISSIPPI 0 1918 2454 2.300000 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 2743129 7359682 2.516667 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 2195263 5523702 2.466667 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 4333 5761 3.200000 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 2695 3651 3.300000 0
Using Galaxy and Managing your Data RStudio in Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/rstudio/tutorial.html 2019-10-08 2025-07-04 15 True False False False interactive_tool_rstudio UseGalaxy.eu, UseGalaxy.org.au 0 4989 7770 2.183333 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 0 140 162 3.233333 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 2900 3759 3.700000 0
Using Galaxy and Managing your Data Use Jupyter notebooks in Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/galaxy-intro-jupyter/tutorial.html 2018-07-02 2025-05-11 10 True False True False interactive_tool_jupyter_notebook UseGalaxy.eu, UseGalaxy.org.au 0 2320 3078 2.433333 0
Using Galaxy and Managing your Data Downloading and Deleting Data in Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/download-delete-data/tutorial.html 2019-10-17 2023-11-09 6 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 7277 9674 1.616667 0
Using Galaxy and Managing your Data Rule Based Uploader: Advanced https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.html 2018-05-25 2024-06-14 11 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 760 1018 4.783333 0
Using Galaxy and Managing your Data Using dataset collections https://training.galaxyproject.org//topics/galaxy-interface/tutorials/collections/tutorial.html Genome indexing, Sequence alignment, Generation, Read mapping 2016-09-30 2024-12-05 20 True False True False bwa_mem, collapse_dataset, snpSift_extractFields, lofreq_call UseGalaxy.eu, UseGalaxy.org.au GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 15472 21220 3.016667 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 0 395 601 2.350000 0
Using Galaxy and Managing your Data Annotate, prepare tests and publish Galaxy workflows in workflow registries https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-fairification/tutorial.html Visualisation, Sequencing quality control, Validation, Read mapping 2025-05-26 2025-05-26 1 True False False False multiqc, falco UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 153 184 1.583333 0
Using Galaxy and Managing your Data JupyterLab in Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/jupyterlab/tutorial.html 2020-03-05 2025-04-25 9 True False False False interactive_tool_jupyter_notebook UseGalaxy.eu, UseGalaxy.org.au 0 2082 3348 2.833333 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 61 74 6.383333 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 0 102 143 4.766667 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 25 27 0.033333 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 1585 2131 2.750000 0
Using Galaxy and Managing your Data Understanding Galaxy history system https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history/tutorial.html 2017-02-20 2025-04-28 12 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 5398 6970 2.850000 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 0 247 300 2.566667 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, Coding region prediction, Genome visualisation, Genome annotation 2018-03-06 2025-03-19 26 True True True True jbrowse, prokka UseGalaxy.be, UseGalaxy.eu Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2761376 7390663 4.433333 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, chromeister, clustalw, gecko UseGalaxy.eu, UseGalaxy.org.au GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz 0 2698382 7199132 4.700000 0
Genome Annotation Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial resistance Read mapping, Genome visualisation, Antimicrobial resistance prediction, Genome annotation 2024-01-23 2025-06-10 9 True False True True bakta, bowtie2, staramr_search, upload1, jbrowse, tbl2gff3, Grep1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi 0 3134 4290 2.983333 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 assembly validation, Sequence alignment, Genome visualisation, Sequence annotation, Gene prediction, Differential protein expression profiling, Genome annotation 2025-06-20 2025-06-25 2 True False False True braker3, omark, gffread, rna_star, helixer, busco, jbrowse 0 218 265 2.150000 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, Repeat sequence detection, Mapping, Editing, RNA-Seq analysis 2021-11-29 2025-06-03 22 True False True True bedtools_maskfastabed, red, repeatmodeler, repeatmasker_wrapper UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 9723 12433 1.383333 0
Genome Annotation Secondary metabolite discovery https://training.galaxyproject.org//topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html Gene prediction, Data handling, Sequence clustering, Service invocation, Differential gene expression analysis 2024-02-21 2024-09-27 2 True False False True ctb_simsearch, ctb_np-likeness-calculator, openbabel_remDuplicates, collapse_dataset, interactive_tool_jupyter_notebook, ncbi_acc_download, antismash, tp_awk_tool, bp_genbank2gff3, Remove beginning1, ctb_silicos_qed, edu.tamu.cpt.gff3.customGbkToGff, ctb_chemfp_mol2fps UseGalaxy.eu 0 595 756 1.333333 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.cz, UseGalaxy.eu, UseGalaxy.no 0 2517913 6582875 5.216667 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 assembly validation, Sequence alignment, Genome visualisation, Sequence annotation, Gene prediction, Differential protein expression profiling, Genome annotation 2025-03-17 2025-06-20 4 True False False True braker3, omark, gffread, rna_star, fasta-stats, busco, jbrowse 0 1084 1360 2.133333 0
Genome Annotation Genome annotation with Helixer https://training.galaxyproject.org//topics/genome-annotation/tutorials/helixer/tutorial.html Biodiversity, Genomics, Zoology, Plant biology Sequence assembly validation, Genome visualisation, Sequence annotation, Gene prediction, Differential protein expression profiling, Genome annotation 2024-08-21 2025-06-04 8 True False False True omark, gffread, jcvi_gff_stats, helixer, busco, jbrowse 0 1064 1281 1.716667 0
Genome Annotation Bacterial Genome Annotation https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements Sequence motif recognition, Scaffolding, Nucleic acid feature detection, Genome assembly, Structural variation detection, Genome visualisation, Protein feature detection, Multilocus sequence typing, Genome annotation 2024-02-01 2024-10-15 6 True False True True bakta, plasmidfinder, Grouping1, tp_tail_tool, isescan, integron_finder, upload1, tp_replace_in_column, jbrowse, tbl2gff3 UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, UseGalaxy.cz 0 5749 7719 2.550000 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 2743129 7359682 2.516667 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 34806 63549 1.450000 0
Genome Annotation Creating an Official Gene Set https://training.galaxyproject.org//topics/genome-annotation/tutorials/official-gene-set/tutorial.html 2023-11-02 2024-02-29 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 38 44 1.750000 0
Genome Annotation Dataset construction for bacterial comparative genomics https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html Genomics, Microbiology Data handling, Sequence database search, Data retrieval 2025-03-14 2025-03-14 1 True False False False sort1, cat1, bg_uniq, Remove beginning1, Cut1, upload1, datasets_download_genome UseGalaxy.fr UseGalaxy.cz 0 63 76 3.933333 0
Genome Annotation Bacterial genome quality control https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html Genomics, Microbiology Sequence assembly validation, Sequencing quality control, Validation, Genome comparison, Statistical calculation, Sequence composition calculation 2025-03-14 2025-03-14 1 True False False False upload1, drep_dereplicate, checkm2 UseGalaxy.eu, UseGalaxy.fr 0 63 70 3.100000 0
Genome Annotation Bacterial pangenomics https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-pangenomics/tutorial.html Genomics, Microbiology Essential dynamics, Rarefaction, Sequence assembly, Genome annotation 2025-03-14 2025-03-14 1 True False False False ppanggolin_msa, ppanggolin_all, upload1 UseGalaxy.eu, UseGalaxy.fr 0 64 76 1.450000 0
Genome Annotation Genome annotation with Funannotate https://training.galaxyproject.org//topics/genome-annotation/tutorials/funannotate/tutorial.html Gene and protein families Sequence assembly validation, Query and retrieval, Sequence motif recognition, Fold recognition, Homology-based gene prediction, Formatting, Sequence alignment, Genome visualisation, Sequence annotation, Protein feature detection, Information extraction, Genome annotation 2021-11-29 2025-06-10 26 True False True True eggnog_mapper, funannotate_predict, picard_MergeSamFiles, rna_star, funannotate_annotate, busco, funannotate_compare, aegean_parseval, jbrowse, interproscan UseGalaxy.eu, UseGalaxy.fr UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org.au 0 10229 14580 1.966667 0
Genome Annotation Comparative gene analysis in unannotated genomes https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html Genomics, Gene and protein families, Sequence analysis, Phylogeny, Comparative genomics De-novo assembly, Transcriptome assembly, Sequence alignment analysis, Multiple sequence alignment, Coding region prediction, Database search, Phylogenetic tree generation 2022-09-08 2025-06-03 10 True False False True collapse_dataset, cat1, Filter1, Add_a_column1, join1, rapidnj, regexColumn1, tp_split_on_column, bg_diamond_view, Cut1, tab2fasta, bg_diamond_makedb, rbc_mafft, gops_intersect_1, bg_diamond, orfipy UseGalaxy.eu UseGalaxy.cz 0 1758 2499 3.150000 0
Genome Annotation Genome annotation with Maker (short) https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html Sequence assembly validation, Genome visualisation, Sequence annotation, Genome annotation 2021-01-12 2024-02-29 3 True False False True gffread, maker_map_ids, maker, fasta-stats, jcvi_gff_stats, busco, jbrowse UseGalaxy.be 0 3817 5388 2.983333 0
Genome Annotation Essential genes detection with Transposon insertion sequencing https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html Genomics, Microbiology, Sequence analysis, Mobile genetic elements Sequence trimming, Primer removal, Read pre-processing, Transposon prediction 2019-07-02 2024-03-18 12 True True False True gff_to_prot, tp_sort_header_tool, Filter1, Add_a_column1, __EXTRACT_DATASET__, cutadapt, tp_easyjoin_tool, transit_gumbel, Cut1, bg_find_subsequences, bowtie_wrapper, deeptools_bam_coverage UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.eu 0 2751052 7374109 4.300000 0
Genome Annotation Genome annotation with Maker https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html Sequence assembly validation, Operation, Homology-based gene prediction, Ab-initio gene prediction, Genome visualisation, Sequence annotation, Gene prediction, Genome annotation 2018-09-24 2024-02-29 14 True False False True gffread, fasta-stats, maker, maker_map_ids, augustus_training, busco, jcvi_gff_stats, jbrowse, snap_training UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no UseGalaxy.cz, UseGalaxy.org.au 0 13575 24131 1.866667 0
Genome Annotation Functional annotation of protein sequences https://training.galaxyproject.org//topics/genome-annotation/tutorials/functional/tutorial.html Function analysis, Protein sites, features and motifs Fold recognition, Information extraction, Sequence motif recognition, Protein feature detection, Sequence alignment analysis, Query and retrieval, Homology-based gene prediction, Genome annotation 2022-07-20 2025-06-03 12 True False False True ncbi_blastp_wrapper, bg_diamond, eggnog_mapper, interproscan UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au UseGalaxy.no 0 3932 5320 1.683333 0
Genome Annotation Refining Genome Annotations with Apollo (eukaryotes) https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo-euk/tutorial.html Genomics Genome visualisation 2022-08-22 2025-06-03 16 True False False False iframe, jbrowse, create_or_update UseGalaxy.no UseGalaxy.cz, UseGalaxy.eu 0 1351 2100 2.483333 0
Genome Annotation Long non-coding RNAs (lncRNAs) annotation with FEELnc https://training.galaxyproject.org//topics/genome-annotation/tutorials/lncrna/tutorial.html Classification, Sequence annotation, Annotation, Transcriptome assembly, RNA-Seq analysis 2022-09-23 2024-09-18 11 True False True True Extract_features1, gffread, feelnc, tp_cat, stringtie UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 1823 2447 2.166667 0
Genome Annotation CRISPR screen analysis https://training.galaxyproject.org//topics/genome-annotation/tutorials/crispr-screen/tutorial.html Primer removal, Read pre-processing, Statistical calculation, Sequence composition calculation, Sequence trimming, Sequencing quality control, Genetic variation analysis, Validation 2021-10-15 2024-08-08 12 True True True True mageck_test, tp_awk_tool, cutadapt, volcanoplot, mageck_mle, multiqc, fastqc, mageck_count UseGalaxy.fr, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2350129 5994247 4.400000 0
Variant Analysis Microbial Variant Calling https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Variant calling, Genome visualisation, Phylogenetic tree visualisation, Phylogenetic tree generation 2018-02-26 2025-03-19 24 True False False True jbrowse, snippy UseGalaxy.be, UseGalaxy.eu GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 14842 23796 2.050000 0
Visualisation Genomic Data Visualisation with JBrowse https://training.galaxyproject.org//topics/visualisation/tutorials/jbrowse/tutorial.html Genome visualisation 2020-01-10 2024-10-15 17 True True False False jbrowse Galaxy@AuBi, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz 0 2747936 7366155 4.850000 0
Imaging Using BioImage.IO models for image analysis in Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/process-image-bioimageio/tutorial.html Visualisation, Image annotation, Data handling, Image analysis 2025-04-09 2025-04-16 5 True False False True ip_split_image, ip_overlay_images, ip_threshold, ip_binary_to_labelimage, __EXTRACT_DATASET__, bioimage_inference, image_math UseGalaxy.eu 0 153 184 3.700000 0
Imaging Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/omero-suite/tutorial.html Image analysis 2024-12-04 2025-04-08 3 True False False False omero_metadata_import, omero_get_id, omero_get_value, omero_import, omero_filter, omero_roi_import 0 155 201 3.350000 0
Imaging Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/parameter-tuning/tutorial.html Visualisation, Image annotation, Data handling, Image analysis 2025-04-28 2025-04-28 1 True False False True collapse_dataset, ip_histogram_equalization, tp_split_on_column, ip_filter_standard, ip_threshold, ip_segmetrics, param_value_from_file UseGalaxy.eu UseGalaxy.cz 0 60 71 2.500000 0
Imaging Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines https://training.galaxyproject.org//topics/imaging/tutorials/2D-spot-detection/tutorial.html Visualisation, Image annotation, Data handling, Image analysis 2025-03-20 2025-03-20 2 True False False True idr_download_by_ids, ip_points_to_label, ip_spot_detection_2d, ip_overlay_images, ip_histogram_equalization, unzip, ip_binary_to_labelimage UseGalaxy.cz, UseGalaxy.eu 0 130 168 1.716667 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 2024-10-15 8 True False False True cp_measure_object_intensity, cp_common, cp_export_to_spreadsheet, cp_save_images, cp_measure_object_size_shape, cp_track_objects, cp_cellprofiler, cp_color_to_gray, cp_overlay_outlines, unzip, cp_tile, cp_identify_primary_objects UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 2117 2647 1.066667 0
Imaging Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools https://training.galaxyproject.org//topics/imaging/tutorials/electrophoresis-gel-bands-image-analysis/tutorial.html Visualisation, Image annotation, Data handling, Image analysis 2025-08-11 2025-08-11 1 True False False True ip_split_image, ip_points_to_label, interactive_tool_qupath, ip_2d_feature_extraction, ip_imageinfo, graphicsmagick_image_convert, __EXTRACT_DATASET__ UseGalaxy.eu 0 117 146 1.383333 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 2024-10-15 9 True True False True cp_common, cp_measure_texture, cp_relate_objects, cp_convert_objects_to_image, cp_measure_image_intensity, cp_export_to_spreadsheet, cp_save_images, cp_measure_granularity, cp_measure_object_intensity, cp_image_math, cp_display_data_on_image, cp_cellprofiler, cp_gray_to_color, cp_enhance_or_suppress_features, cp_identify_primary_objects, cp_measure_image_area_occupied, cp_mask_image, idr_download_by_ids, cp_measure_image_quality, cp_measure_object_size_shape UseGalaxy.be, UseGalaxy.eu Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2746854 7365232 3.766667 0
Imaging Voronoi segmentation https://training.galaxyproject.org//topics/imaging/tutorials/voronoi-segmentation/tutorial.html Visualisation, Image annotation, Data handling, Image analysis 2025-05-13 2025-07-11 4 True False False True voronoi_tessellation, ip_convertimage, ip_count_objects, ip_overlay_images, ip_2d_feature_extraction, unzip, ip_filter_standard, ip_imageinfo, ip_threshold, ip_binary_to_labelimage, colorize_labels, repeat_channels, image_math UseGalaxy.eu 0 214 350 4.583333 0
Imaging Tracking of mitochondria and capturing mitoflashes https://training.galaxyproject.org//topics/imaging/tutorials/detection-of-mitoflashes/tutorial.html Image analysis 2024-11-20 2024-11-20 2 True False False True ip_points_association_nn, ip_spot_detection_2d, ip_curve_fitting UseGalaxy.cz, UseGalaxy.eu 0 131 154 0.916667 0
Imaging Introduction to Image Analysis using Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/imaging-introduction/tutorial.html Visualisation, Image annotation, Data handling, Image analysis 2019-08-13 2025-03-20 14 True False False True ip_count_objects, ip_overlay_images, ip_histogram_equalization, unzip, ip_filter_standard, ip_imageinfo, ip_threshold, ip_binary_to_labelimage UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 2592 3637 1.766667 0
Imaging Training Custom YOLO Models for Segmentation of Bioimages https://training.galaxyproject.org//topics/imaging/tutorials/yolo-segmentation-training/tutorial.html Data handling, Visualisation, Image analysis, Image annotation 2025-07-25 2025-07-31 2 True False False True yolo_training, ip_histogram_equalization, json2yolosegment, unzip, interactive_tool_anylabeling, graphicsmagick_image_convert UseGalaxy.eu 0 154 185 0.433333 0
Imaging End-to-End Tissue Microarray Image Analysis with Galaxy-ME https://training.galaxyproject.org//topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html 2023-02-14 2025-03-14 6 True False False True scimap_phenotyping, palom, ip_convertimage, quantification, unet_coreograph, mesmer, basic_illumination, scanpy_compute_graph, rename_tiff_channels, squidpy_spatial, vitessce_spatial, celesta, scimap_mcmicro_to_anndata, ashlar, gate_finder 0 1313 1793 1.916667 0
Imaging Analyse HeLa fluorescence siRNA screen https://training.galaxyproject.org//topics/imaging/tutorials/hela-screen-analysis/tutorial.html Visualisation, Image annotation, Data handling, Image analysis 2019-08-13 2024-11-07 12 True False False True collapse_dataset, ip_2d_feature_extraction, unzip, ip_filter_standard, ip_threshold, ip_2d_filter_segmentation_by_features, ip_binary_to_labelimage UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no 0 735 948 2.200000 0
Imaging FAIR Bioimage Metadata https://training.galaxyproject.org//topics/imaging/tutorials/bioimage-metadata/tutorial.html 2025-09-28 2025-09-28 0 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 0 0 0.000000 0
Imaging REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data https://training.galaxyproject.org//topics/imaging/tutorials/bioimage-REMBI/tutorial.html 2025-09-28 2025-09-28 0 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 0 0 0.000000 0
Introduction to Galaxy Analyses From peaks to genes https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html 2016-03-29 2025-08-29 64 True False False True CONVERTER_interval_to_bed_0, get_flanks1, tp_sort_header_tool, Add_a_column1, Grouping1, tp_tail_tool, Cut1, upload1, tp_replace_in_column, gops_intersect_1 UseGalaxy.eu, UseGalaxy.fr UseGalaxy.cz, UseGalaxy.no 0 20136 33190 3.333333 0
Introduction to Galaxy Analyses NGS data logistics https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html Genome indexing, Data handling, Formatting, Sequence alignment, Sequencing quality control, Validation, Sequence contamination filtering, SNP detection, Generation, Read mapping 2017-02-22 2025-07-24 38 True False True True bwa_mem2, snpEff, collapse_dataset, lofreq_indelqual, fastp, Filter1, bwa_mem, snpEff_build_gb, snpeff_sars_cov_2, lofreq_viterbi, picard_MarkDuplicates, bwa, fasterq_dump, samtools_view, lofreq_call, multiqc, samtools_stats, snpSift_extractFields UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au MISSISSIPPI, UseGalaxy.cz 0 19565 33528 3.416667 0
Introduction to Galaxy Analyses How to reproduce published Galaxy analyses https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-reproduce/tutorial.html Visualisation 2021-08-25 2024-10-15 12 True False False True csv_to_tabular, Grouping1, Remove beginning1, ggplot2_point, Cut1, datamash_ops, upload1, tp_sorted_uniq Galaxy@AuBi, UseGalaxy.eu MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2138 2863 4.133333 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 tp_sort_header_tool, {{version_split}}, Remove beginning1, Cut1, tp_sorted_uniq, {{version_cat}}, Add_a_column1, join1, {{version_wc}}, {{version_replace_text_line}}, datamash_ops, {{version_filter}}, {{version_join}}, {{version_replace_text_column}}, {{version_cut_columns}}, {{version_datamash}}, {{version_remove_beginning}}, tabular_to_csv, {{version_cut_advanced}}, Filter1, {{version_unique}}, {{version_count}}, {{version_compute}}, Count1, {{version_remove_columns_by_header}}, regexColumn1, {{version_sort}}, Show beginning1, cat1, Grouping1, {{version_paste}}, {{version_select_first}}, tp_split_on_column, tp_cat, upload1, wc_gnu 0 5734 8388 3.516667 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, gene2exon1, gops_intersect_1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au MISSISSIPPI 0 19684 31192 3.566667 0
Introduction to Galaxy Analyses Introduction to Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/introduction/slides.html 2016-09-30 2025-09-23 6 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 2743129 7359754 2.516667 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 2743129 7359754 2.516667 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 7903 11192 1.483333 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 0 422 482 2.800000 0
Introduction to Galaxy Analyses A short introduction to Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-short/tutorial.html Statistical calculation, Sequencing quality control, Sequence composition calculation 2018-08-27 2025-09-23 43 True True True True fastqc, cshl_fastq_quality_filter UseGalaxy.be, UseGalaxy.eu Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2794806 7440239 7.100000 0
Introduction to Galaxy Analyses Galaxy Basics for everyone https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html Visualisation 2019-11-14 2024-12-02 34 True False True True csv_to_tabular, Grouping1, Remove beginning1, ggplot2_point, Cut1, datamash_ops, upload1, tp_sorted_uniq UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz 0 21838 34730 3.983333 0
Introduction to Galaxy Analyses Galaxy Basics for genomics https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-101/tutorial.html Mapping 2016-12-19 2025-04-22 68 True False True True tp_sort_header_tool, upload1, bedtools_intersectbed, datamash_ops, comp1, tp_head_tool UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 46025 74375 3.400000 0
Introduction to Galaxy Analyses Very Short Introductions: QC https://training.galaxyproject.org//topics/introduction/tutorials/vsi_qc/tutorial.html Validation, Sequencing quality control, Sequence contamination filtering 2024-03-26 2024-06-25 4 True False False False multiqc, fastp Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au MISSISSIPPI, UseGalaxy.no 0 282 343 3.316667 0
Materials Science Finding the muon stopping site with pymuon-suite in Galaxy https://training.galaxyproject.org//topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.html 2024-01-22 2024-06-14 2 True False True True pm_uep_opt, pm_muairss_read UseGalaxy.cz, UseGalaxy.eu 0 234 314 2.216667 0
Metabolomics Mass spectrometry: LC-MS analysis https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms/tutorial.html Chromatogram visualisation, Chromatographic alignment, Mass spectrum visualisation, Peak detection, Label-free quantification, Validation, Data filtering 2019-07-02 2025-09-21 13 True False False True abims_CAMERA_annotateDiffreport, abims_xcms_retcor, abims_xcms_fillPeaks, msnbase_readmsdata, wsdl_hmdb, xcms_export_samplemetadata, Univariate, xcms_plot_chromatogram, abims_xcms_xcmsSet, quality_metrics, Batch_correction, xcms_merge, abims_xcms_group, generic_filter UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 12444 20411 1.600000 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 Chromatogram visualisation, Filtering, Formatting, Peak detection, Label-free quantification, Validation, Data filtering, Imputation, Clustering, Chromatographic alignment, Standardisation and normalisation, Mass spectrum visualisation, Format validation, Correlation, Spectral library search 2023-05-08 2023-11-09 5 True False False True abims_xcms_retcor, riassigner, abims_xcms_fillPeaks, msnbase_readmsdata, waveica, msconvert, matchms_formatter, matchms_similarity, abims_xcms_xcmsSet, matchms_filtering, xcms_merge, abims_xcms_group, ramclustr_define_experiment, ramclustr UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au 0 2534 3270 1.533333 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_data_exporter, Filter1, cardinal_spectra_plots, cardinal_quality_report, cardinal_filtering, cardinal_mz_images UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2946 4205 1.750000 0
Metabolomics Predicting EI+ mass spectra with QCxMS https://training.galaxyproject.org//topics/metabolomics/tutorials/qcxms-predictions/tutorial.html 2024-10-01 2024-10-01 1 True True False True qcxms_getres, tp_cut_tool, split_file_to_collection, qcxms_neutral_run, __FILTER_FAILED_DATASETS__, tp_cat, openbabel_compound_convert, xtb_molecular_optimization, qcxms_production_run, param_value_from_file, ctb_im_conformers UseGalaxy.eu UseGalaxy.org.au 0 611169 1470765 3.416667 0
Metabolomics Molecular formula assignment and mass recalibration with MFAssignR package https://training.galaxyproject.org//topics/metabolomics/tutorials/mfassignr/tutorial.html Visualisation 2025-05-19 2025-05-19 1 True False False True mfassignr_findRecalSeries, mfassignr_kmdnoise, mfassignr_recallist, mfassignr_mfassign, mfassignr_recal, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_mfassignCHO, mfassignr_snplot 0 64 81 3.200000 0
Metabolomics Mass spectrometry imaging: Finding differential analytes https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html 2019-04-13 2023-11-09 9 True False False True Summary_Statistics1, Filter1, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, maldi_quant_peak_detection, cardinal_classification, cardinal_mz_images, Grep1, cardinal_combine, maldi_quant_preprocessing, join_files_on_column_fuzzy UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 1942 2793 1.833333 0
Metabolomics Introduction to Metabolomics https://training.galaxyproject.org//topics/metabolomics/tutorials/introduction/slides.html 2018-11-20 2023-01-12 1 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 2743129 7359754 2.516667 0
Metabolomics Mass spectrometry: LC-MS preprocessing with XCMS https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html Chromatogram visualisation, Chromatographic alignment, Mass spectrum visualisation, Peak detection, Label-free quantification, Validation, Data filtering 2020-02-04 2024-10-15 14 True True False False abims_CAMERA_annotateDiffreport, abims_xcms_retcor, abims_xcms_fillPeaks, msnbase_readmsdata, xcms_export_samplemetadata, xcms_plot_chromatogram, abims_xcms_xcmsSet, intens_check, abims_xcms_summary, idchoice, xcms_merge, abims_xcms_group UseGalaxy.fr UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2749071 7369132 4.800000 0
Metabolomics Mass spectrometry : GC-MS analysis with metaMS package https://training.galaxyproject.org//topics/metabolomics/tutorials/gcms/tutorial.html Chromatogram visualisation, Chromatographic alignment, Mass spectrum visualisation, Peak detection, Label-free quantification, Validation, Data filtering 2021-09-22 2023-11-09 7 True False False False abims_xcms_fillPeaks, msnbase_readmsdata, abims_xcms_xcmsSet, xcms_merge, abims_xcms_group UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.no, UseGalaxy.org.au 0 1436 2336 1.650000 0
Metabolomics Mass spectrometry: LC-MS data processing https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html 2021-12-14 2024-10-15 8 True False False False Multivariate, normalization, intens_check, quality_metrics, Batch_correction, generic_filter UseGalaxy.fr UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2707 3665 1.983333 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 2743129 7359754 2.516667 0
Microbiome Analyses of metagenomics data - The global picture https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Visualisation, Phylogenetic analysis, Sequence read processing, Sequence clustering, Sequencing quality control, Taxonomic classification, DNA barcoding 2017-06-22 2024-08-09 4 True False False True humann2_regroup_table, mothur_classify_otu, mothur_pre_cluster, taxonomy_krona_chart, metaphlan2, mothur_filter_seqs, humann2_renorm_table, mothur_classify_seqs, metaphlan2krona, mothur_align_seqs, mothur_summary_seqs, krona-text, mothur_merge_files, mothur_screen_seqs, humann2, mothur_make_biom, mothur_make_group, mothur_cluster_split, mothur_count_seqs, mothur_unique_seqs, mothur_make_shared UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 7736 10511 2.716667 0
Microbiome Antibiotic resistance detection https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial resistance Sequence assembly visualisation, De-novo assembly, Box-Whisker plot plotting, Mapping assembly, Scatter plot plotting, Genome assembly, Aggregation, Sequence analysis, Antimicrobial resistance prediction, Pairwise sequence alignment 2019-06-25 2024-06-14 4 True False True True gfa_to_fa, staramr_search, bandage_image, PlasFlow, miniasm, nanoplot, minimap2, racon, unicycler UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 3024 4258 2.950000 0
Microbiome MGnify v5.0 Amplicon Pipeline https://training.galaxyproject.org//topics/microbiome/tutorials/mgnify-amplicon/tutorial.html Metagenomics, Taxonomy, Sequence analysis Visualisation, k-mer counting, Alignment, Sequence composition calculation, Nucleic acid feature detection, Formatting, Read pre-processing, Validation, Nucleic acid design, Sequence contamination filtering, DNA barcoding, Analysis, Comparison, Statistical calculation, Sequencing quality control, Sequence trimming, Sequence feature detection, Mapping 2025-07-30 2025-07-30 2 True False False True gops_concat_1, __UNZIP_COLLECTION__, taxonomy_krona_chart, fastq_dl, param_value_from_file, multiqc, mapseq, query_tabular, CONVERTER_gz_to_uncompressed, __FILTER_FROM_FILE__, cshl_fasta_formatter, collapse_dataset, tp_awk_tool, Add_a_column1, lotus2, ampvis2_load, collection_column_join, ampvis2_heatmap, biom_convert, fastq_to_fasta_python, tp_find_and_replace, bedtools_maskfastabed, trimmomatic, seqprep, fastp, wc_gnu, prinseq, bedtools_getfastabed, fastqc, infernal_cmsearch, fastq_filter, collection_element_identifiers, Grouping1, __MERGE_COLLECTION__, filter_tabular, cmsearch_deoverlap, __FILTER_EMPTY_DATASETS__, mgnify_seqprep, CONVERTER_uncompressed_to_gz 0 75 95 3.150000 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 Sequence assembly visualisation, Visualisation, Taxonomic classification, Cross-assembly, Data handling, Sequence composition calculation, Mapping assembly, Scatter plot plotting, Phylogenetic tree analysis, Validation, Variant calling, Multiple sequence alignment, Sequence contamination filtering, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation, Antimicrobial resistance prediction, De-novo assembly, Box-Whisker plot plotting, Sequence alignment analysis, Base-calling, Statistical calculation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Genome assembly, Sequencing quality control, Phylogenetic tree reconstruction, Aggregation, Pairwise sequence alignment, Mapping, Multilocus sequence typing, Sequence assembly 2023-01-26 2024-09-27 11 True False True True Remove beginning1, bandage_image, taxonomy_krona_chart, Cut1, snpSift_filter, tp_replace_in_column, param_value_from_file, tp_sorted_uniq, compose_text_param, Paste1, Grep1, fasttree, regex1, CONVERTER_gz_to_uncompressed, krakentools_extract_kraken_reads, multiqc, medaka_consensus_pipeline, snpSift_extractFields, collapse_dataset, fasta2tab, Add_a_column1, bamtools_split_mapped, flye, bcftools_norm, __BUILD_LIST__, newick_display, samtools_fastx, collection_column_join, split_file_to_collection, krakentools_kreport2krona, table_compute, tp_find_and_replace, clustalw, ggplot2_heatmap, samtools_depth, tp_multijoin_tool, fastp, add_line_to_file, abricate, Count1, fasta_merge_files_and_filter_unique_sequences, clair3, minimap2, tab2fasta, regexColumn1, barchart_gnuplot, tp_head_tool, bcftools_consensus, fastqc, bedtools_getfastabed, mlst, porechop, samtools_coverage, collection_element_identifiers, Grouping1, tp_cut_tool, tp_split_on_column, kraken2, nanoplot, __FILTER_FAILED_DATASETS__, __FILTER_EMPTY_DATASETS__ UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org.au 0 4484 6753 3.383333 0
Microbiome Clinical Metaproteomics 2: Discovery https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html Heat map generation, Visualisation, Protein quantification, Statistical calculation, Filtering, Standardisation and normalisation, Formatting, Principal component plotting, Imputation, Clustering 2025-09-28 2025-09-28 0 True False True True peptide_shaker, fasta_cli, Filter1, fasta2tab, Grouping1, msconvert, Remove beginning1, filter_tabular, fasta_merge_files_and_filter_unique_sequences, query_tabular, tp_cat, Cut1, search_gui, maxquant, Grep1, ident_params, dbbuilder UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 1 1 0.000000 0
Microbiome Clinical Metaproteomics 4: Quantitation https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-4-quantitation/tutorial.html Heat map generation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Principal component plotting, Imputation, Clustering 2025-09-28 2025-09-28 0 True False True True maxquant, Grouping1, Grep1, Cut1 UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 0 0 0.000000 0
Microbiome Calculating α and β diversity from microbiome taxonomic data https://training.galaxyproject.org//topics/microbiome/tutorials/diversity/tutorial.html Aggregation, Visualisation 2024-08-01 2025-06-17 7 True False True True krakentools_alpha_diversity, krakentools_beta_diversity Galaxy@Pasteur, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au Galaxy@AuBi 0 5763 6948 1.266667 0
Microbiome Taxonomic Profiling and Visualization of Metagenomic Data https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Visualisation, Aggregation, Statistical calculation, Taxonomic classification, Genome annotation 2023-05-03 2025-04-24 6 True False True True __UNZIP_COLLECTION__, kraken_biom, metaphlan, kraken2, interactive_tool_pavian, taxonomy_krona_chart, est_abundance, krakentools_kreport2krona, interactive_tool_phinch UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 11109 14885 2.016667 0
Microbiome Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Sequence assembly visualisation, Visualisation, Sequence assembly validation, Data handling, Local alignment, Sequence composition calculation, Formatting, Read pre-processing, Variant calling, Sequence contamination filtering, Primer removal, Sequence alignment analysis, Statistical calculation, Sequence file editing, Genome assembly, Sequence trimming, Sequencing quality control, Read mapping 2022-12-05 2025-06-16 6 True False True True megahit_contig2fastg, coverm_contig, megahit, seqtk_subseq, metaspades, bowtie2, bg_uniq, filter_tabular, quast, bandage_image, bandage_info, cutadapt, tp_cat, ngsutils_bam_filter, collection_column_join, random_lines1, fastqc, bamtools UseGalaxy.cz, UseGalaxy.eu 0 3961 5536 2.966667 0
Microbiome Building an amplicon sequence variant (ASV) table from 16S data using DADA2 https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Visualisation, Analysis, Variant calling, Deposition, DNA barcoding 2024-06-05 2025-07-03 11 True False True True __UNZIP_COLLECTION__, dada2_removeBimeraDenovo, dada2_plotQualityProfile, interactive_tool_phyloseq, tp_replace_in_column, Add_a_column1, __SORTLIST__, dada2_mergePairs, phyloseq_from_dada2, dada2_dada, tp_replace_in_line, dada2_learnErrors, dada2_makeSequenceTable, dada2_seqCounts, tp_head_tool, collection_element_identifiers, cat1, Grouping1, dada2_filterAndTrim, dada2_assignTaxonomyAddspecies UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 6078 8557 2.383333 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.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 601 760 1.583333 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 2025-09-28 2025-09-28 0 True False True True msstatstmt, Grep1, unipept UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 0 0 0.000000 0
Microbiome 16S Microbial analysis with Nanopore data https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Visualisation, Sequencing quality control, Sequence composition calculation, Validation, Sequence contamination filtering, Taxonomic classification, Statistical calculation 2020-11-24 2024-07-31 5 True False False True tp_replace_in_line, porechop, fastp, Remove beginning1, datamash_reverse, kraken2, taxonomy_krona_chart, multiqc, fastqc UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr 0 7364 10145 2.633333 0
Microbiome Clinical Metaproteomics 3: Verification https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html 2025-09-28 2025-09-28 0 True False True True collapse_dataset, Filter1, Grouping1, Remove beginning1, fasta_merge_files_and_filter_unique_sequences, pepquery2, tp_cat, Cut1, query_tabular, uniprotxml_downloader, dbbuilder UseGalaxy.cz, UseGalaxy.eu UseGalaxy.org.au 0 0 0 0.000000 43
Microbiome Identification of the micro-organisms in a beer using Nanopore sequencing https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Sequence composition calculation, Visualisation, Sequencing quality control, Aggregation, Statistical calculation, Sequence contamination filtering, Taxonomic classification 2022-09-29 2024-11-29 5 True False True True porechop, fastp, Filter1, kraken2, taxonomy_krona_chart, krakentools_kreport2krona, fastqc GalaxyTrakr, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2460 3586 2.883333 0
Microbiome Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data https://training.galaxyproject.org//topics/microbiome/tutorials/metaplasmidome_query/tutorial.html Genomics, Microbiology, Sequence analysis, Mobile genetic elements Visualisation, Pairwise sequence alignment 2025-01-07 2025-01-07 1 True False False True sort1, add_column_headers, cat1, Filter1, Add_a_column1, Grouping1, join1, MQoutputfilter, tp_tail_tool, CONVERTER_fasta_to_tabular, ggplot2_histogram, histogram_rpy, Cut1, minimap2, tab2fasta, tp_replace_in_column, tp_sorted_uniq, count_gff_features UseGalaxy.fr 0 257 297 0.950000 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 Visualisation, Phylogenetic tree visualisation, Phylogenetic tree editing, Sequence comparison, Sequence composition calculation, Phylogenetic inference, Read pre-processing, Validation, Phylogenetic analysis, Primer removal, Species frequency estimation, Sequence alignment analysis, Statistical calculation, Conversion, Sequencing quality control, Sequence similarity search, Sequence trimming, Taxonomic classification 2020-02-13 2025-06-16 6 True False True True tp_sort_header_tool, humann_split_stratified_table, taxonomy_krona_chart, Cut1, multiqc, Grep1, bg_sortmerna, humann, humann_renorm_table, graphlan, tp_find_and_replace, humann_unpack_pathways, combine_metaphlan2_humann2, humann_rename_table, fastqc, fastq_paired_end_interlacer, cutadapt, metaphlan, humann_regroup_table, graphlan_annotate, export2graphlan UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.no 0 671 855 2.383333 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 Visualisation, Phylogenetic tree visualisation, Phylogenetic tree editing, Sequence comparison, Sequence composition calculation, Phylogenetic inference, Read pre-processing, Validation, Phylogenetic analysis, Primer removal, Species frequency estimation, Sequence alignment analysis, Statistical calculation, Conversion, Sequencing quality control, Sequence similarity search, Sequence trimming, Aggregation, Taxonomic classification 2019-11-21 2025-06-16 6 True True True True combine_metaphlan_humann, tp_sort_header_tool, humann_split_stratified_table, taxonomy_krona_chart, Cut1, multiqc, Grep1, bg_sortmerna, humann, humann_renorm_table, graphlan, tp_find_and_replace, humann_unpack_pathways, humann_rename_table, fastqc, fastq_paired_end_interlacer, Grouping1, cutadapt, metaphlan, humann_regroup_table, graphlan_annotate, export2graphlan UseGalaxy.cz, UseGalaxy.fr UseGalaxy.eu 0 2749177 7367521 4.366667 0
Microbiome Clinical Metaproteomics 1: Database-Generation https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-1-database-generation/tutorial.html Expression analysis, de Novo sequencing, Target-Decoy, Tag-based peptide identification, Protein identification 2025-09-28 2025-09-28 0 True False True True fasta_merge_files_and_filter_unique_sequences, metanovo, uniprotxml_downloader, dbbuilder UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 0 0 0.000000 0
Microbiome Indexing and profiling microbes with MetaSBT https://training.galaxyproject.org//topics/microbiome/tutorials/metasbt/tutorial.html Microbial ecology, Taxonomy 2025-08-25 2025-08-25 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 22 28 4.566667 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 0 372 600 3.266667 0
Microbiome Binning of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html Metagenomics, Sequence assembly Genome assembly, Sequence assembly validation, Sequencing quality control, Validation, Statistical calculation, Sequence composition calculation 2023-12-05 2025-05-15 6 True False True False checkm_lineage_wf, megahit GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.org.au 0 5087 6255 1.516667 0
Microbiome QIIME 2 Moving Pictures https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding 2024-03-14 2024-03-14 1 external False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 499 780 2.783333 0
Microbiome 16S Microbial Analysis with mothur (short) https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Visualisation, Phylogenetic analysis, Sequence read processing, Sequence clustering, Sequencing quality control, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Taxonomic classification, DNA barcoding, Phylogenetic tree generation 2019-05-13 2024-06-14 5 True False True True mothur_chimera_vsearch, mothur_classify_otu, mothur_dist_shared, mothur_pre_cluster, XY_Plot_1, mothur_count_groups, mothur_heatmap_sim, mothur_summary_single, collapse_dataset, mothur_dist_seqs, mothur_tree_shared, mothur_cluster, mothur_remove_groups, mothur_sub_sample, newick_display, mothur_filter_seqs, mothur_classify_seqs, mothur_venn, mothur_summary_seqs, mothur_remove_seqs, mothur_screen_seqs, mothur_remove_lineage, mothur_cluster_split, mothur_count_seqs, mothur_unique_seqs, mothur_make_shared, mothur_rarefaction_single UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 4832 8034 4.600000 0
Microbiome 16S Microbial Analysis with mothur (extended) https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Visualisation, Phylogenetic analysis, Sequence read processing, Sequence clustering, Sequencing quality control, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Taxonomic classification, DNA barcoding, Phylogenetic tree generation 2017-02-12 2024-03-14 4 True False False True mothur_chimera_vsearch, mothur_classify_otu, mothur_dist_shared, mothur_pre_cluster, XY_Plot_1, taxonomy_krona_chart, mothur_count_groups, mothur_make_contigs, mothur_heatmap_sim, mothur_summary_single, mothur_dist_seqs, mothur_tree_shared, mothur_cluster, mothur_remove_groups, mothur_sub_sample, newick_display, mothur_filter_seqs, mothur_classify_seqs, mothur_venn, mothur_align_seqs, mothur_summary_seqs, mothur_remove_seqs, mothur_screen_seqs, mothur_remove_lineage, mothur_make_biom, mothur_taxonomy_to_krona, mothur_cluster_split, mothur_count_seqs, mothur_unique_seqs, mothur_get_groups, mothur_make_shared, mothur_seq_error, mothur_rarefaction_single UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 11146 16361 2.750000 0
Variant Analysis Pox virus genome analysis from tiled-amplicon sequencing data https://training.galaxyproject.org//topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html Primer removal, Sequence alignment analysis, Genome indexing, Local alignment, Sequence alignment, Sequencing quality control, Sequence analysis, Global alignment, Multiple sequence alignment, Sequence contamination filtering, Generation, Read mapping 2023-05-15 2024-03-20 4 True False False True __APPLY_RULES__, samtools_merge, Cut1, compose_text_param, param_value_from_file, Grep1, Add_a_column1, __ZIP_COLLECTION__, EMBOSS: maskseq51, datamash_ops, fasta_regex_finder, qualimap_bamqc, mimodd_info, fasta_compute_length, fastp, rbc_mafft, ivar_consensus, bwa_mem, ivar_trim, samtools_view, upload1, fatovcf UseGalaxy.eu UseGalaxy.cz 0 949 1130 2.483333 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 Phylogenetic tree visualisation, Sequence alignment analysis, Statistical calculation, Local alignment, Sequence composition calculation, Sequencing quality control, Genome visualisation, Sequence alignment, Sequence analysis, Global alignment, Validation, Variant calling, Sequence contamination filtering, Taxonomic classification, Antimicrobial resistance prediction, Phylogenetic tree generation 2020-07-25 2024-07-26 30 True False True True EMBOSS:%20seqret84, multiqc, tp_sed_tool, tp_awk_tool, jbrowse, EMBOSS: seqret84, tb_profiler_profile, qualimap_bamqc, tbvcfreport, tb_variant_filter, fastp, __FLATTEN__, bcftools_consensus, fastqc, jvarkit_wgscoverageplotter, kraken2, mosdepth, upload1, samtools_stats, snippy 0 7353 11397 3.016667 0
Variant Analysis Avian influenza viral strain analysis from gene segment sequencing data https://training.galaxyproject.org//topics/variant-analysis/tutorials/aiv-analysis/tutorial.html Phylogenetic analysis, Primer removal, Data retrieval, De-novo assembly, Data handling, Genome indexing, Sequence alignment analysis, Sequence file editing, Sequence alignment, Sequencing quality control, Multiple sequence alignment, Sequence analysis, Sequence contamination filtering, Generation, Read mapping 2022-11-21 2024-10-04 10 True False False False tp_find_and_replace, ivar_consensus, collapse_dataset, Show beginning1, seqtk_subseq, bamtools_split_ref, bwa_mem, fastp, upload1, __RELABEL_FROM_FILE__, vapor, samtools_view, iqtree, rbc_mafft, Grep1, qualimap_bamqc UseGalaxy.eu UseGalaxy.cz 0 1905 2691 2.550000 0
Transcriptomics Whole transcriptome analysis of Arabidopsis thaliana https://training.galaxyproject.org//topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html Visualisation, Primer removal, RNA-Seq quantification, Validation, Sequence composition calculation, Differential gene expression analysis, Read mapping, Sequence trimming, Sequencing quality control, Read pre-processing, Gene expression analysis, RNA-Seq analysis 2021-04-08 2025-08-10 18 True True True True sort1, filter_by_fasta_ids, deseq2, cat1, Filter1, __MERGE_COLLECTION__, trim_galore, rbc_mirdeep2_mapper, Cut1, sample_seqs, salmon, multiqc, rbc_mirdeep2_quantifier, targetfinder, falco UseGalaxy.cz 0 2603326 6856061 5.100000 0
Sequence analysis Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants https://training.galaxyproject.org//topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html Phylogenetic inference (from molecular sequences), Phylogenetic analysis, Sequence analysis, Phylogenetic tree editing, Multiple sequence alignment 2025-03-26 2025-04-27 2 True False True True filter_by_fasta_ids, trimal, Filter1, tapscan_classify, Remove beginning1, Cut1, iqtree, quicktree, ete_treeviewer, rbc_mafft UseGalaxy.eu 0 186 234 1.133333 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, ncbi_blastx_wrapper, bg_diamond Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au GalaxyTrakr, UseGalaxy.no 0 1555 1967 2.916667 0
Single Cell Analysis of plant scRNA-Seq Data with Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-plant/tutorial.html Principal component visualisation, Expression profile clustering, Differential gene expression analysis 2021-04-08 2025-02-13 7 True False True True scanpy_plot, anndata_import, scanpy_filter, scanpy_inspect, scanpy_remove_confounders, scanpy_cluster_reduce_dimension, scanpy_normalize, anndata_manipulate UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2597 3244 1.483333 0
Proteomics Statistical analysis of DIA data https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.html Differential protein expression profiling, Tag-based peptide identification, Spectrum calculation 2020-12-02 2023-11-09 9 True False False True Filter1, histogram_rpy, Grep1, msstats UseGalaxy.eu, UseGalaxy.no UseGalaxy.cz, UseGalaxy.org.au 0 1292 1821 2.666667 0
Proteomics Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-hla-binding-novel-peptides/tutorial.html 2025-01-14 2025-07-02 1 True False False True Filter1, Remove beginning1, pepquery2, iedb_api, Cut1, query_tabular, table_compute UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 29 31 1.400000 0
Proteomics Proteogenomics 2: Database Search https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html Conversion, Peptide database search 2018-11-20 2025-05-08 24 True False True True peptide_shaker, tab2fasta, search_gui, query_tabular, mz_to_sqlite, ident_params UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 1495 2231 4.750000 0
Proteomics Library Generation for DIA Analysis https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html Heat map generation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Principal component plotting, Imputation, Clustering 2020-12-02 2025-06-02 12 True False False True Filter1, TargetedFileConverter, diapysef, OpenSwathAssayGenerator, maxquant, OpenSwathDecoyGenerator UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 4476 5846 1.366667 0
Proteomics Proteogenomics 3: Novel peptide analysis https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.html 2018-11-20 2025-05-15 20 True False True True ncbi_blastp_wrapper, query_tabular, pep_pointer, peptide_genomic_coordinate UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 1577 2257 2.550000 0
Proteomics metaQuantome 3: Taxonomy https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy Heat map generation, Visualisation, Filtering, Quantification, Functional clustering, Principal component visualisation, Indexing, Query and retrieval, Differential protein expression analysis, Statistical inference 2020-10-29 2024-03-15 14 True False False True metaquantome_sample, metaquantome_stat, metaquantome_db, metaquantome_filter, metaquantome_expand, metaquantome_viz UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 434 572 2.400000 0
Proteomics Neoantigen 1a: Fusion-Database-Generation https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-fusion-database-generation/tutorial.html Sequence alignment 2025-01-14 2025-07-02 1 True False False True CONVERTER_gz_to_uncompressed, tp_awk_tool, rna_star, tab2fasta, arriba, query_tabular, arriba_get_filters, regex1 UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 99 126 1.116667 0
Proteomics Neoantigen 2: Database merge and FragPipe discovery https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.html 2025-01-14 2025-07-02 1 True False False True collapse_dataset, Remove beginning1, fasta_merge_files_and_filter_unique_sequences, fragpipe, validate_fasta_database, query_tabular, Grep1 UseGalaxy.eu UseGalaxy.org.au 0 104 129 1.766667 0
Proteomics Clinical Metaproteomics 2: Discovery https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html Heat map generation, Visualisation, Protein quantification, Statistical calculation, Filtering, Standardisation and normalisation, Formatting, Principal component plotting, Imputation, Clustering 2024-02-06 2025-08-10 5 True False True True peptide_shaker, fasta_cli, Filter1, fasta2tab, Grouping1, msconvert, Remove beginning1, filter_tabular, fasta_merge_files_and_filter_unique_sequences, query_tabular, tp_cat, Cut1, search_gui, maxquant, Grep1, ident_params, dbbuilder UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 319 430 7.483333 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 IDMerger, MzTabExporter, PeptideIndexer, IDConflictResolver, ConsensusID, IDFilter, MSGFPlusAdapter, FalseDiscoveryRate, FileMerger, FileFilter, FeatureFinderMultiplex, IDMapper, HighResPrecursorMassCorrector 0 820 1139 1.433333 0
Proteomics Proteogenomics 1: Database Creation https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html Sequence alignment, Sequence annotation, Statistical calculation, Variant calling, Transcriptome assembly, RNA-Seq analysis 2018-11-20 2025-05-08 29 True False True True custom_pro_db, gffcompare, fasta2tab, translate_bed, filter_tabular, bed_to_protein_map, fasta_merge_files_and_filter_unique_sequences, freebayes, cat_multi_datasets, sqlite_to_tabular, gffcompare_to_bed, tab2fasta, tp_replace_in_column, hisat2, query_tabular, regexColumn1, stringtie UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 5680 9359 2.650000 0
Proteomics Neoantigen 5a: Predicting HLA Binding https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-predicting-hla-binding/tutorial.html Genetic variation analysis, Read mapping 2025-01-14 2025-07-02 1 True False False True tp_awk_tool, query_tabular, seq2hla, optitype UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 39 44 0.066667 0
Proteomics Clinical Metaproteomics 4: Quantitation https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.html Heat map generation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Principal component plotting, Imputation, Clustering 2024-02-06 2025-08-10 5 True False True True maxquant, Grouping1, Grep1, Cut1 UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 167 234 4.083333 0
Proteomics Mass spectrometry imaging: Loading and exploring MSI data https://training.galaxyproject.org//topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.html Proteomics 2018-11-27 2025-04-08 18 True False False True tp_sort_header_tool, cardinal_quality_report, Grep1, cardinal_data_exporter UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2672 4154 1.666667 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, DecoyDatabase, fasta_merge_files_and_filter_unique_sequences, tab2fasta, addValue, dbbuilder UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.no 0 4598 7334 2.133333 0
Proteomics Label-free data analysis using MaxQuant https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-label-free/tutorial.html Heat map generation, Visualisation, Protein quantification, Spectrum calculation, Statistical calculation, Tag-based peptide identification, Standardisation and normalisation, Differential protein expression profiling, Principal component plotting, Imputation, Clustering 2020-04-29 2025-05-21 14 True False False True tp_sort_header_tool, Filter1, Add_a_column1, histogram_rpy, Cut1, maxquant, msstats, Grep1 UseGalaxy.eu, UseGalaxy.no UseGalaxy.cz, UseGalaxy.org.au 0 19606 28670 1.766667 0
Proteomics Machine Learning Modeling of Anticancer Peptides https://training.galaxyproject.org//topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.html 2021-01-22 2023-11-09 8 True False False True pdaug_merge_dataframes, pdaug_sequence_property_based_descriptors, pdaug_ml_models, pdaug_addclasslabel, pdaug_basic_plots UseGalaxy.be 0 1006 1508 2.250000 0
Proteomics Neoantigen 4: Variant Annotation https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-variant-annotation/tutorial.html 2025-01-14 2025-07-02 1 True False False True Convert characters1, tab2fasta, query_tabular, regexColumn1, pep_pointer UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 55 68 1.266667 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 MQoutputfilter, tp_cut_tool, retr_pepatlas1, retrieve_from_hpa, rna_abbased_data, IDconverter, Jvenn, prot_features UseGalaxy.be, UseGalaxy.fr 0 1599 2175 2.583333 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 Heat map generation, Visualisation, Protein quantification, Spectrum calculation, Statistical calculation, Tag-based peptide identification, Standardisation and normalisation, Differential protein expression profiling, Principal component plotting, Imputation, Clustering 2021-02-17 2025-09-22 19 True False True True Summary_Statistics1, Filter1, fasta2tab, tp_easyjoin_tool, uniprot, Cut1, datamash_ops, tp_replace_in_column, maxquant, msstats, Grep1, ggplot2_heatmap2 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 8348 13492 2.683333 0
Proteomics Neoantigen 3: PepQuery2 Verification https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-peptide-verification/tutorial.html Formatting, Filtering 2025-01-14 2025-07-02 1 True False False True ncbi_blastp_wrapper, msconvert, pepquery2, tab2fasta, query_tabular UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 42 50 2.483333 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 cluter_profiler, reactome_analysis, MQoutputfilter, retrieve_from_hpa, rna_abbased_data, IDconverter, Jvenn UseGalaxy.be, UseGalaxy.fr 0 3015 4398 2.800000 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_peptide, pyprophet_score, OpenSwathWorkflow, Grep1, msconvert, pyprophet_protein, pyprophet_export, pyprophet_merge UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 2984 4207 2.383333 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.cz, UseGalaxy.eu, UseGalaxy.org.au 0 1933 2647 1.800000 0
Proteomics Peptide and Protein ID using SearchGUI and PeptideShaker https://training.galaxyproject.org//topics/proteomics/tutorials/protein-id-sg-ps/tutorial.html 2017-06-12 2025-04-08 28 True False False True peptide_shaker, PeakPickerHiRes, FileConverter, search_gui, Grep1 0 2991 4843 1.916667 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 IDMerger, FileInfo, PeptideIndexer, IDScoreSwitcher, ConsensusID, msconvert, IDFilter, MSGFPlusAdapter, PeakPickerHiRes, FalseDiscoveryRate, TextExporter, IDPosteriorErrorProbability, XTandemAdapter, Grep1, FidoAdapter UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 3326 5597 2.883333 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 msstatstmt, Grep1, unipept UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 261 350 2.983333 0
Proteomics Neoantigen 1b: Non-Reference-Database-Generation https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html Sequence alignment, Sequence annotation, Statistical calculation, Variant calling, Transcriptome assembly, RNA-Seq analysis 2025-01-14 2025-07-02 1 True False False True CONVERTER_gz_to_uncompressed, custom_pro_db, gffcompare, fasta2tab, translate_bed, filter_tabular, bed_to_protein_map, fasta_merge_files_and_filter_unique_sequences, freebayes, sqlite_to_tabular, tp_cat, gffcompare_to_bed, tab2fasta, hisat2, query_tabular, regexColumn1, stringtie UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 49 55 0.666667 0
Proteomics Multiomics data analysis using MultiGSEA https://training.galaxyproject.org//topics/proteomics/tutorials/multiGSEA-tutorial/tutorial.html Aggregation, Pathway analysis, Gene-set enrichment analysis 2025-03-10 2025-03-11 2 True False False True Filter1, multigsea, tp_grep_tool UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org.au 0 201 219 2.000000 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 peptide_shaker, unipept, search_gui, query_tabular, sqlite_to_tabular UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz 0 2832 4526 2.683333 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 collapse_dataset, Filter1, Grouping1, Remove beginning1, fasta_merge_files_and_filter_unique_sequences, pepquery2, tp_cat, Cut1, query_tabular, uniprotxml_downloader, dbbuilder UseGalaxy.cz, UseGalaxy.eu UseGalaxy.org.au 0 179 244 6.016667 0
Proteomics Peptide and Protein Quantification via Stable Isotope Labelling (SIL) https://training.galaxyproject.org//topics/proteomics/tutorials/protein-quant-sil/tutorial.html 2017-03-17 2025-04-08 32 True False False True FileInfo, Summary_Statistics1, ProteinQuantifier, XTandemAdapter, PeptideIndexer, IDConflictResolver, IDScoreSwitcher, tp_tail_tool, FalseDiscoveryRate, IDMapper, MultiplexResolver, IDPosteriorErrorProbability, histogram_rpy, TextExporter, FeatureFinderMultiplex, Grep1, FidoAdapter UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 1327 1866 1.583333 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_peptide_sequence_analysis, pdaug_peptide_data_access, pdaug_merge_dataframes, pdaug_sequence_property_based_descriptors, pdaug_tsvtofasta, pdaug_fishers_plot, pdaug_addclasslabel, pdaug_basic_plots UseGalaxy.be 0 705 963 2.416667 0
Proteomics MaxQuant and MSstats for the analysis of TMT data https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.html Heat map generation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Principal component plotting, Imputation, Clustering 2021-08-13 2025-01-08 11 True False False True msstatstmt, maxquant UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 4159 5568 1.633333 0
Proteomics Secretome Prediction https://training.galaxyproject.org//topics/proteomics/tutorials/secretome-prediction/tutorial.html 2017-04-13 2025-04-08 15 True False False True wolf_psort, Filter1, get_subontology_from, tp_cut_tool, bg_uniq, tp_easyjoin_tool, term_id_vs_term_name, uniprot, Convert characters1, comp1, tp_sorted_uniq, Grep1 0 627 946 1.483333 0
Proteomics metaQuantome 2: Function https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics Heat map generation, Visualisation, Filtering, Quantification, Functional clustering, Principal component visualisation, Indexing, Query and retrieval, Differential protein expression analysis, Statistical inference 2020-10-29 2024-03-15 14 True False False True metaquantome_sample, metaquantome_stat, metaquantome_db, metaquantome_filter, metaquantome_expand, metaquantome_viz UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 406 577 4.233333 0
Proteomics metaQuantome 1: Data creation https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Formatting, Visualisation, Label-free quantification, Prediction and recognition, Filtering 2020-10-16 2024-03-14 20 True False False True peptide_shaker, Filter1, msconvert, Remove beginning1, unipept, regex1, flashlfq, Cut1, search_gui, tp_replace_in_column, query_tabular, Grep1, tp_replace_in_line UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 870 1481 3.850000 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 Grouping1, bioconductor_scp UseGalaxy.eu, UseGalaxy.org.au 0 165 213 1.150000 0
Proteomics Clinical Metaproteomics 1: Database-Generation https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.html Expression analysis, de Novo sequencing, Target-Decoy, Tag-based peptide identification, Protein identification 2024-02-06 2025-07-30 7 True False True True fasta_merge_files_and_filter_unique_sequences, metanovo, uniprotxml_downloader, dbbuilder UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 534 825 4.550000 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 2743129 7359755 2.516667 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 7590 12294 0.900000 0
Sequence analysis Mapping https://training.galaxyproject.org//topics/sequence-analysis/tutorials/mapping/tutorial.html Mapping Primer removal, Read pre-processing, Data handling, Sequence alignment analysis, Statistical calculation, Sequence composition calculation, Sequence trimming, Sequencing quality control, Genome visualisation, Validation, Read mapping 2016-10-04 2025-03-31 43 True True True True bamFilter, bowtie2, trim_galore, multiqc, jbrowse, samtools_stats, fastqc UseGalaxy.eu, UseGalaxy.org.au Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2807213 7467764 5.233333 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 Visualisation, Phylogenetic analysis, Sequence read processing, Data handling, Sequence clustering, Sequence file editing, Sequencing quality control, Taxonomic classification, DNA barcoding, Demultiplexing 2024-01-08 2024-03-05 2 True False False True fastq_to_tabular, ncbi_blastn_wrapper, seqtk_trimfq, fastq_groomer, seqtk_mergepe, aligned_to_consensus, qiime_align_seqs, regex1, __FILTER_FROM_FILE__, ab1_fastq_converter, cshl_fastq_to_fasta, __SORTLIST__, fastq_masker_by_quality, mothur_degap_seqs, mothur_merge_files, unzip, tab2fasta, filter_by_fasta_ids, collection_element_identifiers, cshl_fastx_reverse_complement UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 3047 3836 1.766667 0
Sequence analysis Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes https://training.galaxyproject.org//topics/sequence-analysis/tutorials/viral_primer_design/tutorial.html PCR primer design, Sequence alignment, Multiple sequence alignment, Global alignment, Sequence alignment analysis, Sequence analysis, Local alignment 2025-03-20 2025-03-20 2 True False False True fasta_compute_length, EMBOSS: degapseq20, varvamp, split_file_to_collection, rbc_mafft, ncbi_makeblastdb UseGalaxy.eu 0 427 504 1.033333 0
Sequence analysis Quality Control https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-control/tutorial.html Primer removal, Validation, Box-Whisker plot plotting, Statistical calculation, Sequence composition calculation, Scatter plot plotting, Sequencing quality control, Sequence trimming, Read pre-processing 2016-10-04 2025-03-29 48 True True True True pycoqc, cutadapt, fastqe, nanoplot, multiqc, fastqc UseGalaxy.eu, UseGalaxy.org.au Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr 0 2846891 7549890 5.550000 0
Sequence analysis Screening assembled genomes for contamination using NCBI FCS https://training.galaxyproject.org//topics/sequence-analysis/tutorials/ncbi-fcs/tutorial.html Sequence trimming, Sequence assembly validation, Sequence contamination filtering 2024-04-16 2024-04-16 2 True False False True ncbi_fcs_adaptor, ncbi_fcs_gx GalaxyTrakr 0 1671 2276 2.283333 0
Sequence analysis Quality and contamination control in bacterial isolate using Illumina MiSeq Data https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Visualisation, Expression analysis, Cross-assembly, Statistical calculation, Sequencing quality control, Sequence contamination filtering, Taxonomic classification, Read mapping 2024-07-15 2025-03-20 4 True False True True recentrifuge, fastp, upload1, kraken2, est_abundance, falco UseGalaxy.eu, UseGalaxy.fr UseGalaxy.cz 0 1420 1852 2.933333 0
Single Cell Bulk RNA Deconvolution with MuSiC https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music/tutorial.html 2022-02-11 2025-02-14 10 True False True True music_deconvolution, music_construct_eset, music_inspect_eset UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 3757 4769 1.650000 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 2025-05-07 24 True False True True sceasy_convert, alevin, _salmon_kallisto_mtx_to_10x, join1, _ensembl_gtf2gene_list, dropletutils_empty_drops, Cut1, anndata_inspect, _dropletBarcodePlot, dropletutils_read_10x, anndata_manipulate UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 3356 5119 3.533333 0
Single Cell Converting between common single cell data formats https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-data-ingest/tutorial.html Community profiling, Loading 2024-02-13 2025-03-11 4 True False False True sceasy_convert, fastq_to_tabular, Filter1, datamash_transpose, join1, tp_cut_tool, scanpy_filter_cells, tp_tail_tool, seurat_read10x, regexColumn1, dropletutils, monocle3_create, Cut1, tabular_to_fastq, anndata_inspect, anndata_ops, dropletutils_read_10x UseGalaxy.eu 0 2305 2748 1.283333 0
Single Cell Pre-processing of 10X Single-Cell RNA Datasets https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html Sequencing quality control, Sequence alignment, Community profiling, Loading, Validation 2019-09-11 2025-04-29 13 True False True True multiqc, dropletutils, rna_starsolo UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 11945 15432 1.866667 0
Single Cell Pre-processing of Single-Cell RNA Data https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing/tutorial.html Sequence alignment, Sequencing quality control, RNA-Seq quantification, Read summarisation, Data handling, Validation, Sequence alignment analysis 2019-02-22 2025-04-08 5 True True False True featurecounts, bamFilter, tp_sed_tool, collection_column_join, rna_star, umi_tools_extract, __FLATTEN__, multiqc, umi_tools_count, samtools_stats UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2749274 7367747 4.766667 0
Single Cell Pseudobulk Analysis with Decoupler and EdgeR https://training.galaxyproject.org//topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html Principal component visualisation, Expression profile clustering, Differential gene expression analysis 2025-02-12 2025-05-09 8 True False True True column_remove_by_header, tp_awk_tool, decoupler_pseudobulk, edger, scanpy_filter, anndata_inspect, volcanoplot, tp_replace_in_column, __EXTRACT_DATASET__, anndata_manipulate, tp_replace_in_line UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 1304 1520 0.683333 0
Single Cell Single-cell quality control with scater https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scater-qc/tutorial.html Sequence visualisation, Sequencing quality control, Read pre-processing 2019-10-23 2025-02-14 6 True False False True scater_plot_dist_scatter, scater_filter, scater_create_qcmetric_ready_sce, scater_plot_pca UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz 0 679 768 0.716667 0
Single Cell GO Enrichment Analysis on Single-Cell RNA-Seq Data https://training.galaxyproject.org//topics/single-cell/tutorials/GO-enrichment/tutorial.html Gene-set enrichment analysis 2024-09-17 2025-04-08 8 True True False True tp_split_on_column, gprofiler_gost, Cut1, goenrichment UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 636446 1533535 3.266667 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, Genome indexing, Statistical calculation, Peak calling, Sequence composition calculation, Differential gene expression analysis, Gene regulatory network analysis, Sequence alignment, Sequencing quality control, Principal component visualisation, Enrichment analysis, Imputation, Generation, Expression profile clustering, Read mapping 2023-04-24 2025-02-13 9 True False False True scanpy_plot, bwa_mem, episcanpy_preprocess, bedtools_sortbed, sinto_fragments, anndata_inspect, macs2_callpeak, tp_sorted_uniq, episcanpy_build_matrix, sinto_barcode, fastqc UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 5775 6808 1.100000 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 2710683 7245713 2.516667 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 0 584 820 3.883333 0
Single Cell Removing the effects of the cell cycle https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html Principal component visualisation, Expression profile clustering, Differential gene expression analysis 2023-01-25 2025-03-11 14 True False False True sort1, scanpy_plot, cat1, tp_easyjoin_tool, scanpy_inspect, anndata_inspect, scanpy_regress_variable, scanpy_cluster_reduce_dimension, addValue, table_compute, anndata_manipulate 0 2028 2394 0.783333 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 tp_find_and_replace, sceasy_convert, tp_grep_tool, hca_matrix_downloader, seurat_read10x, retrieve_scxa, scanpy_read_10x, anndata_ops, regexColumn1 UseGalaxy.eu 0 524 696 4.000000 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 Genome indexing, Essential dynamics, Differential gene expression analysis, Gene expression profiling, Dimensionality reduction, Sequence alignment, Principal component visualisation, Generation, Expression profile clustering, Read mapping 2024-07-11 2025-07-02 5 True False False True snapatac2_peaks_and_motif, scanpy_plot, fasta_compute_length, bwa_mem, anndata_manipulate, snapatac2_plotting, snapatac2_clustering, scanpy_filter, scanpy_inspect, Cut1, anndata_inspect, anndata_ops, scanpy_normalize, replace_column_with_key_value_file, snapatac2_preprocessing 0 1380 1676 1.100000 0
Single Cell Clustering 3K PBMCs with Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html Principal component visualisation, Expression profile clustering, Differential gene expression analysis 2019-12-19 2025-04-29 16 True True True True scanpy_plot, anndata_import, scanpy_filter, scanpy_inspect, scanpy_remove_confounders, scanpy_cluster_reduce_dimension, anndata_inspect, datamash_ops, scanpy_normalize, anndata_manipulate UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2750909 7370877 4.533333 0
Single Cell Combining single cell datasets after pre-processing https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html 2022-09-08 2025-04-22 22 True False True True anndata_inspect, Cut1, tp_replace_in_column, anndata_ops, Paste1, anndata_manipulate UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be 0 2426 3396 2.533333 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 3110 3559 0.983333 0
Single Cell Understanding Barcodes https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-umis/tutorial.html Statistical calculation, Sequencing quality control, Sequence composition calculation 2019-02-20 2025-02-14 11 True False True True umi_tools_extract, seq_filter_by_id, fastqc UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au Galaxy@AuBi, UseGalaxy.no 0 6149 7666 1.233333 0
Single Cell Downstream Single-cell RNA analysis with RaceID https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-raceid/tutorial.html Expression analysis, Molecular dynamics, Expression profile clustering 2019-03-25 2025-02-14 7 True False False True raceid_inspecttrajectory, tp_sed_tool, raceid_clustering, datamash_transpose, raceid_filtnormconf, raceid_inspectclusters, raceid_trajectory, datamash_ops, tp_head_tool UseGalaxy.eu, UseGalaxy.no UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org.au 0 1043 1234 1.316667 0
Single Cell Comparing inferred cell compositions using MuSiC deconvolution https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music-4-compare/tutorial.html 2023-01-20 2025-02-13 10 True False False True music_compare UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 265 408 1.083333 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 3119 3699 1.483333 0
Single Cell Filter, plot and explore single-cell RNA-seq data with Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html Principal component visualisation, Expression profile clustering, Differential gene expression analysis 2021-03-24 2025-04-23 24 True False True True interactive_tool_cellxgene_vip, scanpy_find_markers, scanpy_compute_graph, scanpy_filter_cells, scanpy_inspect, Cut1, scanpy_cluster_reduce_dimension, anndata_ops, scanpy_plot, join1, scanpy_find_variable_genes, scanpy_run_pca, scanpy_filter_genes, scanpy_scale_data, scanpy_run_tsne, scanpy_filter, anndata_inspect, scanpy_normalize, scanpy_find_cluster, scanpy_normalise_data, scanpy_run_umap, retrieve_scxa, scanpy_plot_embed, anndata_manipulate UseGalaxy.eu 0 5126 7828 2.616667 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 Filter1, seurat_create, seurat_clustering, csv_to_tabular, seurat_preprocessing, seurat_data, seurat_plot, Cut1, seurat_reduce_dimension UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au MISSISSIPPI 0 1042 1235 1.216667 0
Single Cell Filter, plot, and explore single cell RNA-seq data with Seurat https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html 2024-04-09 2025-03-11 10 True False False True seurat_find_variable_genes, seurat_find_clusters, seurat_read10x, seurat_filter_cells, retrieve_scxa, seurat_plot, seurat_find_markers, seurat_run_umap, seurat_normalise_data, seurat_scale_data, seurat_find_neighbours, seurat_run_pca UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 1718 2103 1.266667 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_parameter_iterator, scanpy_run_umap, scanpy_compute_graph, scanpy_run_tsne, scanpy_plot_embed, scanpy_find_cluster UseGalaxy.eu, UseGalaxy.org.au 0 263 297 1.183333 0
Single Cell Converting NCBI Data to the AnnData Format https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html 2023-12-13 2025-03-11 7 True False True True anndata_manipulate, scanpy_filter_cells, unzip, Cut1, anndata_inspect, tp_replace_in_column, anndata_ops, Paste1, anndata_import UseGalaxy.eu, UseGalaxy.org.au 0 412 488 1.800000 0
Single Cell Evaluating Reference Data for Bulk RNA Deconvolution https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html Visualisation, Annotation 2025-02-02 2025-03-11 3 True False False True datamash_transpose, Remove beginning1, Cut1, ggplot2_violin, Paste1, collapse_dataset, music_deconvolution, tp_sed_tool, tp_awk_tool, Add_a_column1, join1, tp_easyjoin_tool, collection_column_join, __DUPLICATE_FILE_TO_COLLECTION__, table_compute, annotatemyids, tp_multijoin_tool, Count1, bg_column_arrange_by_header, tp_cut_tool, ggplot2_point, music_construct_eset UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 90 110 1.150000 0
Single Cell Multi-sample batch correction with Harmony and SnapATAC2 https://training.galaxyproject.org//topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html Gene expression profiling, Dimensionality reduction, Essential dynamics 2025-02-28 2025-07-02 2 True False False True __FILTER_FROM_FILE__, snapatac2_peaks_and_motif, Show beginning1, collection_element_identifiers, fasta_compute_length, snapatac2_plotting, anndata_inspect, snapatac2_clustering, __EXTRACT_DATASET__, anndata_manipulate, snapatac2_preprocessing UseGalaxy.eu, UseGalaxy.org.au 0 390 440 0.900000 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 2743129 7359755 2.516667 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 4377 5188 1.316667 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_run_paga, scanpy_compute_graph, scanpy_run_diffmap, scanpy_plot_embed, scanpy_run_fdg, scanpy_run_dpt, scanpy_plot_trajectory, anndata_manipulate, scanpy_find_cluster UseGalaxy.eu UseGalaxy.org.au 0 1206 1537 2.283333 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 sort1, annotatemyids, music_manipulate_eset, tp_sed_tool, tp_awk_tool, add_line_to_file, join1, tp_cut_tool, datamash_transpose, table_compute, tp_easyjoin_tool, retrieve_scxa, Cut1, scanpy_read_10x, anndata_inspect, music_construct_eset, regex1 UseGalaxy.cz 0 718 1216 2.250000 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 705705 1704526 2.483333 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 6087 6933 0.800000 0
Single Cell Inferring single cell trajectories with Monocle3 https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html 2022-09-30 2025-04-23 24 True False True True monocle3_reduceDim, monocle3_learnGraph, monocle3_orderCells, Filter1, datamash_transpose, join1, tp_cut_tool, monocle3_diffExp, regexColumn1, monocle3_plotCells, monocle3_create, Cut1, monocle3_preprocess, monocle3_partition, anndata_inspect, monocle3_topmarkers UseGalaxy.eu 0 3823 4751 1.516667 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 sort1, annotatemyids, music_manipulate_eset, tp_sed_tool, column_remove_by_header, tp_awk_tool, table_compute, tp_cut_tool, tp_easyjoin_tool, music_construct_eset, regex1 UseGalaxy.cz 0 664 1070 1.650000 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 1786941 4273439 2.416667 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 1184717 2825431 2.466667 0
Statistics and machine learning Machine learning: classification and regression https://training.galaxyproject.org//topics/statistics/tutorials/classification_regression/tutorial.html 2019-03-07 2025-04-08 13 True False False True plotly_ml_performance_plots, plotly_regression_performance_plots, sklearn_ensemble, sklearn_svm_classifier UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 5643 10179 0.783333 0
Statistics and machine learning Clustering in Machine Learning https://training.galaxyproject.org//topics/statistics/tutorials/clustering_machinelearning/tutorial.html Visualisation 2020-05-08 2025-04-08 14 True False False True csv_to_tabular, sklearn_numeric_clustering, ggplot2_point UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 8390 13950 0.933333 0
Statistics and machine learning Deep Learning (Part 3) - Convolutional neural networks (CNN) https://training.galaxyproject.org//topics/statistics/tutorials/CNN/tutorial.html 2021-04-19 2025-05-09 19 True True True True keras_model_config, keras_train_and_eval, model_prediction, keras_model_builder, sklearn_to_categorical, ml_visualization_ex UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 2601099 6827971 3.400000 0
Statistics and machine learning Basics of machine learning https://training.galaxyproject.org//topics/statistics/tutorials/machinelearning/tutorial.html 2018-11-05 2025-05-13 15 True True True True sklearn_svm_classifier UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.fr, UseGalaxy.no 0 2745817 7363394 5.500000 0
Statistics and machine learning Prepare Data from CbioPortal for Flexynesis Integration https://training.galaxyproject.org//topics/statistics/tutorials/flexynesis_cbio_import/tutorial.html 2025-08-10 2025-08-13 2 True False False True tp_sort_header_tool, table_compute, tp_cut_tool, flexynesis_cbioportal_import, flexynesis_utils, __EXTRACT_DATASET__ UseGalaxy.eu 0 22 22 1.683333 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 0 152 195 2.233333 0
Statistics and machine learning PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis https://training.galaxyproject.org//topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html 2021-05-06 2023-11-09 7 True False False True pancancer_external_sample_status_prediction, pancancer_map_mutation_class, pancancer_classifier, pancancer_targene_summary_figures, pancancer_visualize_decisions, pancancer_targene_cell_line_predictions, pancancer_targene_pharmacology, pancancer_within_disease_analysis, pancancer_compare_within_models, pancancer_apply_weights, pancancer_pathway_count_heatmaps, pancancer_alternative_genes_pathwaymapper 0 768 1207 3.216667 0
Statistics and machine learning Text-mining with the SimText toolset https://training.galaxyproject.org//topics/statistics/tutorials/text-mining_simtext/tutorial.html 2021-04-05 2025-05-07 8 True False False True pmids_to_pubtator_matrix, interactive_tool_simtext_app, pubmed_by_queries UseGalaxy.eu 0 453 621 2.333333 0
Statistics and machine learning Age prediction using machine learning https://training.galaxyproject.org//topics/statistics/tutorials/age-prediction-with-ml/tutorial.html 2019-01-25 2025-04-08 12 True False False True sklearn_build_pipeline, plotly_regression_performance_plots, sklearn_ensemble, sklearn_searchcv, plotly_parallel_coordinates_plot UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.no 0 13115 21176 0.683333 0
Statistics and machine learning Modeling Breast Cancer Subtypes with Flexynesis https://training.galaxyproject.org//topics/statistics/tutorials/flexynesis_classification/tutorial.html 2025-08-13 2025-09-02 3 True False False True Show beginning1, tp_sort_header_tool, datamash_transpose, table_compute, join1, tp_cut_tool, tabpfn, tp_easyjoin_tool, flexynesis_plot, flexynesis, __EXTRACT_DATASET__, pick_value UseGalaxy.eu 0 39 64 2.116667 0
Statistics and machine learning Regression in Machine Learning https://training.galaxyproject.org//topics/statistics/tutorials/regression_machinelearning/tutorial.html 2020-01-25 2025-05-14 19 True True True True sklearn_generalized_linear, sklearn_build_pipeline, plotly_regression_performance_plots, sklearn_ensemble, Remove beginning1, sklearn_searchcv UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no 0 2746327 7363795 3.800000 0
Statistics and machine learning Building the LORIS LLR6 PanCancer Model Using PyCaret https://training.galaxyproject.org//topics/statistics/tutorials/loris_model/tutorial.html 2024-12-13 2025-05-08 2 True True True True PyCaret_Model_Comparison 0 493533 1164023 4.450000 0
Statistics and machine learning Deep Learning (Part 1) - Feedforward neural networks (FNN) https://training.galaxyproject.org//topics/statistics/tutorials/FNN/tutorial.html 2021-04-28 2024-06-14 12 True True True True keras_model_config, plotly_regression_performance_plots, keras_train_and_eval, model_prediction, keras_model_builder UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no 0 2605545 6816890 3.250000 0
Statistics and machine learning Image classification in Galaxy with fruit 360 dataset https://training.galaxyproject.org//topics/statistics/tutorials/fruit_360/tutorial.html 2021-12-01 2024-07-09 8 True True True True keras_model_config, keras_train_and_eval, model_prediction, tp_cut_tool, keras_model_builder, sklearn_to_categorical, ml_visualization_ex UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 2261841 5730844 3.200000 0
Statistics and machine learning Introduction to deep learning https://training.galaxyproject.org//topics/statistics/tutorials/intro_deep_learning/tutorial.html 2020-03-26 2025-04-08 9 True False False True keras_model_config, keras_train_and_eval, model_prediction, keras_model_builder, ml_visualization_ex UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 2378 3049 1.633333 0
Statistics and machine learning Identifing Survival Markers of Brain tumor with Flexynesis https://training.galaxyproject.org//topics/statistics/tutorials/flexynesis_survival/tutorial.html 2025-08-13 2025-08-13 2 True False False True Add_a_column1, flexynesis_plot, flexynesis, datamash_ops, tp_replace_in_column, __EXTRACT_DATASET__ UseGalaxy.eu 0 17 19 2.416667 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_generalized_linear, sklearn_build_pipeline, sklearn_svm_classifier, plotly_ml_performance_plots, sklearn_ensemble, Remove beginning1, sklearn_searchcv, sklearn_nn_classifier UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no 0 2745840 7363738 4.766667 0
Statistics and machine learning Deep Learning (Part 2) - Recurrent neural networks (RNN) https://training.galaxyproject.org//topics/statistics/tutorials/RNN/tutorial.html 2021-02-23 2025-05-10 15 True True True True keras_model_config, keras_train_and_eval, model_prediction, keras_model_builder, ml_visualization_ex UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no 0 2676150 7109336 3.316667 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, flexynesis, flexynesis_utils, __EXTRACT_DATASET__ UseGalaxy.eu 0 17 21 8.750000 0
Statistics and machine learning A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy https://training.galaxyproject.org//topics/statistics/tutorials/gpu_jupyter_lab/tutorial.html 2022-04-06 2025-04-08 9 True False False True Filter1, Cut1, interactive_tool_ml_jupyter_notebook UseGalaxy.eu 0 1170 1491 1.483333 0
Statistics and machine learning Interval-Wise Testing for omics data https://training.galaxyproject.org//topics/statistics/tutorials/iwtomics/tutorial.html Peak calling, Differential gene expression analysis, Differentially-methylated region identification, Comparison, Genome annotation 2018-06-14 2023-11-09 17 True False False True iwtomics_testandplot, iwtomics_plotwithscale, iwtomics_loadandplot UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 360 482 3.050000 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 763886 1846238 3.566667 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 0 421 525 0.716667 0
Statistics and machine learning Introduction to Machine Learning using R https://training.galaxyproject.org//topics/statistics/tutorials/intro-to-ml-with-r/tutorial.html 2021-05-21 2024-10-15 15 True False True False interactive_tool_rstudio UseGalaxy.eu, UseGalaxy.org.au 0 3989 5980 1.083333 0
Synthetic Biology Evaluating and ranking a set of pathways based on multiple metrics https://training.galaxyproject.org//topics/synthetic-biology/tutorials/pathway_analysis/tutorial.html 2022-09-26 2024-06-14 7 True False True True rpfba, rpranker, rpscore, rpthermo 0 608 915 3.116667 0
Synthetic Biology Designing plasmids encoding predicted pathways by using the BASIC assembly method https://training.galaxyproject.org//topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.html 2022-05-12 2024-06-14 8 True False True True selenzy-wrapper, dnabot, rpbasicdesign 0 958 1485 2.633333 0
Synthetic Biology Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools https://training.galaxyproject.org//topics/synthetic-biology/tutorials/retrosynthesis_analysis/tutorial.html 2022-06-23 2024-06-14 8 True False True True rp2paths, get_sbml_model, rpextractsink, rpcompletion, retropath2, rrparser 0 525 772 2.550000 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 1796387 4300472 2.416667 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 2743129 7359756 2.516667 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 0 273 494 2.833333 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 20 20 0.100000 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 0 143 156 2.816667 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 19 21 0.016667 0
Teaching and Hosting Galaxy training Organizing a workshop https://training.galaxyproject.org//topics/teaching/tutorials/organize-workshop/tutorial.html 2018-11-15 2023-11-09 4 True False False False 0 247 268 1.083333 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 6 6 0.000000 0
Teaching and Hosting Galaxy training Training Infrastructure as a Service https://training.galaxyproject.org//topics/teaching/tutorials/setup-tiaas-for-training/tutorial.html 2018-11-15 2023-12-20 4 True False False False 0 210 401 6.550000 0
Teaching and Hosting Galaxy training Running a workshop as instructor https://training.galaxyproject.org//topics/teaching/tutorials/running-workshop/tutorial.html 2018-11-15 2025-04-08 6 True False False False 0 151 279 1.416667 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 0 301 346 4.083333 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 0 116 136 2.516667 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 81 85 0.300000 0
Transcriptomics RNA-RNA interactome data analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-interactome/tutorial.html Sequence trimming, Sequencing quality control, Primer removal, Read pre-processing, Sequence composition calculation, Statistical calculation 2020-03-23 2023-11-09 12 True False False True chira_extract, chira_collapse, cutadapt, chira_merge, chira_map, query_tabular, chira_quantify, fastqc UseGalaxy.be, UseGalaxy.no UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 1441 2193 2.833333 0
Transcriptomics CLIP-Seq data analysis from pre-processing to motif detection https://training.galaxyproject.org//topics/transcriptomics/tutorials/clipseq/tutorial.html Sequencing quality control, Sequence alignment, Sequence trimming, Primer removal, Read pre-processing, Statistical calculation, Sequence composition calculation, Mapping 2018-08-17 2023-11-09 23 True False False True sort1, wig_to_bigWig, deeptools_plot_fingerprint, peakachu, bctools_extract_alignment_ends, tp_awk_tool, __SORTLIST__, umi_tools_extract, rcas, deeptools_plot_correlation, umi_tools_dedup, rna_star, deeptools_multi_bam_summary, meme_chip, fastqc, __MERGE_COLLECTION__, bedtools_slopbed, cutadapt, bedtools_genomecoveragebed_bedgraph, Extract genomic DNA 1 UseGalaxy.no 0 8118 16093 1.883333 0
Transcriptomics Genome-wide alternative splicing analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html Visualisation, Sequence assembly validation, Data handling, Sequence comparison, Sequence composition calculation, Formatting, Protein sequence analysis, Sequence alignment, Validation, Sequence analysis, Sequence contamination filtering, Transcriptome assembly, RNA-Seq analysis, De-novo assembly, Statistical calculation, Sequencing quality control, Sequence annotation 2023-05-17 2025-03-28 11 True True False True sort1, Remove beginning1, tp_uniq_tool, pygenomeTracks, Cut1, gtftobed12, addValue, multiqc, rseqc_geneBody_coverage, isoformswitchanalyzer, __FILTER_FROM_FILE__, gffcompare, tp_awk_tool, Add_a_column1, gffread, pfamscan, gene2exon1, stringtie_merge, rseqc_junction_annotation, rseqc_infer_experiment, fastp, Filter1, rseqc_read_distribution, rseqc_inner_distance, rna_star, rna_quast, __FLATTEN__, cpat, fastqc, collection_element_identifiers, cat1, tp_grep_tool, tp_cat, stringtie, rseqc_junction_saturation UseGalaxy.cz, UseGalaxy.fr 0 1388429 3265386 4.366667 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 tp_sort_header_tool, egsea, Add_a_column1, join1, tp_cut_tool, fgsea, Cut1, goseq UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz 0 25803 41489 1.916667 0
Transcriptomics De novo transcriptome assembly, annotation, and differential expression analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/full-de-novo/tutorial.html de Novo sequencing, De-novo assembly, Statistical calculation, Sequence composition calculation, Gene functional annotation, Sequencing quality control, Validation, Coding region prediction, Transcriptome assembly 2020-02-13 2023-11-09 8 True False False True trinity_align_and_estimate_abundance, trimmomatic, trinity_run_de_analysis, transdecoder, trinity_filter_low_expr_transcripts, trinity_abundance_estimates_to_matrix, trinity, describe_samples, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, trinotate, trinity_samples_qccheck, multiqc, fastqc UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 14301 26028 2.433333 0
Transcriptomics Visualization of RNA-Seq results with heatmap2 https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html 2018-12-31 2023-11-09 13 True False False True datamash_transpose, join1, Cut1, ggplot2_heatmap2 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 76970 127022 1.366667 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, RNA-Seq analysis, Differential gene expression analysis 2025-05-28 2025-06-16 5 True False False True length_and_gc_content, Multivariate, Show beginning1, tp_sort_header_tool, cat1, deseq2, Filter1, Add_a_column1, Grouping1, tp_easyjoin_tool, deg_annotate, Cut1, volcanoplot, goseq, table_compute, ggplot2_heatmap2 UseGalaxy.eu, UseGalaxy.fr UseGalaxy.cz, UseGalaxy.no 0 618 750 1.166667 0
Transcriptomics 1: RNA-Seq reads to counts https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html Read summarisation, RNA-Seq quantification, Primer removal, Data handling, Validation, Statistical calculation, Sequence composition calculation, Formatting, Sequence trimming, Sequencing quality control, Sequence alignment, Read pre-processing 2018-09-23 2024-08-09 33 True False False True rseqc_geneBody_coverage, featurecounts, rseqc_read_distribution, cutadapt, picard_MarkDuplicates, multiqc, collection_column_join, hisat2, samtools_idxstats, rseqc_infer_experiment, fastqc UseGalaxy.eu MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 77170 140734 2.583333 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 blockclust, tp_sort_header_tool, blockbuster, samtools_sort UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 1011 1383 3.050000 0
Transcriptomics Differential abundance testing of small RNAs https://training.galaxyproject.org//topics/transcriptomics/tutorials/srna/tutorial.html Primer removal, RNA-Seq quantification, Statistical calculation, Sequence composition calculation, Differential gene expression analysis, Sequence trimming, Sequence alignment, Sequencing quality control, Read pre-processing, Gene expression analysis, RNA-Seq analysis 2017-06-29 2023-11-09 26 True False False True deseq2, Filter1, trim_galore, fastq_manipulation, samtool_filter2, salmon, hisat2, bedtools_bamtofastq, fastqc UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 6858 12067 2.083333 0
Transcriptomics Network analysis with Heinz https://training.galaxyproject.org//topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html RNA-Seq analysis, Pathway or network analysis, Differential gene expression analysis 2018-10-11 2024-01-15 16 True True False True deseq2, heinz_visualization, heinz_bum, Cut1, heinz, heinz_scoring UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 2745148 7362909 5.783333 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 annotatemyids, mergeCols1, tp_cut_tool, limma_voom, tp_replace_in_line UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au 0 42913 72758 2.266667 0
Transcriptomics GO Enrichment Analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/goenrichment/tutorial.html Gene-set enrichment analysis 2019-01-23 2024-03-05 12 True False False True Filter1, goslimmer, goenrichment Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 22881 37258 1.333333 0
Transcriptomics Visualization of RNA-Seq results with Volcano Plot https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.html 2018-12-31 2025-04-17 16 True False True True volcanoplot UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 151504 249355 1.333333 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 2743129 7359758 2.516667 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 2745653 7363577 4.283333 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 2744123 7361030 6.266667 0
Transcriptomics RNA Seq Counts to Viz in R https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.html 2019-10-08 2024-10-15 21 True False True False interactive_tool_rstudio UseGalaxy.eu, UseGalaxy.org.au 0 4202 5388 1.933333 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 21912 34369 2.183333 0
Transcriptomics RNA-seq Alignment with STAR https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.html 2023-05-15 2023-11-09 6 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 10363 12711 1.450000 0
Transcriptomics Visualization of RNA-Seq results with Volcano Plot in R https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot-r/tutorial.html 2021-06-14 2024-06-14 8 True False True False volcanoplot, interactive_tool_rstudio UseGalaxy.eu, UseGalaxy.org.au 0 30774 42062 1.683333 0
Transcriptomics Reference-based RNA-Seq data analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/ref-based/tutorial.html Visualisation, Pathway or network analysis, Data handling, Differential gene expression analysis, Formatting, Sequence alignment, Exonic splicing enhancer prediction, Read pre-processing, Validation, RNA-Seq analysis, RNA-Seq quantification, Read summarisation, Pathway or network visualisation, Primer removal, Gene functional annotation, Sequencing quality control, Sequence trimming, Enrichment analysis, Read mapping 2016-10-05 2025-06-16 103 True False True True length_and_gc_content, tp_sort_header_tool, pygenomeTracks, Cut1, gtftobed12, rseqc_geneBody_coverage, goseq, multiqc, ggplot2_heatmap2, __FILTER_FROM_FILE__, featurecounts, Add_a_column1, join1, dexseq, deg_annotate, ChangeCase, table_compute, rseqc_infer_experiment, tp_replace_in_line, __TAG_FROM_FILE__, deseq2, Filter1, rseqc_read_distribution, picard_MarkDuplicates, rna_star, __FLATTEN__, dexseq_count, collection_element_identifiers, cat1, tp_grep_tool, pathview, Grouping1, __MERGE_COLLECTION__, __EXTRACT_DATASET__, tp_tail_tool, cutadapt, samtools_view, tp_cat, samtools_idxstats, falco UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au UseGalaxy.cz 0 181974 343682 2.800000 0
Transcriptomics Pathway analysis with the MINERVA Platform https://training.galaxyproject.org//topics/transcriptomics/tutorials/minerva-pathways/tutorial.html RNA-Seq quantification, Read summarisation, Read pre-processing, Data handling, Statistical calculation, Primer removal, Sequence composition calculation, Annotation, Gene functional annotation, Sequencing quality control, Sequence trimming, Sequence alignment, Validation, RNA-Seq analysis 2024-03-28 2024-07-26 3 True False False True tp_sort_header_tool, fasterq_dump, Cut1, rseqc_geneBody_coverage, goseq, multiqc, tp_sorted_uniq, Grep1, featurecounts, Add_a_column1, join1, collection_column_join, tp_replace_in_line, annotatemyids, rseqc_read_distribution, fastqc, cutadapt, hisat2, limma_voom, __EXTRACT_DATASET__ UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 571 688 1.700000 0
Transcriptomics De novo transcriptome reconstruction with RNA-Seq https://training.galaxyproject.org//topics/transcriptomics/tutorials/de-novo/tutorial.html RNA-Seq quantification, Read summarisation, Statistical calculation, Sequence composition calculation, Differential gene expression analysis, Sequence alignment, Sequencing quality control, Sequence annotation, Transcriptome assembly, RNA-Seq analysis 2017-02-19 2024-06-14 36 True False True True trimmomatic, featurecounts, deseq2, gffcompare, Filter1, stringtie, hisat2, stringtie_merge, deeptools_bam_coverage, fastqc Galaxy@AuBi, UseGalaxy.fr UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 16467 28454 2.650000 0
Variant Analysis Introduction to Variant analysis https://training.galaxyproject.org//topics/variant-analysis/tutorials/introduction/slides.html 2016-08-19 2023-03-05 2 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 2743129 7359758 2.516667 0
Variant Analysis Calling very rare variants https://training.galaxyproject.org//topics/variant-analysis/tutorials/dunovo/tutorial.html Genome indexing, Statistical calculation, Sequence composition calculation, Sequence alignment, Sequencing quality control, Variant calling, Generation, Read mapping 2017-02-22 2024-12-09 21 True False False True naive_variant_caller, Filter1, bwa_mem, align_families, correct_barcodes, bamleftalign, make_families, dunovo, allele_counts_1, sequence_content_trimmer, fastqc 0 1934 3036 1.766667 0
Variant Analysis Mapping and molecular identification of phenotype-causing mutations https://training.galaxyproject.org//topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html 2018-03-07 2023-11-09 16 True False False True tp_find_and_replace, snpEff, mimodd_vcf_filter, mimodd_map, mimodd_varcall, snpEff_download, mimodd_varextract, mimodd_varreport UseGalaxy.be, UseGalaxy.eu GalaxyTrakr, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 4270 6297 2.733333 0
Variant Analysis Trio Analysis using Synthetic Datasets from RD-Connect GPAP https://training.galaxyproject.org//topics/variant-analysis/tutorials/trio-analysis/tutorial.html Genetic variation analysis, Sequence analysis 2022-05-19 2024-09-17 13 True False True True CONVERTER_gz_to_uncompressed, snpEff, tp_grep_tool, Filter1, pyega3, bcftools_norm, gene_iobio_display_generation_iframe, bcftools_merge, gemini_inheritance, regexColumn1, CONVERTER_uncompressed_to_gz, gemini_load UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org.au 0 1887 3370 3.750000 0
Variant Analysis Identification of somatic and germline variants from tumor and normal sample pairs https://training.galaxyproject.org//topics/variant-analysis/tutorials/somatic-variants/tutorial.html Visualisation, Data handling, Statistical calculation, Genome indexing, Sequence alignment analysis, Sequence composition calculation, Sequence alignment, Sequencing quality control, Validation, Variant calling, Generation, Read mapping 2019-03-13 2025-03-20 16 True False False True gemini_load, snpEff, bg_column_arrange_by_header, samtools_calmd, varscan_somatic, bamFilter, trimmomatic, bwa_mem, tp_easyjoin_tool, bamleftalign, samtools_rmdup, multiqc, gemini_annotate, gemini_query, falco, fastqc UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 14100 25468 2.516667 0
Variant Analysis Calling variants in diploid systems https://training.galaxyproject.org//topics/variant-analysis/tutorials/dip/tutorial.html Genetic variation analysis, Statistical calculation, Variant calling, Sequence analysis 2017-02-20 2025-04-28 17 True False False True snpEff, freebayes, vcfallelicprimitives, gemini_query, gemini_db_info, gemini_load UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au 0 15118 26034 3.233333 0
Variant Analysis Somatic Variant Discovery from WES Data Using Control-FREEC https://training.galaxyproject.org//topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html Visualisation, Copy number estimation, Genome indexing, Statistical calculation, Sequence composition calculation, Sequence visualisation, Sequence alignment, Sequencing quality control, Validation, Variant calling, Genome alignment, Generation, Read mapping 2022-10-05 2025-03-20 14 True False False True trimmomatic, samtools_calmd, bwa_mem, Grep1, circos, __RELABEL_FROM_FILE__, falco, __BUILD_LIST__, bamleftalign, samtools_view, samtools_rmdup, tp_text_file_with_recurring_lines, multiqc, control_freec, __EXTRACT_DATASET__, fastqc, tp_replace_in_line UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 1803 2319 2.033333 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 Data handling, Genome indexing, Sequence alignment analysis, Statistical calculation, Sequence composition calculation, Formatting, Sequence alignment, Sequencing quality control, Variant calling, Generation, Read mapping 2017-02-16 2024-03-15 23 True False False True vcffilter2, bamFilter, bwa_mem, picard_MergeSamFiles, picard_MarkDuplicates, freebayes, bamleftalign, Cut1, vcf2tsv, fastqc UseGalaxy.eu, UseGalaxy.fr UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 8428 15272 2.166667 0
Variant Analysis Exome sequencing data analysis for diagnosing a genetic disease https://training.galaxyproject.org//topics/variant-analysis/tutorials/exome-seq/tutorial.html Genome indexing, Statistical calculation, Sequence composition calculation, Sequence alignment, Sequencing quality control, Sequence analysis, Genetic variation analysis, Validation, Variant calling, Generation, Read mapping 2016-08-19 2025-05-11 29 True False True True gemini_load, snpEff, trimmomatic, bwa_mem, bcftools_norm, freebayes, snpEff_download, samtools_view, samtools_rmdup, multiqc, gemini_inheritance, fastqc UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au 0 34328 62707 2.766667 0
Variant Analysis Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates https://training.galaxyproject.org//topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html Visualisation, Primer removal, Genome indexing, Data handling, Sequence alignment, Sequence trimming, Read pre-processing, Generation, Read mapping 2025-02-24 2025-02-24 1 True False False True bcftools_mpileup, collapse_dataset, ncbi_acc_download, Filter1, tp_awk_tool, bwa_mem, trim_galore, ggplot2_point, bcftools_call, fastq_dump, tp_replace_in_column, vcf2tsv, tp_replace_in_line UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au UseGalaxy.cz 0 223 314 1.066667 0
Variant Analysis Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs) https://training.galaxyproject.org//topics/variant-analysis/tutorials/beacon_cnv_query/tutorial.html Genetic variation analysis, Database search, Service discovery 2024-08-06 2024-09-27 3 True False False False beacon2_cnv UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 154 191 2.766667 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 Genetic variation analysis, Database search, Service discovery 2024-08-06 2024-09-27 3 True False False False beacon2_import, cnv_vcf2json, beacon2_cnv, cnv_phenopacket UseGalaxy.eu 0 287 325 0.466667 0
Visualisation Visualisation with Circos https://training.galaxyproject.org//topics/visualisation/tutorials/circos/tutorial.html Sequence visualisation 2020-01-10 2024-10-15 22 True True True True Remove beginning1, circos, Cut1, upload1, random_lines1, Grep1 Galaxy@AuBi, Galaxy@Pasteur, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.no 0 2773076 7407668 4.183333 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, gff2bed1, circos_interval_to_tile, circos, Cut1, deeptools_bam_coverage, circos_wiggle_to_scatter, circos_interval_to_text UseGalaxy.cz, UseGalaxy.fr Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 1351 1711 1.966667 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 1100540 2641459 2.483333 0
Visualisation Visualisations in Galaxy https://training.galaxyproject.org//topics/visualisation/tutorials/introduction/slides.html 2020-01-10 2023-01-12 1 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 2743129 7359761 2.516667 0