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 3443320 8403082 2.166667 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 3445174 8405710 5.483333 0
Galaxy Server administration Galaxy Installation with Ansible https://training.galaxyproject.org//topics/admin/tutorials/ansible-galaxy/tutorial.html Database management, Informatics, Data management 2019-01-28 2026-01-23 109 True True True False 0 3469164 8450939 3.900000 0
Galaxy Server administration Connecting Galaxy to a compute cluster https://training.galaxyproject.org//topics/admin/tutorials/connect-to-compute-cluster/tutorial.html 2018-01-07 2025-11-24 65 True True True False 0 3447461 8410172 5.416667 0
Galaxy Server administration Galaxy Monitoring with gxadmin https://training.galaxyproject.org//topics/admin/tutorials/gxadmin/tutorial.html 2019-01-28 2025-11-13 27 True True True False 0 3444248 8404518 4.850000 0
Galaxy Server administration Reference Data with CVMFS https://training.galaxyproject.org//topics/admin/tutorials/cvmfs/tutorial.html 2019-01-27 2026-01-23 55 True True True False 0 3445582 8406386 5.183333 0
Galaxy Server administration Galaxy Monitoring with Telegraf and Grafana https://training.galaxyproject.org//topics/admin/tutorials/monitoring/tutorial.html 2019-01-31 2025-11-24 54 True True True False 0 3446272 8408498 3.033333 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 3443320 8403083 2.166667 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 3444715 8405250 3.700000 0
Galaxy Server administration Galaxy Interactive Tools https://training.galaxyproject.org//topics/admin/tutorials/interactive-tools/tutorial.html 2020-02-27 2026-01-23 30 True True True False 0 3445714 8406648 4.800000 0
Galaxy Server administration Gearing towards production https://training.galaxyproject.org//topics/admin/tutorials/production/slides.html 2019-01-28 2025-11-20 11 False True True False 0 3443320 8403083 2.166667 0
Galaxy Server administration Data Libraries https://training.galaxyproject.org//topics/admin/tutorials/data-library/tutorial.html 2021-01-14 2025-11-24 35 True True True False 0 3427526 8340387 4.133333 0
Galaxy Server administration Server Maintenance: Cleanup, Backup, and Restoration https://training.galaxyproject.org//topics/admin/tutorials/backup-cleanup/tutorial.html Database management, Informatics, Data management 2019-01-31 2025-11-24 10 True True True False 0 3443941 8403902 10.250000 0
Galaxy Server administration Running Jobs on Remote Resources with Pulsar https://training.galaxyproject.org//topics/admin/tutorials/pulsar/tutorial.html 2019-01-28 2026-01-23 59 True True True False 0 3445963 8407388 4.983333 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 3449895 8414752 3.833333 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 3443320 8403083 2.166667 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 3443320 8403083 2.166667 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 3443320 8403083 2.166667 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 3443320 8403083 2.166667 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 3444052 8404218 2.950000 0
Galaxy Server administration Galactic Database https://training.galaxyproject.org//topics/admin/tutorials/database/slides.html 2019-01-28 2025-11-20 6 False True True False 0 3443320 8403083 2.166667 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 3443320 8403083 2.166667 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 3443320 8403083 2.166667 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 1436378 2807168 1.666667 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 3443320 8403083 2.166667 0
Galaxy Server administration Reference Data with Data Managers https://training.galaxyproject.org//topics/admin/tutorials/reference-genomes/tutorial.html Genome indexing, Generation, Sequence alignment, Read mapping 2019-01-28 2026-01-23 7 True True False False bwa, bwa_mem_index_builder_data_manager, data_manager_fetch_genome_all_fasta_dbkey 0 3443972 8403919 6.066667 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 3443320 8403084 2.166667 0
Galaxy Server administration Setting up Celery Workers for Galaxy https://training.galaxyproject.org//topics/admin/tutorials/celery/tutorial.html 2022-07-16 2025-11-24 19 True True False False 0 2588140 5582634 3.500000 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 3443320 8403084 2.166667 0
Galaxy Server administration Deploying a Beacon v1 in Galaxy https://training.galaxyproject.org//topics/admin/tutorials/beacon/tutorial.html 2023-04-16 2025-11-22 7 True False False False 0 166 184 2.083333 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 78 85 1.983333 0
Galaxy Server administration Enable upload via FTP https://training.galaxyproject.org//topics/admin/tutorials/ftp/tutorial.html 2021-06-18 2025-12-18 29 True False False False 0 1298 1761 1.650000 0
Galaxy Server administration Upgrading Galaxy https://training.galaxyproject.org//topics/admin/tutorials/upgrading/tutorial.html 2021-06-08 2026-01-23 11 True False True False 0 771 1164 2.733333 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 66 73 1.733333 0
Galaxy Server administration Performant Uploads with TUS https://training.galaxyproject.org//topics/admin/tutorials/tus/tutorial.html 2022-03-01 2025-11-22 22 True False True False 0 916 1327 5.383333 0
Galaxy Server administration Monitoring Galaxy and Pulsar with Sentry https://training.galaxyproject.org//topics/admin/tutorials/sentry/tutorial.html 2023-04-19 2025-12-18 13 True False False False 0 249 297 1.533333 0
Galaxy Server administration Galaxy Monitoring with Reports https://training.galaxyproject.org//topics/admin/tutorials/reports/tutorial.html 2019-01-31 2026-01-23 49 True False False False 0 537 707 2.500000 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 0 709 812 0.583333 0
Galaxy Server administration Training Infrastructure as a Service (TIaaS) https://training.galaxyproject.org//topics/admin/tutorials/tiaas/tutorial.html 2020-02-12 2025-11-24 45 True False True False 0 587 776 3.116667 0
Galaxy Server administration Mapping Jobs to Destinations using TPV https://training.galaxyproject.org//topics/admin/tutorials/job-destinations/tutorial.html 2021-01-17 2026-01-23 44 True False True False 0 1756 2714 3.250000 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 0 223 265 1.833333 0
Galaxy Server administration Customizing the look of Galaxy https://training.galaxyproject.org//topics/admin/tutorials/customization/tutorial.html 2023-04-16 2025-11-22 8 True False False False 0 628 767 4.183333 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 86 96 1.616667 0
Galaxy Server administration Use Apptainer containers for running Galaxy jobs https://training.galaxyproject.org//topics/admin/tutorials/apptainer/tutorial.html 2021-01-08 2025-11-24 19 True False True False 0 1138 1446 2.566667 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 3080 5008 1.050000 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 71 89 2.883333 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 8349 16499 0.716667 0
Galaxy Server administration Reference Data with CVMFS without Ansible https://training.galaxyproject.org//topics/admin/tutorials/cvmfs-manual/tutorial.html 2020-06-17 2026-01-23 10 True False False False 0 455 600 2.366667 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 1650 2703 2.233333 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 0 686 996 2.066667 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 0 101 120 1.383333 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 93 101 0.883333 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 1135 1289 0.316667 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 2411 3099 0.433333 0
Galaxy Server administration Deploying a compute cluster in OpenStack via Terraform https://training.galaxyproject.org//topics/admin/tutorials/terraform/tutorial.html 2018-10-27 2024-12-19 15 True True False False 0 3459438 8433344 3.116667 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 2082186 4294942 1.883333 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 2096460 4327318 1.883333 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 2139670 4430714 1.900000 0
Assembly An Introduction to Genome Assembly https://training.galaxyproject.org//topics/assembly/tutorials/general-introduction/tutorial.html Formatting, Statistical calculation, Sequencing quality control, Visualisation, Validation, Sequence composition calculation, De-novo assembly, Sequence assembly validation 2017-05-23 2026-01-23 30 True True True True fastqc, quast, multiqc, fastq_paired_end_interlacer, velvetg, velveth Galaxy@AuBi, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 3480201 8463254 5.016667 0
Assembly Genome Assembly Quality Control https://training.galaxyproject.org//topics/assembly/tutorials/assembly-quality-control/tutorial.html Biodiversity, Sequence assembly, Data quality management Visualisation, De-novo assembly, Genome assembly, k-mer counting, Phasing, Scaffolding, Sequence assembly validation 2022-08-26 2025-06-04 6 True True False True quast, merqury, busco, chromeister, meryl UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au UseGalaxy.cz 0 2542971 5449699 4.183333 0
Assembly Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial resistance Statistical calculation, Genome assembly, Sequence alignment, Sequence contamination filtering, Sequence assembly validation, Cross-assembly, Sequence composition calculation, Scatter plot plotting, Filtering, Mapping assembly, Visualisation, De-novo assembly, Box-Whisker plot plotting, Read mapping, Sequence assembly visualisation, Sequencing quality control, Sequencing error detection 2021-03-24 2026-01-05 16 True False False True fastqc, __FLATTEN__, bwa_mem2, fastp, quast, bandage_image, __EXTRACT_DATASET__, filtlong, nanoplot, polypolish, CONVERTER_bz2_to_uncompressed, flye, porechop, upload1 UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr 0 10807 16115 3.366667 0
Assembly Large genome assembly and polishing https://training.galaxyproject.org//topics/assembly/tutorials/largegenome/tutorial.html Genomics, Sequence assembly, Biodiversity Statistical calculation, Genome assembly, Sequence contamination filtering, Variant calling, Sequence assembly, Cross-assembly, Sequence composition calculation, Scatter plot plotting, Sequencing quality control, Mapping assembly, Visualisation, De-novo assembly, Box-Whisker plot plotting, Validation, Sequence assembly visualisation, Pairwise sequence alignment, Base-calling, Sequence assembly validation 2023-03-06 2026-01-23 15 True False True True fastqc, fastp, quast, bandage_image, busco, multiqc, barchart_gnuplot, fasta-stats, minimap2, meryl, nanoplot, medaka_consensus_pipeline, racon, genomescope, flye UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 7914 10216 1.933333 0
Assembly Hybrid genome assembly - Nanopore and Illumina https://training.galaxyproject.org//topics/assembly/tutorials/hybrid_denovo_assembly/tutorial.html Genome assembly, Genome indexing, Read alignment, Mapping assembly, Visualisation, Analysis, Generation, De-novo assembly, Sequence alignment, Validation, Read mapping, Sequence assembly validation, Sequence assembly, Cross-assembly, Sequencing quality control, Aggregation 2025-11-03 2025-11-06 2 True False False True unicycler, quast, busco, pilon, multiqc, bwa_mem, flye UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.no 0 613 750 1.450000 0
Assembly ERGA post-assembly QC https://training.galaxyproject.org//topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html Genomics, Sequence assembly, Biodiversity Sequence alignment analysis, Genotyping, Genome assembly, Data handling, Sequence assembly visualisation, Pairwise sequence alignment, Scaffolding, Phasing, Visualisation, Sequence alignment, k-mer counting, Data deposition, Sequence trimming, Data parsing, De-novo assembly, Sequence assembly validation 2023-06-23 2025-06-04 8 True False True True smudgeplot, tp_find_and_replace, collapse_dataset, gfastats, samtools_stats, pretext_snapshot, genomescope, busco, pretext_map, minimap2, __EXTRACT_DATASET__, blobtoolkit, interactive_tool_blobtoolkit, meryl, bwa_mem2, bg_diamond, CONVERTER_gz_to_uncompressed, bellerophon, merqury, bandage_image UseGalaxy.eu UseGalaxy.org (Main), UseGalaxy.org.au 0 2170 2799 1.933333 0
Assembly Chloroplast genome assembly https://training.galaxyproject.org//topics/assembly/tutorials/chloroplast-assembly/tutorial.html Genome assembly, Analysis, Coding region prediction, Sequence alignment, Sequence assembly, Cross-assembly, Scatter plot plotting, Genome visualisation, Genome indexing, Read alignment, Gene prediction, Mapping assembly, Generation, Box-Whisker plot plotting, Read mapping, Sequence assembly visualisation, Genome annotation, De-novo assembly 2020-12-04 2026-01-23 22 True False True True pilon, jbrowse, fasta-stats, bwa_mem, upload1, prokka, nanoplot, bandage_image, flye, bandage_info UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 8276 12814 2.766667 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.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 1023 1228 1.616667 0
Assembly Decontamination of a genome assembly https://training.galaxyproject.org//topics/assembly/tutorials/assembly-decontamination/tutorial.html Genomics, Sequence assembly, Biodiversity Data handling, Taxonomic classification 2024-09-04 2025-06-04 5 True False True True ncbi_dustmasker_wrapper, Cut1, tp_sed_tool, gfastats, ncbi_blastn_wrapper, parse_mito_blast, Filter1, kraken2, tp_cat UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 1848 2267 2.316667 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 Visualisation, Genome assembly, Sequence contamination filtering, Sequence assembly visualisation, Read mapping, Sequencing quality control, Sequence assembly validation 2021-03-24 2026-01-05 18 True False True True shovill, fastp, quast, falco, upload1, bandage_image, bandage_info UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 10653 16340 3.566667 0
Assembly Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Sequence alignment analysis, Statistical calculation, Genome assembly, Sequence file editing, Local alignment, Sequence contamination filtering, Variant calling, Sequence trimming, Sequence composition calculation, Formatting, Data handling, Primer removal, Visualisation, Read pre-processing, Read mapping, Sequence assembly visualisation, Sequencing quality control, Sequence assembly validation 2026-02-10 2026-02-10 0 True False True True bowtie2, fastqc, bg_uniq, quast, coverm_contig, metaspades, collection_column_join, filter_tabular, bamtools, cutadapt, megahit, ngsutils_bam_filter, bandage_image, megahit_contig2fastg, tp_cat, seqtk_subseq, random_lines1, bandage_info UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 2 3 0.000000 0
Assembly De Bruijn Graph Assembly https://training.galaxyproject.org//topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html Formatting, Genome assembly, Sequence assembly visualisation, Sequence assembly, Optimisation and refinement, De-novo assembly 2017-05-24 2026-01-07 26 True True False True fasta-stats, spades, velvetg, bandage_image, velveth, velvetoptimiser UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz 0 3450119 8413832 4.933333 0
Assembly Unicycler Assembly https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html Sequence assembly, Genomics, Microbiology Aggregation, Statistical calculation, Genome assembly, Gene prediction, Visualisation, Validation, Coding region prediction, Genome annotation, Sequence composition calculation, Sequencing quality control, Sequence assembly validation 2017-10-11 2026-01-23 25 True True False True fastqc, quast, multiqc, prokka, unicycler UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3456485 8425505 4.233333 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 Scatter plot plotting, Genome assembly, Sequence file editing, Data handling, Pairwise sequence alignment, Validation, Box-Whisker plot plotting, Sequence contamination filtering, Sequence assembly visualisation, Read mapping, Sequencing quality control, Aggregation 2020-04-21 2025-05-15 14 True True True True bowtie2, unicycler, fastp, collapse_dataset, fasta_filter_by_length, multiqc, fasterq_dump, samtools_stats, seqtk_sample, __ZIP_COLLECTION__, minimap2, samtools_view, bandage_image, samtools_fastx, nanoplot, bandage_info UseGalaxy.eu, UseGalaxy.org.au Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 3449616 8413481 5.283333 0
Assembly Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step https://training.galaxyproject.org//topics/assembly/tutorials/vgp_genome_assembly/tutorial.html Genomics, Sequence assembly, Biodiversity Genome assembly, Mapping, Data handling, Sequence trimming, Primer removal, Scaffolding, k-mer counting, Visualisation, Read pre-processing, Sequence alignment, Read binning, Pairwise sequence alignment, Phasing, De-novo assembly, Sequence assembly validation 2021-06-04 2026-01-23 58 True False True True tp_find_and_replace, collapse_dataset, gfastats, pretext_snapshot, tp_grep_tool, genomescope, quast, busco, pretext_map, purge_dups, minimap2, yahs, cutadapt, hifiasm, meryl, bwa_mem2, sort1, bionano_scaffold, collection_column_join, salsa, Convert characters1, bellerophon, merqury, cat1, Add_a_column1, bedtools_bamtobed, gfa_to_fa, tp_cut_tool UseGalaxy.cz 0 16710 25030 1.966667 0
Assembly Genome assembly using PacBio data https://training.galaxyproject.org//topics/assembly/tutorials/hifi-assembly/tutorial.html Genomics, Sequence assembly, Biodiversity Visualisation, Mapping assembly, Genome assembly, Cross-assembly, De-novo assembly, Sequence assembly validation 2021-11-29 2025-06-04 2 True False False True quast, busco, fasta-stats, gfa_to_fa, hifiasm, flye UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.no 0 1124 1346 1.716667 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 (Main), UseGalaxy.org.au 0 3837 5279 2.566667 0
Assembly Making sense of a newly assembled genome https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html Sequence assembly, Genomics, Microbiology Genome visualisation, Sequence alignment, Mapping, Sequence visualisation, Read mapping 2018-06-14 2024-06-24 29 True False False True collapse_dataset, jbrowse, circos_aln_to_links, tp_grep_tool, join1, tp_cat, tp_sed_tool, addValue, Filter1, fasta_compute_length, bedtools_sortbed, fasta_filter_by_length, bedtools_intersectbed, circos_interval_to_tiles, tp_sort_header_tool, mergeCols1, lastz_wrapper_2, random_lines1, upload1, tp_replace_in_column, Cut1, datamash_ops, cat1, tp_replace_in_line, bedtools_complementbed, Grep1, circos 0 6820 13073 2.916667 0
Assembly Genome assembly and assembly QC - Introduction short version https://training.galaxyproject.org//topics/assembly/tutorials/assembly_and_qc_short/slides.html 2025-04-22 2026-01-30 3 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 983252 1694120 1.216667 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 3422610 8334564 2.166667 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 2961733 6778046 2.083333 0
Climate Sentinel 5P data visualisation https://training.galaxyproject.org//topics/climate/tutorials/sentinel5_data/tutorial.html 2024-01-26 2025-05-10 2 True False False True interactive_tool_copernicus, interactive_tool_copernicus_notebook, interactive_tool_panoply 0 338 385 0.483333 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 2836788 6378763 3.816667 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, argo_getdata, xarray_coords_info, timeseries_extraction UseGalaxy.eu 0 342 404 1.033333 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__, graphicsmagick_image_montage, climate_stripes, ggplot2_point, __EXTRACT_DATASET__, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select, regexColumn1, xarray_coords_info UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 2836522 6378201 4.750000 0
Climate Ocean's variables study https://training.galaxyproject.org//topics/climate/tutorials/ocean-variables/tutorial.html 2023-11-29 2025-05-10 5 True False False True interactive_tool_odv, divand_full_analysis, interactive_tool_divand UseGalaxy.eu 0 253 300 1.483333 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_odv_history, harmonize_insitu_to_netcdf, interactive_tool_odv, tool_odv, tool_biogeochemical_calibration UseGalaxy.eu 0 78 91 1.283333 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, xarray_select, ggplot2_point, ctsm_fates UseGalaxy.eu, UseGalaxy.org (Main) 0 3444842 8405476 3.916667 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 datamash_ops, climate_stripes, tp_awk_tool, interactive_tool_panoply, cds_essential_variability, ggplot2_point, Grep1, psy_maps UseGalaxy.eu 0 1124 1535 1.233333 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 3443320 8403102 2.166667 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 0 459 552 1.150000 0
Climate Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab https://training.galaxyproject.org//topics/climate/tutorials/fates-jupyterlab/tutorial.html 2020-10-25 2025-05-10 16 True False False False interactive_tool_jupyter_notebook UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 575 985 1.700000 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, obis_data, c3s, argo_getdata UseGalaxy.eu UseGalaxy.be 0 138 172 1.450000 0
Climate Collaboration with JupyterGIS https://training.galaxyproject.org//topics/climate/tutorials/jupytergis_collaboration/tutorial.html 2025-04-03 2025-05-10 4 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 206 253 0.800000 0
Climate Visualize Climate data with Panoply netCDF viewer https://training.galaxyproject.org//topics/climate/tutorials/panoply/tutorial.html 2020-03-05 2025-05-10 18 True False False False interactive_tool_panoply UseGalaxy.eu, UseGalaxy.org (Main) 0 6473 10460 0.800000 0
Galaxy Community Building Creation of the labs in the different Galaxy instances for your community https://training.galaxyproject.org//topics/community/tutorials/community-lab/tutorial.html 2025-10-04 2026-01-28 4 True False False False 0 79 100 3.033333 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 95 111 0.316667 0
Galaxy Community Building Creation of resources listing Galaxy workflow for your community https://training.galaxyproject.org//topics/community/tutorials/community-workflow-table/tutorial.html 2025-09-17 2025-11-27 3 True False False False 0 33 35 0.600000 0
Galaxy Community Building Make your tools available on your subdomain https://training.galaxyproject.org//topics/community/tutorials/tools_subdomains/tutorial.html 2024-12-03 2024-12-20 2 True False False False 0 56 71 5.650000 0
Galaxy Community Building Creation of resources listing all the tools and their metadata relevant to your community https://training.galaxyproject.org//topics/community/tutorials/community-tool-table/tutorial.html 2024-03-13 2025-10-28 5 True False False False 0 125 150 1.800000 0
Galaxy Community Building Creation of a Galaxy tutorial table for your community https://training.galaxyproject.org//topics/community/tutorials/community-tutorial-table/tutorial.html 2025-09-17 2025-10-28 2 True False False False 0 44 48 1.016667 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 0 132 167 2.183333 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 0 169 182 1.400000 0
Computational chemistry Protein target prediction of a bioactive ligand with Align-it and ePharmaLib https://training.galaxyproject.org//topics/computational-chemistry/tutorials/zauberkugel/tutorial.html 2022-02-15 2024-06-14 10 True False False True split_file_to_collection, sort1, openbabel_addh, rdconf, tp_cat, ctb_alignit UseGalaxy.cz 0 1328 1898 2.316667 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 get_pdb, chembl, openbabel_compound_convert, ctb_silicos_qed, ctb_im_rxn_maker, md_converter, openbabel_svg_depiction UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no 0 520 620 1.533333 0
Computational chemistry Protein-ligand docking https://training.galaxyproject.org//topics/computational-chemistry/tutorials/cheminformatics/tutorial.html 2019-10-19 2025-12-04 17 True False False True tp_find_and_replace, ctb_online_data_fetch, collapse_dataset, tp_grep_tool, sdf_to_tab, ctb_remDuplicates, tp_cat, prepare_receptor, ctb_obgrep, get_pdb, prepare_box, ctb_np-likeness-calculator, ctb_chemfp_butina_clustering, openbabel_compound_convert, fpocket, ctb_remIons, chembl, ctb_chemfp_nxn_clustering, ctb_filter, openbabel_svg_depiction, ctb_compound_convert, docking, ctb_chemfp_mol2fps, ctb_change_title UseGalaxy.org (Main) 0 20478 34651 1.633333 0
Computational chemistry Analysis of molecular dynamics simulations https://training.galaxyproject.org//topics/computational-chemistry/tutorials/analysis-md-simulations/tutorial.html 2019-06-03 2023-11-09 13 True False False True mdanalysis_rdf, mdanalysis_cosine_analysis, mdanalysis_distance, bio3d_rmsf, mdanalysis_ramachandran_plot, bio3d_pca, bio3d_rmsd, mdanalysis_dihedral UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 33006 58204 1.250000 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, rxdock_rbcavity, split_file_to_collection, collapse_dataset, xchem_pose_scoring, rxdock_rbdock, xchem_transfs_scoring, ctb_frankenstein_ligand, rdock_rbdock, enumerate_charges, openbabel_compound_convert, sucos_max_score 0 3242 5298 3.000000 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 get_pdb, gmx_editconf, gmx_em, gmx_solvate, gmx_sim, tp_grep_tool, gmx_setup UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 27495 48755 1.416667 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 get_pdb, gmx_merge_topology_files, bio3d_pca_visualize, gmx_editconf, gmx_setup, gmx_energy, ambertools_acpype, gmx_em, mdanalysis_cosine_analysis, bio3d_rmsf, gmx_solvate, vmd_hbonds, bio3d_pca, gmx_sim, tp_grep_tool, bio3d_rmsd, openbabel_compound_convert, md_converter UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 11219 19520 2.416667 0
Computational chemistry Running molecular dynamics simulations using NAMD https://training.galaxyproject.org//topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.html 2019-06-03 2023-11-09 9 True False False True namd_nvt, minimizer, setup, namd_npt 0 4329 7192 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 1878 2520 1.600000 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 3443466 8403272 3.700000 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 3443320 8403107 2.166667 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 5529 6633 0.766667 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 0 343 650 2.450000 0
Contributing to the Galaxy Training Material Adding auto-generated video to your slides https://training.galaxyproject.org//topics/contributing/tutorials/slides-with-video/tutorial.html 2020-10-20 2023-11-09 12 True False False False 0 286 369 3.350000 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 0 700 1052 2.383333 0
Contributing to the Galaxy Training Material Generating PDF artefacts of the website https://training.galaxyproject.org//topics/contributing/tutorials/generating-pdf/tutorial.html 2018-06-04 2023-11-09 12 True False False False 0 90 108 3.016667 0
Contributing to the Galaxy Training Material Preview the GTN website as you edit your training material https://training.galaxyproject.org//topics/contributing/tutorials/rendering_gtn/tutorial.html 2025-03-14 2026-02-04 4 True False True False 0 479 642 4.550000 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 0 315 473 2.283333 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 0 286 373 2.500000 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 86 128 0.516667 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 0 574 765 1.616667 0
Contributing to the Galaxy Training Material Including a new topic https://training.galaxyproject.org//topics/contributing/tutorials/create-new-topic/tutorial.html 2018-06-04 2025-12-01 33 True False False False 0 1278 1738 0.550000 0
Contributing to the Galaxy Training Material Design and plan session, course, materials https://training.galaxyproject.org//topics/contributing/tutorials/design/tutorial.html 2022-09-23 2025-03-11 12 True False False False 0 651 863 2.600000 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 54 59 0.416667 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 0 127 143 0.233333 0
Contributing to the Galaxy Training Material Creating a new tutorial https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial/tutorial.html Read pre-processing, Sequence file editing, Read mapping, Data handling, Primer removal, Sequence trimming 2018-06-20 2025-11-20 33 True False True True bowtie2, Cut1, tp_sed_tool, seqtk_subseq, Filter1, c3s, bam_to_sam, fastq_to_tabular, tp_cut_tool, cutadapt, tp_cat, tp_sorted_uniq, random_lines1 0 1891 2760 4.683333 0
Contributing to the Galaxy Training Material FAIR Galaxy Training Material https://training.galaxyproject.org//topics/contributing/tutorials/fair-gtn/tutorial.html 2026-02-10 2026-02-10 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 68 70 0.316667 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 60 60 0.050000 0
Contributing to the Galaxy Training Material Creating content in Markdown https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-content/tutorial.html Sequencing quality control, Validation 2017-06-25 2025-04-08 85 True False False False multiqc, upload1 0 3833 9871 2.083333 0
Contributing to the Galaxy Training Material Creating Slides https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-slides/slides.html 2018-06-13 2024-11-08 17 False True True False 0 3443320 8403109 2.166667 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 0 129 150 3.100000 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 Visualisation, Tree-based sequence alignment, Validation, Sequence contamination filtering, Variant classification, Read mapping, Sequencing quality control 2021-06-08 2025-12-18 11 True False True True fastp, pangolin, compose_text_param, multiqc, collapse_dataset, falco, bcftools_consensus, snpSift_filter UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 3025 3668 1.966667 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 3122572 7312687 3.450000 0
Variant Analysis Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html Variant classification, Variant calling, Tree-based sequence alignment, Methylation analysis 2021-06-30 2025-03-28 18 True False True False datamash_ops, pangolin, fasta_regex_finder, nextclade, Filter1, upload1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 7573 13460 3.400000 0
Variant Analysis From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2/tutorial.html Formatting, Sequence contamination filtering, Data handling, Genome indexing, Generation, Sequence alignment, Validation, Read mapping, SNP detection, Sequencing quality control 2020-06-24 2024-06-14 16 True False True True fastp, lofreq_viterbi, snpeff_sars_cov_2, lofreq_call, multiqc, fasterq_dump, samtools_stats, picard_MarkDuplicates, bwa_mem, lofreq_indelqual, Filter1, snpSift_extractFields, tp_cut_tool, Grep1 UseGalaxy.eu, UseGalaxy.org (Main) MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 13930 20883 2.866667 0
Sequence analysis Removal of human reads from SARS-CoV-2 sequencing data https://training.galaxyproject.org//topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html Sequence file editing, Sequence alignment, Read mapping, Data handling, Genome indexing, Generation 2021-08-04 2023-11-09 5 True False False True __UNZIP_COLLECTION__, __ZIP_COLLECTION__, seqtk_subseq, bwa_mem, tp_replace_in_line, trimmomatic, samtools_fastx, Grep1 UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 4151 5871 2.400000 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 jq, snpeff_sars_cov_2, fasterq_dump, fastq_dump, fastq_to_fasta_python, tp_cat, query_tabular UseGalaxy.be, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3224020 7648652 3.750000 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 Genome visualisation, Statistical calculation, Sequence alignment, Read mapping, Sequencing quality control, Genome indexing, Sequence composition calculation, Generation 2023-07-10 2024-02-29 2 True False False False bwa_mem, jbrowse, fastqc UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz 0 1384 1799 3.833333 0
Foundations of Data Science Data Manipulation Olympics https://training.galaxyproject.org//topics/data-science/tutorials/data-manipulation-olympics/tutorial.html 2026-02-10 2026-02-10 0 True False False True {{version_paste}}, {{version_cat}}, {{version_split}}, Count1, wc_gnu, join1, tp_cat, {{version_replace_text_line}}, Remove beginning1, {{version_cut_columns}}, Filter1, {{version_datamash}}, tp_split_on_column, {{version_remove_beginning}}, {{version_join}}, {{version_filter}}, {{version_cut_advanced}}, {{version_compute}}, tp_sort_header_tool, {{version_replace_text_column}}, {{version_sort}}, upload1, {{version_remove_columns_by_header}}, datamash_ops, Cut1, tabular_to_csv, cat1, Add_a_column1, Show beginning1, {{version_select_first}}, regexColumn1, {{version_count}}, {{version_unique}}, tp_sorted_uniq, {{version_wc}}, Grouping1 0 0 0 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 1724280 3502092 2.083333 0
Foundations of Data Science Learning about one gene across biological resources and formats https://training.galaxyproject.org//topics/data-science/tutorials/online-resources-gene/tutorial.html 2023-09-07 2023-11-09 3 True True True False ncbi_blastp_wrapper Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, PepSimili, UseGalaxy.no 0 1879963 3852461 4.250000 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 0 339 572 0.550000 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 0 174 204 1.800000 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 0 523 705 0.450000 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 0 715 775 0.400000 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 9488 12388 2.050000 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 1009 1274 2.183333 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 0 634 779 1.366667 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 1508 1958 1.766667 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 1209 1683 2.700000 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 0 520 560 0.866667 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 1021 1259 1.216667 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 3469 4456 0.933333 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 2213 2507 0.533333 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 0 176 422 0.250000 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 2850 3849 2.133333 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 1453 1818 0.566667 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 0 638 799 0.500000 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 0 678 775 1.016667 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 1659 2583 2.750000 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 0 997 1169 0.766667 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 0 283 346 1.750000 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 0 564 744 1.200000 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 0 413 691 5.750000 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 0 155 168 0.900000 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 0 656 846 0.783333 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 0 599 721 1.450000 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 0 867 964 0.533333 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 0 409 461 0.733333 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 0 156 168 0.350000 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 2189 2574 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 0 161 175 0.750000 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 0 291 342 0.700000 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 0 407 482 1.550000 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 68 74 0.633333 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 15 15 0.050000 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 0 574 664 0.633333 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 0 622 708 0.350000 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 0 247 291 1.516667 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 0 734 788 0.516667 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 1364 1481 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 0 229 251 1.016667 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 0 639 676 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 0 238 261 0.350000 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 0 555 598 0.433333 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 1180 1365 0.300000 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 0 205 220 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 0 902 967 0.283333 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 3443320 8403122 2.166667 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 3443320 8403122 2.166667 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 3444095 8404120 4.233333 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 3444059 8403998 3.083333 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 3443320 8403122 2.166667 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 3443320 8403122 2.166667 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 3443320 8403122 2.166667 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 3443691 8403644 3.850000 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 3231767 7673925 4.533333 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 3443522 8403391 3.416667 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 3443320 8403125 2.166667 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 3443324 8403130 2.633333 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 3443320 8403125 2.166667 0
Development in Galaxy nb2workflow: Generating Galaxy Tools From Jupyter Notebooks https://training.galaxyproject.org//topics/dev/tutorials/tool-from-notebook/tutorial.html 2025-12-04 2025-12-04 1 True False False False 0 20 22 0.750000 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 0 456 540 1.366667 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 0 241 351 2.700000 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 1281 1692 2.650000 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 0 259 349 2.816667 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 2815 4513 2.533333 0
Development in Galaxy Debugging Galaxy https://training.galaxyproject.org//topics/dev/tutorials/debugging/tutorial.html 2021-06-15 2025-11-05 15 True False False False 0 624 1228 2.650000 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 0 306 361 2.150000 0
Development in Galaxy Contributing a New Feature to Galaxy Core https://training.galaxyproject.org//topics/dev/tutorials/core-contributing/tutorial.html 2021-06-08 2025-11-05 10 True False False False 0 770 1139 2.566667 0
Development in Galaxy Writing Automated Tests for Galaxy https://training.galaxyproject.org//topics/dev/tutorials/writing_tests/tutorial.html 2022-07-15 2025-11-05 6 True False False False 0 299 727 1.850000 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 45 48 1.166667 0
Digital Humanities Introduction to Digital Humanities in Galaxy https://training.galaxyproject.org//topics/digital-humanities/tutorials/introduction_to_dh/tutorial.html 2025-09-11 2025-11-25 5 True False False True diff, tp_find_and_replace, Remove beginning1, tp_replace_in_line, wordcloud, tp_grep_tool, wc_gnu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 95 112 1.500000 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 datamash_ops, Cut1, sort1, diff, Add_a_column1, tp_replace_in_line, Filter1, wordcloud UseGalaxy.cz 0 181 208 1.300000 0
Digital Humanities OpenRefine Tutorial for researching cultural data https://training.galaxyproject.org//topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html 2025-09-24 2025-10-21 2 True False False True datamash_ops, Cut1, compose_text_param, barchart_gnuplot, Remove beginning1, tp_head_tool, param_value_from_file, filter_tabular, tp_sort_header_tool, wordcloud, regexColumn1, tp_grep_tool, interactive_tool_openrefine UseGalaxy.eu 0 72 79 0.183333 0
Ecology Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities https://training.galaxyproject.org//topics/ecology/tutorials/MetaShARK_tutorial/tutorial.html 2024-03-04 2026-01-30 8 True False False False interactive_tool_metashark UseGalaxy.eu, UseGalaxy.fr 0 232 277 1.616667 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 crsconverter, phylogenetic_occupancy_matcher, estimate_endem, phylo_index UseGalaxy.eu 0 115 140 1.066667 0
Ecology Sentinel 2 biodiversity https://training.galaxyproject.org//topics/ecology/tutorials/remote-sensing/tutorial.html 2023-04-13 2025-12-08 7 True False False True srs_pca, srs_preprocess_s2, srs_process_data, srs_diversity_maps, srs_global_indices, srs_spectral_indices UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 654 830 1.533333 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 pampa_presabs, pampa_communitymetrics, pampa_glmcomm, tp_sort_header_tool, mergeCols1, Filter1, pampa_glmsp, regexColumn1, tp_easyjoin_tool, tp_cut_tool, regex1, Count1, tp_cat, datamash_transpose, pampa_plotglm UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au 0 1145 1516 1.866667 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 0 929 1291 1.283333 0
Ecology Champs blocs indicators https://training.galaxyproject.org//topics/ecology/tutorials/champs-blocs/tutorial.html 2023-01-04 2025-12-02 12 True False False True cb_eco, cb_div, cb_qecb, cb_ivr, cb_dissim 0 190 340 1.700000 0
Ecology Species distribution modeling https://training.galaxyproject.org//topics/ecology/tutorials/species-distribution-modeling/tutorial.html 2019-07-04 2025-06-03 18 True False False True tabular_to_csv, tp_find_and_replace, interactive_tool_wallace, spocc_occ, Filter1, tp_cut_tool UseGalaxy.eu, UseGalaxy.fr 0 3294 4976 1.183333 0
Ecology Visualization of Climate Data using  NetCDF xarray Map Plotting https://training.galaxyproject.org//topics/ecology/tutorials/x-array-map-plot/tutorial.html 2022-10-26 2024-06-27 9 True False False True graphicsmagick_image_montage, cdo_operations, xarray_mapplot, xarray_metadata_info, xarray_coords_info UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz 0 2452 2828 0.450000 0
Ecology RAD-Seq de-novo data analysis https://training.galaxyproject.org//topics/ecology/tutorials/de-novo-rad-seq/tutorial.html Statistical calculation, Data handling, Sequence composition calculation, Sequencing quality control 2017-02-14 2025-06-03 14 True False False True fastqc, stacks_populations, stacks_procrad, stacks_denovomap UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 2752 4356 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 regionalgam_flight_curve, regionalgam_gls, tab2csv_R, Remove beginning1, regionalgam_autocor_acf, regionalgam_glmmpql, ggplot2_point, tp_awk_tool, csv2tab_R, flight-curve, mergeCols1, Filter1, regionalgam_plot_trend, regexColumn1, regionalgam_ab_index, Paste1, Count1 0 360 478 3.250000 0
Ecology Metabarcoding/eDNA through Obitools https://training.galaxyproject.org//topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html Statistical calculation, Sequence analysis, Sequence composition calculation, Sequencing quality control 2022-02-28 2025-06-03 12 True False True True fastqc, obi_ngsfilter, obi_stat, Cut1, obi_illumina_pairend, obi_grep, seq_filter_by_id, wc_gnu, ncbi_blastn_wrapper, obi_uniq, obi_annotate, Filter1, fastq_groomer, unzip, obi_clean, obi_tab, join1 UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 4701 6521 1.933333 0
Ecology Obis marine indicators https://training.galaxyproject.org//topics/ecology/tutorials/obisindicators/tutorial.html Biodiversity, Ecology, Data mining 2023-04-11 2025-06-03 9 True False False True obis_data, obisindicators, tp_cut_tool UseGalaxy.eu UseGalaxy.be 0 333 413 1.900000 0
Ecology Preparing genomic data for phylogeny reconstruction https://training.galaxyproject.org//topics/ecology/tutorials/phylogeny-data-prep/tutorial.html Genetic variation analysis, Sequence clustering, Sequence analysis, Genome annotation, Multiple sequence alignment, Sequence assembly validation 2022-10-21 2025-06-03 5 True False False True funannotate_predict, busco, collapse_dataset, clustalw, proteinortho, proteinortho_grab_proteins, tp_replace_in_line, Filter1, clipkit, regex1, phykit_alignment_based, glimmer_gbk_to_orf, repeatmasker_wrapper 0 2328 3193 2.783333 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_clara_cluster, ecoregion_GeoNearestNeighbor, filter_tabular, interactive_tool_jupyter_notebook, ecoregion_taxa_seeker, mergeCols1, ecoregion_eco_map, regexColumn1, unzip, tp_cut_tool, ecoregion_cluster_estimate, ecoregion_brt_analysis UseGalaxy.eu 0 343 443 2.183333 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_GeoNearestNeighbor, WormsMeasurements, column_remove_by_header, ClaraGuess, ecoregion_taxa_seeker, ecoregion_eco_map, Filter1, regexColumn1, unzip, tp_cut_tool, ecoregion_brt_analysis UseGalaxy.eu 0 59 62 1.550000 0
Ecology Checking expected species and contamination in bacterial isolate https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Statistical calculation, Expression analysis, Cross-assembly, Taxonomic classification 2024-03-04 2025-12-18 5 True False False True est_abundance, kraken2, recentrifuge, upload1 UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main) 0 947 1266 3.183333 0
Ecology RAD-Seq Reference-based data analysis https://training.galaxyproject.org//topics/ecology/tutorials/ref-based-rad-seq/tutorial.html Statistical calculation, Sequencing quality control, Data handling, Genome indexing, Validation, Sequence alignment, Read mapping, Sequence composition calculation, Generation 2017-02-14 2025-11-06 15 True False False True fastqc, bwa, Cut1, stacks_procrad, multiqc, cat1, regex_replace, addValue, bwa_wrapper, Summary_Statistics1, tp_replace_in_line, Filter1, tp_sort_header_tool, Grep1, stacks_refmap, Count1, stacks_populations, Convert characters1 0 3267 5045 1.816667 0
Ecology Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS https://training.galaxyproject.org//topics/ecology/tutorials/Metashrimps_tutorial/tutorial.html 2024-01-22 2025-06-03 6 True False False False interactive_tool_metashrimps UseGalaxy.eu 0 126 136 1.216667 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 cshl_fastq_to_fasta, Count1, ncbi_blastn_wrapper, fastp UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 556 698 0.816667 0
Ecology Cleaning GBIF data for the use in Ecology https://training.galaxyproject.org//topics/ecology/tutorials/gbif_cleaning/tutorial.html 2022-10-28 2025-06-03 6 True False False True Summary_Statistics1, spocc_occ, Filter1, gdal_ogr2ogr, Count1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no 0 695 853 0.850000 0
Ecology From NDVI data with OpenEO to time series visualisation with Holoviews https://training.galaxyproject.org//topics/ecology/tutorials/ndvi_openeo/tutorial.html 2024-01-24 2024-06-29 3 True False False True interactive_tool_holoviz, interactive_tool_copernicus_notebook UseGalaxy.eu 0 244 284 0.850000 0
Ecology Marine Omics identifying biosynthetic gene clusters https://training.galaxyproject.org//topics/ecology/tutorials/marine_omics_bgc/tutorial.html Sequence motif recognition, Genome annotation, Protein feature detection 2024-08-19 2025-06-03 3 True False False True prodigal, SanntiS_marine, sanntis_marine, regex1, interproscan 0 231 266 1.833333 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_beta_diversity, ecology_stat_presence_abs, tool_anonymization, Remove beginning1, ecology_link_between_var, ecology_homogeneity_normality, regexColumn1, tp_cut_tool, ecology_presence_abs_abund UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr 0 1682 2338 2.616667 0
Ecology Data submission using ENA upload Tool https://training.galaxyproject.org//topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html Visualisation, Read pre-processing, Validation, Sequence trimming, Primer removal, Read mapping, Sequencing quality control 2024-12-13 2025-03-20 2 True False False False bg_uniq, __RELABEL_FROM_FILE__, fastq_filter, collection_element_identifiers, multiqc, ncbi_blastn_wrapper, ab1_fastq_converter, falco, cutadapt, fastq_to_fasta_python, fastq_groomer, regex1, Paste1, __FILTER_EMPTY_DATASETS__ UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz 0 297 318 0.733333 0
Ecology Visualize EBV cube data with Panoply netCDF viewer https://training.galaxyproject.org//topics/ecology/tutorials/panoply_ebv/tutorial.html 2022-10-28 2024-06-27 9 True False False False interactive_tool_panoply UseGalaxy.eu, UseGalaxy.org (Main) 0 261 324 1.116667 0
Ecology Audio data annotation with NEAL (Nature + Energy Audio labeler) https://training.galaxyproject.org//topics/ecology/tutorials/NEAL_tutorial/tutorial.html 2025-10-14 2025-11-06 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 48 56 0.166667 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 0 204 246 1.166667 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 0 318 365 1.533333 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 0 818 1028 1.416667 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 1349 1637 1.500000 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 1985 2372 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 0 116 137 0.966667 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 1666 1964 0.733333 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 1322 1539 0.783333 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 0 762 886 1.233333 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 1066173 1886284 1.600000 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 0 249 278 1.450000 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 1066170 1886280 1.600000 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 0 207 235 0.733333 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 48 57 0.833333 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 1066217 1886341 2.150000 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 Genome visualisation, Statistical calculation, Structure visualisation, Mapping, Peak calling, Primer removal, Pathway visualisation, Gene regulatory network analysis, Read pre-processing, Enrichment analysis, Read mapping, Sequence trimming, Sequence composition calculation, Sequencing quality control 2018-09-17 2025-12-18 15 True True False True deeptools_plot_fingerprint, bedtools_mergebed, deeptools_bam_coverage, fastqc, deeptools_bam_compare, Filter1, macs2_callpeak, trim_galore, bedtools_sortbed, jbrowse2, bbgtobigwig, bowtie2, __FLATTEN__, cat1, deeptools_multi_bam_summary, deeptools_plot_heatmap, deeptools_compute_matrix, samtools_idxstats, deeptools_plot_correlation UseGalaxy.eu, UseGalaxy.org (Main) 0 3449433 8415096 5.750000 0
Epigenetics CUT&RUN data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/cut_and_run/tutorial.html Formatting, Sequence alignment analysis, Mapping, Data handling, Peak calling, Primer removal, Gene regulatory network analysis, Read pre-processing, Visualisation, Validation, Enrichment analysis, Read mapping, Sequence trimming, Sequencing quality control 2024-03-06 2025-03-19 5 True False False True deeptools_plot_fingerprint, meme_chip, bamFilter, idr, multiqc, picard_MarkDuplicates, __EXTRACT_DATASET__, macs2_callpeak, trim_galore, bedtools_intersectbed, Extract genomic DNA 1, falco, pe_histogram, datamash_transpose, bowtie2, __FLATTEN__, wig_to_bigWig, bedtools_bamtobed, deeptools_plot_heatmap, deeptools_compute_matrix, Grep1 0 6964 8852 1.400000 0
Epigenetics ATAC-Seq data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/atac-seq/tutorial.html Formatting, Sequence alignment analysis, Statistical calculation, Mapping, Data handling, Primer removal, Peak calling, Gene regulatory network analysis, Read pre-processing, Visualisation, Enrichment analysis, Sequence trimming, Read mapping, Sequence composition calculation, Sequencing quality control 2019-09-02 2025-12-18 24 True True True True bamFilter, fastqc, picard_MarkDuplicates, Filter1, cutadapt, macs2_callpeak, bedtools_intersectbed, tp_sort_header_tool, pe_histogram, bowtie2, __FLATTEN__, Cut1, wig_to_bigWig, bedtools_bamtobed, samtools_idxstats, deeptools_plot_heatmap, deeptools_compute_matrix, pygenomeTracks, Grep1 0 3509177 8521033 3.950000 0
Epigenetics Hi-C analysis of Drosophila melanogaster cells using HiCExplorer https://training.galaxyproject.org//topics/epigenetics/tutorials/hicexplorer/tutorial.html Visualisation, Formatting, Read mapping 2018-02-23 2025-08-11 30 True False False True hicexplorer_hicbuildmatrix, hicexplorer_hicpca, bowtie2, hicexplorer_hicfindrestrictionsites, hicexplorer_hicmergematrixbins, hicexplorer_hicfindtads, hicexplorer_hiccorrectmatrix, hicexplorer_hicdetectloops, pygenomeTracks, hicexplorer_hicplotmatrix, hicexplorer_hicinfo UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.no, UseGalaxy.org (Main) 0 7739 12847 1.500000 0
Epigenetics Identification of the binding sites of the Estrogen receptor https://training.galaxyproject.org//topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html Statistical calculation, Sequence trimming, Peak calling, Primer removal, Gene regulatory network analysis, Read pre-processing, Enrichment analysis, Read mapping, Sequence composition calculation, Sequencing quality control 2017-09-18 2025-04-08 10 True False False True bowtie2, fastqc, deeptools_compute_gc_bias, deeptools_bam_compare, deeptools_multi_bam_summary, deeptools_plot_fingerprint, deeptools_plot_heatmap, samtools_idxstats, macs2_callpeak, bam_to_sam, deeptools_compute_matrix, trim_galore, deeptools_bam_coverage, deeptools_plot_correlation UseGalaxy.be Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 1966 2883 2.733333 0
Epigenetics Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) https://training.galaxyproject.org//topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html ChIP-seq Statistical calculation, Sequencing quality control, Mapping, Genome indexing, Peak calling, Gene regulatory network analysis, Enrichment analysis, Sequence alignment, Read mapping, Sequence composition calculation, Generation 2016-12-20 2025-04-08 11 True False False True fastqc, bwa, deeptools_compute_gc_bias, bedtools_intersectbed, deeptools_bam_compare, deeptools_multi_bam_summary, deeptools_correct_gc_bias, deeptools_plot_fingerprint, deeptools_plot_heatmap, deeptools_compute_matrix, trimmomatic, macs2_callpeak, samtools_idxstats, deeptools_plot_correlation UseGalaxy.be, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 7514 13819 3.350000 0
Epigenetics Infinium Human Methylation BeadChip https://training.galaxyproject.org//topics/epigenetics/tutorials/ewas-suite/tutorial.html 2018-08-27 2024-10-15 21 True True False True Cut1, Remove beginning1, clusterprofiler_bitr, chipeakanno_annopeaks, minfi_analysis, clusterprofiler_go UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3445449 8406456 4.000000 0
Epigenetics DNA Methylation data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/methylation-seq/tutorial.html Epigenomics Visualisation, Statistical calculation, Read mapping, Sequence composition calculation, Sequencing quality control 2017-02-16 2025-04-03 24 True False False True fastqc, pileometh, deeptools_plot_profile, wig_to_bigWig, tp_awk_tool, falco, replace_column_with_key_value_file, deeptools_compute_matrix, tp_tail_tool, bwameth, metilene 0 15542 25591 2.033333 0
Epigenetics Introduction to ChIP-Seq data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/introduction-chip-seq/slides.html 2017-06-12 2024-03-05 2 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3443320 8403140 2.166667 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 3443320 8403140 2.166667 0
Evolution Phylogenetics - Back to basics https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo/tutorial.html Phylogenetic tree generation, Phylogenetic tree reconstruction, Sequence analysis, Phylogenetic analysis, Phylogenetic tree generation (from molecular sequences), Multiple sequence alignment, Phylogenetic tree analysis, Phylogenetic tree generation (maximum likelihood and Bayesian methods) 2024-05-10 2024-05-10 1 True False False True rbc_mafft, fasttree, newick_display, iqtree UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 5857 7557 1.883333 0
Evolution Identifying tuberculosis transmission links: from SNPs to transmission clusters https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html Genomics, Microbiology, Infectious disease, DNA polymorphism Phylogenetic tree generation, Variant calling, Phylogenetic tree visualisation, Antimicrobial resistance prediction 2022-03-16 2025-05-26 13 True False False True collapse_dataset, bcftools_consensus, clustering_from_distmat, trimmomatic, tp_grep_tool, addName, tp_cat, tp_sed_tool, tb_profiler_profile, snp_sites, tb_variant_filter, upload1, __MERGE_COLLECTION__, tp_replace_in_line, tp_easyjoin_tool, snp_dists, snippy, samtools_view, Grep1 UseGalaxy.eu 0 3112 4436 2.600000 0
Evolution Tree thinking for tuberculosis evolution and epidemiology https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html Genomics, Microbiology, Phylogeny, Infectious disease Sequence analysis, Phylogenetic tree analysis 2022-03-16 2025-06-04 12 True False False True interactive_tool_rstudio, upload1, raxml UseGalaxy.eu 0 2341 3360 2.450000 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 1523726 3024443 1.716667 0
Evolution Phylogenetic analysis for bacterial comparative genomics https://training.galaxyproject.org//topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html Genomics, Microbiology, Phylogeny Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) 2025-03-14 2025-03-14 1 True False False False fasttree, upload1 Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) GalaxyTrakr 0 133 155 1.900000 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 1523726 3024443 1.716667 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 1523726 3024443 1.716667 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 1523726 3024444 1.716667 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 1523726 3024444 1.716667 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 1523726 3024444 1.716667 0
FAIR Data, Workflows, and Research Data management in Medicinal Chemistry https://training.galaxyproject.org//topics/fair/tutorials/med-chem-data/tutorial.html 2026-02-10 2026-02-10 0 True False True True get_pdb, chembl, openbabel_compound_convert, ctb_silicos_qed, ctb_im_rxn_maker, md_converter, openbabel_svg_depiction UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, 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 1216026 2254747 1.466667 0
FAIR Data, Workflows, and Research Uploading Data to Zenodo from Galaxy https://training.galaxyproject.org//topics/fair/tutorials/zenodo-in-galaxy/tutorial.html 2025-11-06 2025-11-06 1 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 53 56 0.283333 0
FAIR Data, Workflows, and Research Integrating InvenioRDM-compatible Repositories with Galaxy https://training.galaxyproject.org//topics/fair/tutorials/inveniordm-integration/tutorial.html 2025-11-06 2025-11-06 1 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 32 33 0.750000 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 0 654 849 1.633333 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 0 927 1181 1.583333 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 0 659 763 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 0 122 153 1.783333 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 0 388 486 1.316667 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 0 174 193 0.416667 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 0 361 465 1.483333 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 1277476 2399186 2.633333 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 0 400 489 2.350000 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 0 264 296 1.250000 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 0 305 373 2.883333 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 0 222 263 1.266667 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 0 167 201 1.933333 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 0 102 107 1.483333 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 0 396 454 1.050000 0
FAIR Data, Workflows, and Research FAIR Bioimage Metadata https://training.galaxyproject.org//topics/fair/tutorials/bioimage-metadata/tutorial.html 2023-09-13 2025-11-27 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 335 396 2.066667 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 78 88 1.566667 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 63 72 2.733333 0
FAIR Data, Workflows, and Research REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data https://training.galaxyproject.org//topics/fair/tutorials/bioimage-REMBI/tutorial.html 2023-09-13 2025-11-27 9 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 327 377 2.050000 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 0 279 345 1.316667 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 0 296 355 1.066667 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 datamash_ops, Cut1, Remove beginning1, csv_to_tabular, upload1, ggplot2_point, tp_sorted_uniq, Grouping1 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz 0 923 1267 2.633333 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, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au MISSISSIPPI 0 6205 7712 2.966667 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 0 208 270 2.416667 0
Using Galaxy and Managing your Data Using Workflow Parameters https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-parameters/tutorial.html 2019-06-27 2024-06-14 15 True False True True tp_head_tool Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au MISSISSIPPI 0 2041 2595 2.283333 0
Using Galaxy and Managing your Data Getting data into Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/get-data/slides.html 2017-05-24 2022-10-18 4 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3443320 8403147 2.166667 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 2895491 6567167 2.066667 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 5146 6713 2.783333 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 2790 3761 3.266667 0
Using Galaxy and Managing your Data RStudio in Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/rstudio/tutorial.html 2019-10-08 2025-07-04 15 True False False False interactive_tool_rstudio UseGalaxy.eu, UseGalaxy.org.au 0 5305 8193 2.200000 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 0 269 323 1.150000 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 3100 4006 3.550000 0
Using Galaxy and Managing your Data Use Jupyter notebooks in Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/galaxy-intro-jupyter/tutorial.html 2018-07-02 2025-12-17 11 True False True False interactive_tool_jupyter_notebook UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 2571 3395 2.316667 0
Using Galaxy and Managing your Data Downloading and Deleting Data in Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/download-delete-data/tutorial.html 2019-10-17 2026-01-23 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 7630 10068 1.600000 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 0 839 1128 4.383333 0
Using Galaxy and Managing your Data Using dataset collections https://training.galaxyproject.org//topics/galaxy-interface/tutorials/collections/tutorial.html Genome indexing, Generation, Sequence alignment, Read mapping 2016-09-30 2024-12-05 20 True False True False bwa_mem, snpSift_extractFields, lofreq_call, collapse_dataset UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 16542 22535 2.950000 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 0 435 655 2.050000 0
Using Galaxy and Managing your Data Annotate, prepare tests and publish Galaxy workflows in workflow registries https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-fairification/tutorial.html Visualisation, Validation, Read mapping, Sequencing quality control 2025-05-26 2025-05-26 1 True False False False falco, multiqc UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr 0 278 328 2.016667 0
Using Galaxy and Managing your Data JupyterLab in Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/jupyterlab/tutorial.html 2020-03-05 2025-04-25 9 True False False False interactive_tool_jupyter_notebook UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 2199 3497 2.750000 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 0 118 139 2.650000 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 0 206 262 2.200000 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 66 74 0.500000 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 1729 2307 2.733333 0
Using Galaxy and Managing your Data Understanding Galaxy history system https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history/tutorial.html 2017-02-20 2025-04-28 12 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 5656 7270 2.800000 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 0 292 356 2.250000 0
Genome Annotation Genome annotation with Prokka https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Coding region prediction, Genome annotation, Genome visualisation, Gene prediction 2018-03-06 2026-01-23 27 True True True True jbrowse, prokka UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 3462475 8435376 4.100000 0
Genome Annotation From small to large-scale genome comparison https://training.galaxyproject.org//topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.html Multiple sequence alignment 2021-02-08 2024-07-31 8 True True False True clustalw, chromeister, gecko, tp_awk_tool UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz 0 3398854 8242937 4.366667 0
Genome Annotation Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial resistance Genome annotation, Genome visualisation, Antimicrobial resistance prediction, Read mapping 2024-01-23 2025-12-18 10 True False True True bowtie2, tbl2gff3, jbrowse, staramr_search, upload1, Grep1, bakta Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.org (Main) 0 3781 5160 2.866667 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 Differential protein expression profiling, Genome visualisation, Gene prediction, Sequence alignment, Sequence annotation, Genome annotation, Sequence assembly validation 2025-06-20 2025-06-25 2 True False False True gffread, rna_star, omark, busco, jbrowse, helixer, braker3 0 498 585 1.450000 0
Genome Annotation Masking repeats with RepeatMasker https://training.galaxyproject.org//topics/genome-annotation/tutorials/repeatmasker/tutorial.html Sequence composition, complexity and repeats, Genomics Repeat sequence detection, Editing, Mapping, RNA-Seq analysis, Genome annotation 2021-11-29 2025-06-03 22 True False True True bedtools_maskfastabed, red, repeatmodeler, repeatmasker_wrapper UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 10577 13422 1.350000 0
Genome Annotation Secondary metabolite discovery https://training.galaxyproject.org//topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html Service invocation, Data handling, Sequence clustering, Differential gene expression analysis, Gene prediction 2024-02-21 2024-09-27 2 True False False True openbabel_remDuplicates, collapse_dataset, ctb_silicos_qed, bp_genbank2gff3, Remove beginning1, ctb_chemfp_mol2fps, ctb_np-likeness-calculator, tp_awk_tool, interactive_tool_jupyter_notebook, edu.tamu.cpt.gff3.customGbkToGff, antismash, ncbi_acc_download, ctb_simsearch UseGalaxy.eu 0 769 973 1.266667 0
Genome Annotation Refining Genome Annotations with Apollo (prokaryotes) https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Genome visualisation 2021-06-04 2025-05-15 22 True True True True iframe, list_organism, jbrowse, create_account, create_or_update UseGalaxy.be UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3218354 7626702 4.933333 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 Differential protein expression profiling, Genome visualisation, Sequence alignment, Sequence annotation, Genome annotation, Gene prediction, Sequence assembly validation 2025-03-17 2025-06-20 4 True False False True gffread, rna_star, omark, busco, jbrowse, fasta-stats, braker3 0 1665 2031 1.766667 0
Genome Annotation Genome annotation with Helixer https://training.galaxyproject.org//topics/genome-annotation/tutorials/helixer/tutorial.html Biodiversity, Genomics, Zoology, Plant biology Differential protein expression profiling, Genome visualisation, Sequence annotation, Genome annotation, Gene prediction, Sequence assembly validation 2024-08-21 2025-06-04 8 True False False True gffread, omark, busco, jcvi_gff_stats, jbrowse, helixer 0 1409 1674 1.566667 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 Multilocus sequence typing, Sequence motif recognition, Genome visualisation, Genome assembly, Nucleic acid feature detection, Scaffolding, Protein feature detection, Genome annotation, Structural variation detection 2024-02-01 2024-10-15 6 True False True True tbl2gff3, tp_replace_in_column, integron_finder, jbrowse, isescan, upload1, plasmidfinder, tp_tail_tool, Grouping1, bakta UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main) 0 7182 9815 2.650000 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 3443320 8403155 2.166667 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 35249 64095 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 48 54 1.266667 0
Genome Annotation Dataset construction for bacterial comparative genomics https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html Genomics, Microbiology Data handling, Data retrieval, Sequence database search 2025-03-14 2025-03-14 1 True False False False bg_uniq, datasets_download_genome, Cut1, sort1, cat1, Remove beginning1, upload1 UseGalaxy.fr UseGalaxy.cz 0 94 112 2.333333 0
Genome Annotation Bacterial genome quality control https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html Genomics, Microbiology Genome comparison, Statistical calculation, Validation, Sequence composition calculation, Sequencing quality control, Sequence assembly validation 2025-03-14 2025-03-14 1 True False False False upload1, drep_dereplicate, checkm2 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz 0 117 129 1.616667 0
Genome Annotation Bacterial pangenomics https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-pangenomics/tutorial.html Genomics, Microbiology Essential dynamics, Rarefaction, Genome annotation, Sequence assembly 2025-03-14 2025-03-14 1 True False False False ppanggolin_all, ppanggolin_msa, upload1 UseGalaxy.eu, UseGalaxy.fr 0 113 128 1.066667 0
Genome Annotation Genome annotation with Funannotate https://training.galaxyproject.org//topics/genome-annotation/tutorials/funannotate/tutorial.html Gene and protein families Formatting, Sequence motif recognition, Genome visualisation, Fold recognition, Homology-based gene prediction, Sequence alignment, Information extraction, Protein feature detection, Sequence annotation, Genome annotation, Query and retrieval, Sequence assembly validation 2021-11-29 2025-06-10 26 True False True True funannotate_predict, rna_star, busco, eggnog_mapper, funannotate_compare, jbrowse, picard_MergeSamFiles, interproscan, funannotate_annotate, aegean_parseval UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org.au 0 11181 15733 1.916667 0
Genome Annotation Comparative gene analysis in unannotated genomes https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html Genomics, Gene and protein families, Sequence analysis, Phylogeny, Comparative genomics Sequence alignment analysis, Transcriptome assembly, Database search, Phylogenetic tree generation, Coding region prediction, Multiple sequence alignment, De-novo assembly 2022-09-08 2025-06-03 10 True False False True tp_split_on_column, rbc_mafft, Cut1, orfipy, bg_diamond_view, collapse_dataset, cat1, Add_a_column1, bg_diamond, gops_intersect_1, tab2fasta, Filter1, regexColumn1, bg_diamond_makedb, join1, rapidnj UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 1948 2707 2.983333 0
Genome Annotation Genome annotation with Maker (short) https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html Genome visualisation, Sequence annotation, Genome annotation, Sequence assembly validation 2021-01-12 2024-02-29 3 True False False True gffread, busco, jcvi_gff_stats, maker, jbrowse, fasta-stats, maker_map_ids UseGalaxy.be 0 4125 5771 2.883333 0
Genome Annotation Essential genes detection with Transposon insertion sequencing https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html Genomics, Microbiology, Sequence analysis, Mobile genetic elements Transposon prediction, Read pre-processing, Primer removal, Sequence trimming 2019-07-02 2024-03-18 12 True True False True Cut1, Add_a_column1, bowtie_wrapper, transit_gumbel, __EXTRACT_DATASET__, gff_to_prot, tp_sort_header_tool, bg_find_subsequences, Filter1, cutadapt, tp_easyjoin_tool, deeptools_bam_coverage UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.eu 0 3451941 8418427 3.900000 0
Genome Annotation Genome annotation with Maker https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html Genome visualisation, Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Sequence annotation, Genome annotation, Operation, Sequence assembly validation 2018-09-24 2024-02-29 14 True False False True gffread, busco, jcvi_gff_stats, maker, jbrowse, augustus_training, fasta-stats, maker_map_ids, snap_training UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.org.au 0 14005 24650 1.850000 0
Genome Annotation Functional annotation of protein sequences https://training.galaxyproject.org//topics/genome-annotation/tutorials/functional/tutorial.html Function analysis, Protein sites, features and motifs Sequence alignment analysis, Sequence motif recognition, Homology-based gene prediction, Protein feature detection, Information extraction, Fold recognition, Genome annotation, Query and retrieval 2022-07-20 2025-06-03 12 True False False True ncbi_blastp_wrapper, eggnog_mapper, bg_diamond, interproscan UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 4609 6123 1.633333 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.be, UseGalaxy.no UseGalaxy.cz, UseGalaxy.eu 0 1536 2308 2.416667 0
Genome Annotation Long non-coding RNAs (lncRNAs) annotation with FEELnc https://training.galaxyproject.org//topics/genome-annotation/tutorials/lncrna/tutorial.html Annotation, RNA-Seq analysis, Transcriptome assembly, Sequence annotation, Classification 2022-09-23 2024-09-18 11 True False True True gffread, feelnc, stringtie, Extract_features1, tp_cat UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 1992 2644 2.066667 0
Genome Annotation CRISPR screen analysis https://training.galaxyproject.org//topics/genome-annotation/tutorials/crispr-screen/tutorial.html Statistical calculation, Genetic variation analysis, Primer removal, Read pre-processing, Validation, Sequence trimming, Sequence composition calculation, Sequencing quality control 2021-10-15 2024-08-08 12 True True True True fastqc, multiqc, mageck_count, tp_awk_tool, volcanoplot, mageck_mle, cutadapt, mageck_test UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3052067 7039912 3.950000 0
Variant Analysis Microbial Variant Calling https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Phylogenetic tree generation, Variant calling, Genome visualisation, Phylogenetic tree visualisation 2018-02-26 2026-01-23 25 True False False True snippy, jbrowse UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 15579 24719 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 (Main), UseGalaxy.org.au Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz 0 3448789 8410339 4.433333 0
Imaging Using BioImage.IO models for image analysis in Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/process-image-bioimageio/tutorial.html Image analysis 2025-04-09 2026-02-05 9 True False False True ip_split_image, bioimage_inference, ip_binary_to_labelimage, image_math, __EXTRACT_DATASET__, ip_threshold, ip_overlay_images UseGalaxy.be, UseGalaxy.eu 0 227 270 2.833333 0
Imaging Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/omero-suite/tutorial.html Image analysis 2024-12-04 2026-01-21 7 True False False False omero_roi_import, omero_filter, omero_import, omero_metadata_import, omero_get_id, omero_get_value 0 230 293 2.433333 0
Imaging Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/parameter-tuning/tutorial.html Image analysis, Image annotation, Visualisation, Data handling 2025-04-28 2026-01-21 4 True False False True collapse_dataset, ip_filter_standard, param_value_from_file, ip_segmetrics, ip_threshold, ip_histogram_equalization, tp_split_on_column UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz 0 120 134 1.283333 0
Imaging Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines https://training.galaxyproject.org//topics/imaging/tutorials/2D-spot-detection/tutorial.html Image analysis, Image annotation, Visualisation, Data handling 2025-03-20 2025-11-26 5 True False False True idr_download_by_ids, ip_binary_to_labelimage, __EXTRACT_DATASET__, unzip, ip_overlay_images, ip_histogram_equalization, ip_spot_detection_2d, ip_points_to_label UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu 0 234 280 1.500000 0
Imaging Object tracking using CellProfiler https://training.galaxyproject.org//topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html Image analysis, Parsing, Quantification 2021-03-17 2025-11-26 11 True False False True cp_track_objects, cp_save_images, cp_overlay_outlines, cp_measure_object_intensity, cp_cellprofiler, cp_measure_object_size_shape, cp_tile, cp_color_to_gray, cp_common, cp_export_to_spreadsheet, unzip, cp_identify_primary_objects UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 2246 2788 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 Image analysis, Image annotation, Visualisation, Data handling 2025-08-11 2025-11-26 3 True False False True ip_split_image, __EXTRACT_DATASET__, ip_imageinfo, ip_2d_feature_extraction, interactive_tool_qupath, ip_points_to_label, graphicsmagick_image_convert UseGalaxy.eu 0 362 427 0.916667 0
Imaging Nucleoli segmentation and feature extraction using CellProfiler https://training.galaxyproject.org//topics/imaging/tutorials/tutorial-CP/tutorial.html Image analysis, Parsing, Quantification 2020-07-01 2025-11-26 12 True True False True cp_measure_object_size_shape, cp_common, cp_measure_image_area_occupied, cp_convert_objects_to_image, cp_identify_primary_objects, cp_measure_texture, cp_gray_to_color, cp_cellprofiler, cp_display_data_on_image, cp_save_images, cp_relate_objects, cp_image_math, cp_measure_object_intensity, cp_export_to_spreadsheet, cp_measure_image_quality, cp_enhance_or_suppress_features, idr_download_by_ids, cp_measure_image_intensity, cp_measure_granularity, cp_mask_image UseGalaxy.be, UseGalaxy.eu Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 3447473 8409143 3.366667 0
Imaging Voronoi segmentation https://training.galaxyproject.org//topics/imaging/tutorials/voronoi-segmentation/tutorial.html Image analysis, Image annotation, Visualisation, Data handling 2025-05-13 2025-11-26 7 True False False True ip_count_objects, ip_filter_standard, ip_binary_to_labelimage, image_math, ip_overlay_images, voronoi_tessellation, colorize_labels, ip_threshold, ip_convertimage, unzip, ip_imageinfo, ip_2d_feature_extraction, repeat_channels UseGalaxy.be, UseGalaxy.eu 0 348 500 3.083333 0
Imaging Tracking of mitochondria and capturing mitoflashes https://training.galaxyproject.org//topics/imaging/tutorials/detection-of-mitoflashes/tutorial.html Image analysis 2024-11-20 2025-11-26 5 True False False True ip_spot_detection_2d, ip_curve_fitting, ip_points_association_nn UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 211 243 1.083333 0
Imaging Introduction to Image Analysis using Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/imaging-introduction/tutorial.html Image analysis, Image annotation, Visualisation, Data handling 2019-08-13 2026-01-18 18 True False False True ip_count_objects, ip_filter_standard, ip_binary_to_labelimage, ip_overlay_images, ip_threshold, unzip, ip_imageinfo, ip_histogram_equalization UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 2765 3834 1.700000 0
Imaging Training Custom YOLO Models for Segmentation of Bioimages https://training.galaxyproject.org//topics/imaging/tutorials/yolo-segmentation-training/tutorial.html Image analysis, Image annotation, Visualisation, Data handling 2025-07-25 2025-11-26 7 True False False True interactive_tool_anylabeling, yolo_training, json2yolosegment, unzip, ip_histogram_equalization, graphicsmagick_image_convert UseGalaxy.eu 0 298 361 0.900000 0
Imaging End-to-End Tissue Microarray Image Analysis with Galaxy-ME https://training.galaxyproject.org//topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html 2023-02-14 2025-11-26 9 True False False True scimap_mcmicro_to_anndata, celesta, scimap_phenotyping, squidpy_spatial, gate_finder, unet_coreograph, palom, quantification, mesmer, ip_convertimage, ashlar, basic_illumination, rename_tiff_channels, vitessce_spatial, scanpy_compute_graph 0 1522 2046 1.783333 0
Imaging Analyse HeLa fluorescence siRNA screen https://training.galaxyproject.org//topics/imaging/tutorials/hela-screen-analysis/tutorial.html Image analysis, Image annotation, Visualisation, Data handling 2019-08-13 2026-01-18 16 True False False True collapse_dataset, ip_filter_standard, ip_binary_to_labelimage, ip_2d_filter_segmentation_by_features, ip_threshold, unzip, ip_2d_feature_extraction UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.no 0 819 1061 1.966667 0
Introduction to Galaxy Analyses From peaks to genes https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html 2016-03-29 2025-11-05 66 True False True True tp_replace_in_column, Cut1, Add_a_column1, CONVERTER_interval_to_bed_0, gops_intersect_1, get_flanks1, tp_sort_header_tool, upload1, tp_tail_tool, Grouping1 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no 0 20802 34102 3.283333 0
Introduction to Galaxy Analyses NGS data logistics https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html Formatting, SNP detection, Sequence contamination filtering, Data handling, Genome indexing, Generation, Sequence alignment, Validation, Read mapping, Sequencing quality control 2017-02-22 2026-01-06 40 True False True True bwa_mem2, bwa, fastp, lofreq_viterbi, snpEff, multiqc, snpeff_sars_cov_2, snpEff_build_gb, fasterq_dump, samtools_stats, collapse_dataset, picard_MarkDuplicates, bwa_mem, lofreq_indelqual, Filter1, snpSift_extractFields, samtools_view, lofreq_call UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au MISSISSIPPI, UseGalaxy.cz 0 20729 35227 3.400000 0
Introduction to Galaxy Analyses How to reproduce published Galaxy analyses https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-reproduce/tutorial.html Visualisation 2021-08-25 2024-10-15 12 True False False True datamash_ops, Cut1, Remove beginning1, csv_to_tabular, upload1, ggplot2_point, tp_sorted_uniq, Grouping1 Galaxy@AuBi, UseGalaxy.eu, UseGalaxy.org (Main) MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2252 2985 3.966667 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 {{version_paste}}, {{version_cat}}, {{version_split}}, Count1, wc_gnu, join1, tp_cat, {{version_replace_text_line}}, Remove beginning1, {{version_cut_columns}}, Filter1, {{version_datamash}}, tp_split_on_column, {{version_remove_beginning}}, {{version_join}}, {{version_filter}}, {{version_cut_advanced}}, {{version_compute}}, tp_sort_header_tool, {{version_replace_text_column}}, {{version_sort}}, upload1, {{version_remove_columns_by_header}}, datamash_ops, Cut1, tabular_to_csv, cat1, Add_a_column1, Show beginning1, {{version_select_first}}, regexColumn1, {{version_count}}, {{version_unique}}, tp_sorted_uniq, {{version_wc}}, Grouping1 0 6321 9173 3.383333 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, gops_intersect_1, gene2exon1, Filter1, tp_cat UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au MISSISSIPPI 0 20579 32383 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 3443591 8403486 2.166667 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 3443591 8403486 2.166667 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 8295 11635 1.450000 0
Introduction to Galaxy Analyses Best Practices for Citing Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-cite/tutorial.html 2025-11-06 2025-11-06 1 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 107 119 0.600000 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 0 468 530 2.500000 0
Introduction to Galaxy Analyses A short introduction to Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-short/tutorial.html Statistical calculation, Sequence composition calculation, Sequencing quality control 2018-08-27 2026-01-23 44 True True True True fastqc, cshl_fastq_quality_filter UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 3499969 8491095 6.866667 0
Introduction to Galaxy Analyses Galaxy Basics for everyone https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html Visualisation 2019-11-14 2025-11-06 35 True False True True datamash_ops, Cut1, Remove beginning1, csv_to_tabular, upload1, ggplot2_point, tp_sorted_uniq, Grouping1 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz 0 24442 38654 3.900000 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 comp1, datamash_ops, bedtools_intersectbed, tp_head_tool, tp_sort_header_tool, upload1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.no 0 50890 81783 3.400000 0
Introduction to Galaxy Analyses Very Short Introductions: QC https://training.galaxyproject.org//topics/introduction/tutorials/vsi_qc/tutorial.html Sequence contamination filtering, Sequencing quality control, Validation 2024-03-26 2024-06-25 4 True False False False multiqc, fastp Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 365 435 2.516667 0
Materials Science Finding the muon stopping site with pymuon-suite in Galaxy https://training.galaxyproject.org//topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.html 2024-01-22 2024-06-14 2 True False True True pm_muairss_read, pm_uep_opt UseGalaxy.cz, UseGalaxy.eu UseGalaxy.be 0 303 390 1.700000 0
Metabolomics Mass spectrometry: LC-MS analysis https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms/tutorial.html Data filtering, Label-free quantification, Peak detection, Validation, Mass spectrum visualisation, Chromatogram visualisation, Chromatographic alignment 2019-07-02 2025-09-21 13 True False False True abims_xcms_xcmsSet, quality_metrics, Batch_correction, xcms_plot_chromatogram, wsdl_hmdb, abims_xcms_fillPeaks, abims_CAMERA_annotateDiffreport, abims_xcms_group, xcms_merge, generic_filter, abims_xcms_retcor, xcms_export_samplemetadata, Univariate, msnbase_readmsdata UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 13097 21249 1.583333 0
Metabolomics Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) https://training.galaxyproject.org//topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html Imputation, Chromatogram visualisation, Clustering, Formatting, Filtering, Label-free quantification, Format validation, Spectral library search, Peak detection, Validation, Mass spectrum visualisation, Data filtering, Chromatographic alignment, Standardisation and normalisation, Correlation 2023-05-08 2023-11-09 5 True False False True abims_xcms_xcmsSet, matchms_similarity, ramclustr, matchms_formatter, abims_xcms_fillPeaks, abims_xcms_group, xcms_merge, ramclustr_define_experiment, msconvert, abims_xcms_retcor, riassigner, waveica, matchms_filtering, msnbase_readmsdata UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au 0 2854 3650 1.483333 0
Metabolomics Mass spectrometry imaging: Examining the spatial distribution of analytes https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html 2019-02-21 2024-10-15 18 True False False True cardinal_quality_report, cardinal_spectra_plots, cardinal_filtering, Filter1, cardinal_data_exporter, cardinal_mz_images UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 3114 4399 1.700000 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_neutral_run, split_file_to_collection, qcxms_production_run, ctb_im_conformers, param_value_from_file, __FILTER_FAILED_DATASETS__, qcxms_getres, tp_cut_tool, xtb_molecular_optimization, tp_cat, openbabel_compound_convert UseGalaxy.eu UseGalaxy.be, UseGalaxy.org.au 0 1316030 2514672 2.550000 0
Metabolomics Molecular formula assignment and mass recalibration with MFAssignR package https://training.galaxyproject.org//topics/metabolomics/tutorials/mfassignr/tutorial.html Annotation, Visualisation, Deisotoping, Mass spectra calibration 2025-05-19 2025-05-19 1 True False False True mfassignr_mfassignCHO, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_isofiltr, mfassignr_findRecalSeries, mfassignr_recallist, mfassignr_recal, mfassignr_snplot, mfassignr_histnoise 0 192 219 1.516667 0
Metabolomics Mass spectrometry imaging: Finding differential analytes https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html 2019-04-13 2023-11-09 9 True False False True cardinal_quality_report, join_files_on_column_fuzzy, cardinal_segmentations, cardinal_classification, cardinal_preprocessing, Summary_Statistics1, cardinal_combine, Filter1, maldi_quant_peak_detection, maldi_quant_preprocessing, cardinal_mz_images, Grep1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2060 2931 1.783333 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 3443591 8403491 2.166667 0
Metabolomics Mass spectrometry: LC-MS preprocessing with XCMS https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html Data filtering, Label-free quantification, Peak detection, Validation, Mass spectrum visualisation, Chromatogram visualisation, Chromatographic alignment 2020-02-04 2024-10-15 14 True True False False abims_xcms_xcmsSet, xcms_plot_chromatogram, abims_xcms_fillPeaks, abims_CAMERA_annotateDiffreport, abims_xcms_group, xcms_merge, abims_xcms_summary, abims_xcms_retcor, intens_check, xcms_export_samplemetadata, msnbase_readmsdata, idchoice UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3449924 8413373 4.416667 0
Metabolomics Mass spectrometry: GC-MS analysis with the metaMS package https://training.galaxyproject.org//topics/metabolomics/tutorials/gcms/tutorial.html Data filtering, Label-free quantification, Peak detection, Validation, Mass spectrum visualisation, Chromatogram visualisation, Chromatographic alignment 2021-09-22 2025-10-01 8 True False False False abims_xcms_xcmsSet, metams_runGC, xcms_plot_chromatogram, abims_xcms_fillPeaks, abims_xcms_group, xcms_merge, xcms_export_samplemetadata, msnbase_readmsdata UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.no 0 1734 2690 1.633333 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 quality_metrics, Batch_correction, normalization, generic_filter, intens_check, Multivariate UseGalaxy.fr UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3069 4100 1.850000 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 3443591 8403492 2.166667 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 Sequence clustering, Phylogenetic analysis, Sequence read processing, Taxonomic classification, Visualisation, DNA barcoding, Sequencing quality control 2017-06-22 2024-08-09 4 True False False True metaphlan2krona, mothur_filter_seqs, mothur_unique_seqs, humann2_regroup_table, mothur_classify_seqs, mothur_merge_files, mothur_screen_seqs, metaphlan2, mothur_align_seqs, mothur_count_seqs, mothur_cluster_split, mothur_pre_cluster, krona-text, taxonomy_krona_chart, humann2_renorm_table, mothur_make_biom, mothur_summary_seqs, humann2, mothur_make_shared, mothur_make_group, mothur_classify_otu UseGalaxy.be UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 9597 13111 2.650000 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 Scatter plot plotting, Aggregation, Genome assembly, Sequence analysis, Mapping assembly, Box-Whisker plot plotting, Sequence assembly visualisation, Pairwise sequence alignment, De-novo assembly, Antimicrobial resistance prediction 2019-06-25 2024-06-14 4 True False True True PlasFlow, unicycler, bandage_image, miniasm, minimap2, gfa_to_fa, staramr_search, racon, nanoplot UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 3658 5104 2.883333 0
Microbiome Remove contamination and host reads https://training.galaxyproject.org//topics/microbiome/tutorials/host-removal/tutorial.html Validation, Sequencing quality control, Read mapping 2025-12-18 2025-12-18 1 True False False True bowtie2, multiqc, __ZIP_COLLECTION__ Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 88 98 1.350000 0
Microbiome MGnify v5.0 Amplicon Pipeline https://training.galaxyproject.org//topics/microbiome/tutorials/mgnify-amplicon/tutorial.html Metagenomics, Taxonomy, Sequence analysis Statistical calculation, Nucleic acid feature detection, Mapping, Analysis, Sequence contamination filtering, Alignment, Sequence trimming, Sequence composition calculation, Formatting, Visualisation, Comparison, Sequence feature detection, Read pre-processing, Validation, k-mer counting, DNA barcoding, Nucleic acid design, Sequencing quality control 2025-07-30 2025-11-18 3 True False False True cmsearch_deoverlap, biom_convert, tp_find_and_replace, collapse_dataset, trimmomatic, seqprep, wc_gnu, bedtools_maskfastabed, fastqc, lotus2, fastp, fastq_dl, multiqc, tp_awk_tool, ampvis2_heatmap, infernal_cmsearch, __FILTER_EMPTY_DATASETS__, cshl_fasta_formatter, fastq_filter, collection_element_identifiers, collection_column_join, param_value_from_file, filter_tabular, gops_concat_1, fastq_to_fasta_python, taxonomy_krona_chart, CONVERTER_gz_to_uncompressed, __FILTER_FROM_FILE__, bedtools_getfastabed, __MERGE_COLLECTION__, __UNZIP_COLLECTION__, Add_a_column1, ampvis2_load, mapseq, prinseq, CONVERTER_uncompressed_to_gz, mgnify_seqprep, query_tabular, Grouping1 0 272 353 3.650000 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 alignment analysis, Phylogenetic tree reconstruction, Statistical calculation, Genome assembly, Mapping, Antimicrobial resistance prediction, Sequence contamination filtering, Variant calling, Sequence assembly, Cross-assembly, Sequence composition calculation, Phylogenetic tree generation, Aggregation, Scatter plot plotting, Multilocus sequence typing, Sequencing quality control, Data handling, Multiple sequence alignment, Taxonomic classification, Phylogenetic tree analysis, Visualisation, Mapping assembly, De-novo assembly, Box-Whisker plot plotting, Validation, Phylogenetic tree generation (from molecular sequences), Sequence assembly visualisation, Pairwise sequence alignment, Base-calling, Phylogenetic tree generation (maximum likelihood and Bayesian methods) 2023-01-26 2025-11-18 12 True False True True split_file_to_collection, bamtools_split_mapped, clair3, tp_find_and_replace, compose_text_param, table_compute, collapse_dataset, tp_head_tool, tab2fasta, bcftools_consensus, snpSift_extractFields, snpSift_filter, Grep1, Count1, medaka_consensus_pipeline, tp_cut_tool, samtools_fastx, fastqc, krakentools_kreport2krona, fastp, tp_sorted_uniq, multiqc, fasta_merge_files_and_filter_unique_sequences, Remove beginning1, minimap2, __FILTER_FAILED_DATASETS__, __BUILD_LIST__, fasttree, Paste1, tp_split_on_column, __FILTER_EMPTY_DATASETS__, tp_multijoin_tool, bcftools_norm, ggplot2_heatmap, clustalw, collection_element_identifiers, krakentools_extract_kraken_reads, collection_column_join, param_value_from_file, mlst, samtools_depth, samtools_coverage, kraken2, regex1, nanoplot, CONVERTER_gz_to_uncompressed, taxonomy_krona_chart, fasta2tab, porechop, tp_replace_in_column, Cut1, bedtools_getfastabed, barchart_gnuplot, Add_a_column1, abricate, regexColumn1, add_line_to_file, bandage_image, newick_display, flye, Grouping1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org.au 0 5208 7681 3.200000 0
Microbiome Clinical Metaproteomics 2: Discovery https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html Formatting, Heat map generation, Statistical calculation, Filtering, Protein quantification, Visualisation, Principal component plotting, Imputation, Clustering, Standardisation and normalisation 2026-02-10 2026-02-10 0 True False True True peptide_shaker, search_gui, Cut1, maxquant, fasta_merge_files_and_filter_unique_sequences, Remove beginning1, fasta_cli, dbbuilder, msconvert, filter_tabular, Filter1, ident_params, query_tabular, tp_cat, Grep1, fasta2tab, Grouping1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 0 0 0.000000 0
Microbiome Clinical Metaproteomics 4: Quantitation https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-4-quantitation/tutorial.html Heat map generation, Statistical calculation, Protein quantification, Visualisation, Principal component plotting, Imputation, Clustering, Standardisation and normalisation 2026-02-10 2026-02-10 0 True False True True maxquant, Cut1, Grep1, Grouping1 UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 0 0 0.000000 0
Microbiome Calculating α and β diversity from microbiome taxonomic data https://training.galaxyproject.org//topics/microbiome/tutorials/diversity/tutorial.html Visualisation, Aggregation 2024-08-01 2025-06-17 7 True False True True krakentools_alpha_diversity, krakentools_beta_diversity Galaxy@Pasteur, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, GalaxyTrakr 0 7759 9390 1.216667 0
Microbiome Taxonomic Profiling and Visualization of Metagenomic Data https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Visualisation, Statistical calculation, Genome annotation, Taxonomic classification, Aggregation 2023-05-03 2025-12-18 7 True False True True est_abundance, krakentools_kreport2krona, interactive_tool_pavian, __UNZIP_COLLECTION__, interactive_tool_phinch, metaphlan, kraken2, kraken_biom, taxonomy_krona_chart UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 13113 17458 1.983333 0
Microbiome Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Sequence alignment analysis, Statistical calculation, Genome assembly, Sequence file editing, Local alignment, Sequence contamination filtering, Variant calling, Sequence trimming, Sequence composition calculation, Formatting, Data handling, Primer removal, Visualisation, Read pre-processing, Read mapping, Sequence assembly visualisation, Sequencing quality control, Sequence assembly validation 2022-12-05 2025-12-08 8 True False True True bowtie2, fastqc, bg_uniq, quast, coverm_contig, metaspades, collection_column_join, filter_tabular, bamtools, cutadapt, megahit, ngsutils_bam_filter, bandage_image, megahit_contig2fastg, tp_cat, seqtk_subseq, random_lines1, bandage_info UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 4744 6551 2.883333 0
Microbiome Building an amplicon sequence variant (ASV) table from 16S data using DADA2 https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Analysis, Visualisation, DNA barcoding, Variant calling, Deposition 2024-06-05 2025-07-03 11 True False True True interactive_tool_phyloseq, dada2_filterAndTrim, dada2_mergePairs, tp_head_tool, dada2_assignTaxonomyAddspecies, phyloseq_from_dada2, dada2_makeSequenceTable, dada2_dada, dada2_removeBimeraDenovo, __SORTLIST__, dada2_plotQualityProfile, collection_element_identifiers, dada2_learnErrors, dada2_seqCounts, tp_replace_in_column, __UNZIP_COLLECTION__, cat1, Add_a_column1, tp_replace_in_line, Grouping1 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 7686 10865 2.350000 0
Microbiome Binning of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html Metagenomics, Sequence assembly Genome comparison, Statistical calculation, Sequencing quality control, Sequence clustering, Validation, Read binning, Genome annotation, Sequence assembly, Sequence composition calculation, Read mapping, Sequence assembly validation 2023-12-05 2025-12-02 7 True False True True bowtie2, maxbin2, samtools_sort, concoct, das_tool, metabat2_jgi_summarize_bam_contig_depths, concoct_cut_up_fasta, concoct_coverage_table, drep_dereplicate, concoct_merge_cut_up_clustering, __BUILD_LIST__, checkm_lineage_wf, metabat2, semibin, concoct_extract_fasta_bins, Fasta_to_Contig2Bin, binette UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.org (Main), UseGalaxy.org.au 0 6118 7485 1.433333 0
Microbiome Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2 https://training.galaxyproject.org//topics/microbiome/tutorials/lotus2-identifying-fungi/tutorial.html DNA barcoding, Sequence feature detection 2024-09-30 2024-09-30 2 True False False True lotus2 UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 836 1046 1.633333 0
Microbiome Clinical Metaproteomics 5: Data Interpretation https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-5-data-interpretation/tutorial.html Visualisation, Prediction and recognition 2026-02-10 2026-02-10 0 True False True True unipept, msstatstmt, Grep1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 0 0 0.000000 0
Microbiome 16S Microbial analysis with Nanopore data https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Visualisation, Statistical calculation, Validation, Sequence contamination filtering, Taxonomic classification, Sequence composition calculation, Sequencing quality control 2020-11-24 2024-07-31 5 True False False True fastqc, fastp, multiqc, Remove beginning1, tp_replace_in_line, kraken2, datamash_reverse, taxonomy_krona_chart, porechop UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr 0 9037 12557 2.650000 0
Microbiome Clinical Metaproteomics 3: Verification https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html 2026-02-10 2026-02-10 0 True False True True pepquery2, Cut1, collapse_dataset, fasta_merge_files_and_filter_unique_sequences, Remove beginning1, dbbuilder, Filter1, query_tabular, tp_cat, uniprotxml_downloader, Grouping1 UseGalaxy.cz, UseGalaxy.eu UseGalaxy.org (Main), UseGalaxy.org.au 0 0 0 0.000000 0
Microbiome Identification of the micro-organisms in a beer using Nanopore sequencing https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Visualisation, Statistical calculation, Sequence contamination filtering, Taxonomic classification, Sequence composition calculation, Sequencing quality control, Aggregation 2022-09-29 2024-11-29 5 True False True True fastqc, krakentools_kreport2krona, fastp, Filter1, kraken2, taxonomy_krona_chart, porechop UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3083 4474 2.800000 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 MQoutputfilter, ggplot2_histogram, tp_replace_in_column, Cut1, sort1, cat1, Add_a_column1, count_gff_features, histogram_rpy, minimap2, tab2fasta, add_column_headers, Filter1, CONVERTER_fasta_to_tabular, tp_tail_tool, join1, tp_sorted_uniq, Grouping1 UseGalaxy.fr 0 363 411 0.716667 0
Microbiome Metatranscriptomics analysis using microbiome RNA-seq data (short) https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis Sequence similarity search, Sequence alignment analysis, Species frequency estimation, Statistical calculation, Phylogenetic analysis, Phylogenetic tree visualisation, Sequence trimming, Sequence composition calculation, Phylogenetic tree editing, Conversion, Sequence comparison, Primer removal, Taxonomic classification, Read pre-processing, Visualisation, Validation, Phylogenetic inference, Sequencing quality control 2020-02-13 2025-06-16 6 True False True True humann_rename_table, graphlan_annotate, tp_find_and_replace, fastq_paired_end_interlacer, metaphlan, graphlan, fastqc, humann_split_stratified_table, multiqc, bg_sortmerna, humann_regroup_table, cutadapt, export2graphlan, combine_metaphlan2_humann2, humann_renorm_table, tp_sort_header_tool, taxonomy_krona_chart, Cut1, humann, humann_unpack_pathways, Grep1 UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.no 0 859 1115 2.366667 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 Sequence similarity search, Sequence alignment analysis, Species frequency estimation, Statistical calculation, Phylogenetic analysis, Phylogenetic tree visualisation, Sequence trimming, Sequence composition calculation, Phylogenetic tree editing, Conversion, Sequence comparison, Primer removal, Taxonomic classification, Read pre-processing, Visualisation, Validation, Phylogenetic inference, Sequencing quality control, Aggregation 2019-11-21 2025-06-16 6 True True True True humann_rename_table, graphlan_annotate, tp_find_and_replace, fastq_paired_end_interlacer, metaphlan, graphlan, fastqc, humann_split_stratified_table, multiqc, bg_sortmerna, humann_regroup_table, cutadapt, export2graphlan, humann_renorm_table, tp_sort_header_tool, taxonomy_krona_chart, Cut1, humann, humann_unpack_pathways, Grep1, combine_metaphlan_humann, Grouping1 UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.eu 0 3450732 8412774 4.066667 0
Microbiome Clinical Metaproteomics 1: Database-Generation https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-1-database-generation/tutorial.html Tag-based peptide identification, Target-Decoy, de Novo sequencing, Expression analysis, Protein identification 2026-02-10 2026-02-10 0 True False True True fasta_merge_files_and_filter_unique_sequences, metanovo, uniprotxml_downloader, dbbuilder UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.org (Main) 0 1 1 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 84 92 1.416667 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 0 444 716 3.083333 0
Microbiome Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads https://training.galaxyproject.org//topics/microbiome/tutorials/mags-building/tutorial.html Metagenomics, Sequence assembly Genome comparison, Statistical calculation, Data handling, Validation, Genome annotation, Sequence composition calculation, Sequencing quality control, Sequence assembly validation 2025-12-18 2025-12-18 1 True False False False tp_replace_in_column, Cut1, collapse_dataset, multiqc, cat1, Remove beginning1, fasterq_dump, collection_column_join, drep_dereplicate, __EXTRACT_DATASET__, Summary_Statistics1, tp_sort_header_tool, checkm_lineage_wf, bakta, join1, Grouping1 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 221 262 1.433333 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 0 670 1007 2.400000 0
Microbiome 16S Microbial Analysis with mothur (short) https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic analysis, Sequence read processing, Taxonomic classification, Phylogenetic tree analysis, Visualisation, DNA barcoding, Phylogenetic tree generation, Sequencing quality control 2019-05-13 2025-12-18 6 True False True True mothur_summary_single, mothur_filter_seqs, collapse_dataset, mothur_dist_seqs, mothur_remove_seqs, mothur_cluster, mothur_unique_seqs, mothur_classify_seqs, mothur_dist_shared, mothur_tree_shared, mothur_screen_seqs, mothur_chimera_vsearch, mothur_remove_lineage, mothur_count_groups, XY_Plot_1, mothur_count_seqs, mothur_venn, mothur_cluster_split, mothur_pre_cluster, mothur_rarefaction_single, mothur_heatmap_sim, mothur_remove_groups, mothur_summary_seqs, mothur_make_shared, mothur_sub_sample, newick_display, mothur_classify_otu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.fr 0 6078 10180 4.466667 0
Microbiome 16S Microbial Analysis with mothur (extended) https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Phylogenetic tree reconstruction, Sequence clustering, Phylogenetic analysis, Sequence read processing, Taxonomic classification, Phylogenetic tree analysis, Visualisation, DNA barcoding, Phylogenetic tree generation, Sequencing quality control 2017-02-12 2025-12-18 5 True False False True mothur_summary_single, mothur_filter_seqs, mothur_dist_seqs, mothur_remove_seqs, mothur_cluster, mothur_unique_seqs, mothur_classify_seqs, mothur_seq_error, mothur_dist_shared, mothur_tree_shared, mothur_make_contigs, mothur_screen_seqs, mothur_get_groups, mothur_chimera_vsearch, mothur_align_seqs, mothur_remove_lineage, mothur_count_groups, XY_Plot_1, mothur_count_seqs, mothur_venn, mothur_cluster_split, mothur_pre_cluster, taxonomy_krona_chart, mothur_rarefaction_single, mothur_make_biom, mothur_heatmap_sim, mothur_remove_groups, mothur_summary_seqs, mothur_make_shared, mothur_sub_sample, mothur_taxonomy_to_krona, newick_display, mothur_classify_otu UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 12935 18943 2.733333 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 Sequence alignment analysis, Global alignment, Sequence analysis, Genome indexing, Primer removal, Multiple sequence alignment, Local alignment, Generation, Sequence alignment, Sequence contamination filtering, Read mapping, Sequencing quality control 2023-05-15 2024-03-20 4 True False False True rbc_mafft, fatovcf, qualimap_bamqc, compose_text_param, ivar_trim, fastp, __ZIP_COLLECTION__, fasta_compute_length, param_value_from_file, __APPLY_RULES__, samtools_merge, ivar_consensus, upload1, datamash_ops, Cut1, Add_a_column1, fasta_regex_finder, mimodd_info, EMBOSS: maskseq51, bwa_mem, samtools_view, Grep1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org (Main) 0 1122 1324 2.216667 0
Variant Analysis M. tuberculosis Variant Analysis https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease Sequence alignment analysis, Genome visualisation, Statistical calculation, Global alignment, Sequence analysis, Taxonomic classification, Local alignment, Phylogenetic tree visualisation, Validation, Sequence alignment, Sequence contamination filtering, Phylogenetic tree generation, Variant calling, Sequence composition calculation, Sequencing quality control, Antimicrobial resistance prediction 2020-07-25 2026-01-06 32 True False True True qualimap_bamqc, jbrowse, samtools_stats, bcftools_consensus, fastqc, fastp, EMBOSS: seqret84, multiqc, tp_sed_tool, tp_awk_tool, tb_profiler_profile, EMBOSS:%20seqret84, jvarkit_wgscoverageplotter, kraken2, tb_variant_filter, upload1, tbvcfreport, __FLATTEN__, mosdepth, snippy 0 7924 12096 2.900000 0
Variant Analysis Avian influenza viral strain analysis from gene segment sequencing data https://training.galaxyproject.org//topics/variant-analysis/tutorials/aiv-analysis/tutorial.html Sequence alignment analysis, Data retrieval, Sequence file editing, Sequencing quality control, Data handling, Genome indexing, Phylogenetic analysis, Sequence analysis, Primer removal, Multiple sequence alignment, Generation, Sequence alignment, Sequence contamination filtering, Read mapping, De-novo assembly 2022-11-21 2024-10-04 10 True False False False rbc_mafft, fastp, __RELABEL_FROM_FILE__, bamtools_split_ref, qualimap_bamqc, tp_find_and_replace, vapor, collapse_dataset, seqtk_subseq, bwa_mem, Show beginning1, samtools_view, iqtree, Grep1, ivar_consensus, upload1 UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 2170 3118 2.866667 0
Transcriptomics Whole transcriptome analysis of Arabidopsis thaliana https://training.galaxyproject.org//topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html Sequence trimming, Differential gene expression analysis, RNA-Seq analysis, Primer removal, Visualisation, RNA-Seq quantification, Read pre-processing, Validation, Sequence composition calculation, Read mapping, Gene expression analysis, Sequencing quality control 2021-04-08 2025-08-10 18 True True True True rbc_mirdeep2_quantifier, Cut1, sort1, __MERGE_COLLECTION__, rbc_mirdeep2_mapper, multiqc, cat1, targetfinder, filter_by_fasta_ids, salmon, falco, Filter1, deseq2, sample_seqs, trim_galore UseGalaxy.cz 0 3304604 7900939 4.716667 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 tree editing, Phylogenetic inference (from molecular sequences), Phylogenetic analysis, Multiple sequence alignment, Sequence analysis 2025-03-26 2025-04-27 2 True False True True rbc_mafft, Cut1, trimal, Remove beginning1, filter_by_fasta_ids, ete_treeviewer, Filter1, quicktree, iqtree, tapscan_classify UseGalaxy.eu 0 322 430 1.966667 0
Sequence analysis NCBI BLAST+ against the MAdLand https://training.galaxyproject.org//topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.html Sequence alignment analysis 2023-01-16 2024-07-31 9 True False False False ncbi_blastp_wrapper, bg_diamond, ncbi_blastx_wrapper Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 1832 2338 3.133333 0
Single Cell Analysis of plant scRNA-Seq Data with Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-plant/tutorial.html Expression profile clustering, Differential gene expression analysis, Principal component visualisation 2021-04-08 2025-02-13 7 True False True True anndata_import, scanpy_remove_confounders, scanpy_plot, anndata_manipulate, scanpy_filter, scanpy_normalize, scanpy_cluster_reduce_dimension, scanpy_inspect UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2906 3615 1.566667 0
Proteomics Statistical analysis of DIA data https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.html Tag-based peptide identification, Differential protein expression profiling, Spectrum calculation 2020-12-02 2023-11-09 9 True False False True histogram_rpy, Filter1, Grep1, msstats UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.org.au 0 1389 1929 2.516667 0
Proteomics Neoantigen 5b: IEDB binding Validated Neopeptides https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-hla-binding-novel-peptides/tutorial.html 2025-01-14 2025-12-03 5 True False False False iedb_api, table_compute, Filter1, fasta_to_tabular, query_tabular 0 92 97 0.350000 0
Proteomics Proteogenomics 2: Database Search https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html Peptide database search, Conversion 2018-11-20 2025-05-08 24 True False True True search_gui, mz_to_sqlite, tab2fasta, ident_params, query_tabular, peptide_shaker UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 1617 2388 4.766667 0
Proteomics Library Generation for DIA Analysis https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html Heat map generation, Statistical calculation, Protein quantification, Visualisation, Principal component plotting, Imputation, Clustering, Standardisation and normalisation 2020-12-02 2025-06-02 12 True False False True TargetedFileConverter, diapysef, maxquant, Filter1, OpenSwathDecoyGenerator, OpenSwathAssayGenerator UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 4703 6133 1.350000 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, peptide_genomic_coordinate, pep_pointer, query_tabular UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.no 0 1787 2569 2.716667 0
Proteomics metaQuantome 3: Taxonomy https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy Statistical inference, Functional clustering, Query and retrieval, Principal component visualisation, Heat map generation, Filtering, Visualisation, Indexing, Quantification, Differential protein expression analysis 2020-10-29 2024-03-15 14 True False False True metaquantome_viz, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_db, metaquantome_filter UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 458 598 2.216667 0
Proteomics Neoantigen 1a: Fusion-Database-Generation https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-fusion-database-generation/tutorial.html Sequence alignment 2025-01-14 2025-12-03 4 True False False False rna_star, arriba, arriba_get_filters, tp_awk_tool, tab2fasta, regex1, CONVERTER_gz_to_uncompressed, query_tabular UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 212 260 1.266667 0
Proteomics Neoantigen 2: Database merge and FragPipe discovery https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.html 2025-01-14 2025-12-03 4 True False False False fragpipe, collapse_dataset, validate_fasta_database, fasta_merge_files_and_filter_unique_sequences, Remove beginning1, fragpipe_manifest_generator, query_tabular, Grep1 UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 261 301 1.133333 0
Proteomics Clinical Metaproteomics 2: Discovery https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html Formatting, Heat map generation, Statistical calculation, Filtering, Protein quantification, Visualisation, Principal component plotting, Imputation, Clustering, Standardisation and normalisation 2024-02-06 2025-08-10 5 True False True True peptide_shaker, search_gui, Cut1, maxquant, fasta_merge_files_and_filter_unique_sequences, Remove beginning1, fasta_cli, dbbuilder, msconvert, filter_tabular, Filter1, ident_params, query_tabular, tp_cat, Grep1, fasta2tab, Grouping1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 372 487 5.533333 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 FalseDiscoveryRate, FileFilter, HighResPrecursorMassCorrector, FeatureFinderMultiplex, IDConflictResolver, IDMapper, PeptideIndexer, MSGFPlusAdapter, MzTabExporter, ConsensusID, FileMerger, IDFilter, IDMerger 0 896 1221 1.366667 0
Proteomics Proteogenomics 1: Database Creation https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html RNA-Seq analysis, Transcriptome assembly, Statistical calculation, Sequence alignment, Sequence annotation, Variant calling 2018-11-20 2025-05-08 29 True False True True tp_replace_in_column, freebayes, custom_pro_db, fasta_merge_files_and_filter_unique_sequences, translate_bed, cat_multi_datasets, bed_to_protein_map, tab2fasta, filter_tabular, gffcompare_to_bed, gffcompare, hisat2, sqlite_to_tabular, regexColumn1, stringtie, query_tabular, fasta2tab UseGalaxy.be, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 6075 9841 2.583333 0
Proteomics Neoantigen 5a: Predicting HLA Binding https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-predicting-hla-binding/tutorial.html Genetic variation analysis, Read mapping 2025-01-14 2025-12-03 4 True False False False seq2hla, query_tabular, tp_awk_tool, optitype UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 97 103 0.016667 0
Proteomics Clinical Metaproteomics 4: Quantitation https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.html Heat map generation, Statistical calculation, Protein quantification, Visualisation, Principal component plotting, Imputation, Clustering, Standardisation and normalisation 2024-02-06 2025-08-10 5 True False True True maxquant, Cut1, Grep1, Grouping1 UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 196 262 2.100000 0
Proteomics Mass spectrometry imaging: Loading and exploring MSI data https://training.galaxyproject.org//topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.html Proteomics 2018-11-27 2025-04-08 18 True False False True cardinal_quality_report, tp_sort_header_tool, Grep1, cardinal_data_exporter UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2881 4389 1.616667 0
Proteomics Protein FASTA Database Handling https://training.galaxyproject.org//topics/proteomics/tutorials/database-handling/tutorial.html Proteomics 2017-02-14 2025-04-08 30 True False False True fasta_merge_files_and_filter_unique_sequences, addValue, dbbuilder, tab2fasta, DecoyDatabase, fasta2tab UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 4895 7734 2.150000 0
Proteomics Label-free data analysis using MaxQuant https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-label-free/tutorial.html Heat map generation, Tag-based peptide identification, Differential protein expression profiling, Statistical calculation, Protein quantification, Visualisation, Principal component plotting, Imputation, Clustering, Standardisation and normalisation, Spectrum calculation 2020-04-29 2025-05-21 14 True False False True Cut1, maxquant, Add_a_column1, histogram_rpy, tp_sort_header_tool, Filter1, msstats, Grep1 UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.org.au 0 20313 29584 1.750000 0
Proteomics Machine Learning Modeling of Anticancer Peptides https://training.galaxyproject.org//topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.html 2021-01-22 2023-11-09 8 True False False True pdaug_basic_plots, pdaug_addclasslabel, pdaug_merge_dataframes, pdaug_ml_models, pdaug_sequence_property_based_descriptors UseGalaxy.be 0 1067 1578 2.100000 0
Proteomics Neoantigen 4: Variant Annotation https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-variant-annotation/tutorial.html 2025-01-14 2025-12-03 5 True False False False select, column_regex_find_and_replace, tab2fasta, regexColumn1, query_tabular, pep_pointer, Convert characters1, cut 0 104 121 1.016667 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 retr_pepatlas1, Jvenn, retrieve_from_hpa, IDconverter, tp_cut_tool, rna_abbased_data, prot_features, MQoutputfilter UseGalaxy.be, UseGalaxy.fr 0 1741 2355 2.433333 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, Tag-based peptide identification, Differential protein expression profiling, Statistical calculation, Protein quantification, Visualisation, Principal component plotting, Imputation, Clustering, Standardisation and normalisation, Spectrum calculation 2021-02-17 2025-09-22 19 True False True True tp_replace_in_column, Cut1, datamash_ops, ggplot2_heatmap2, maxquant, Summary_Statistics1, Filter1, tp_easyjoin_tool, msstats, uniprot, Grep1, fasta2tab UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 8729 14079 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 2025-12-03 4 True False False False pepquery2, msconvert, tab2fasta, ncbi_blastp_wrapper, query_tabular UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 91 100 1.366667 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, IDconverter, Jvenn, rna_abbased_data, retrieve_from_hpa, reactome_analysis, MQoutputfilter UseGalaxy.be UseGalaxy.fr 0 3144 4544 2.733333 0
Proteomics DIA Analysis using OpenSwathWorkflow https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html Formatting, Filtering 2020-12-02 2025-05-20 12 True False False True pyprophet_protein, OpenSwathWorkflow, pyprophet_merge, msconvert, pyprophet_score, pyprophet_export, pyprophet_peptide, Grep1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 3299 4675 2.500000 0
Proteomics EncyclopeDIA https://training.galaxyproject.org//topics/proteomics/tutorials/encyclopedia/tutorial.html Formatting, Filtering 2021-06-21 2025-05-19 12 True False True True encyclopedia_searchtolib, msconvert, encyclopedia_quantify UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 2040 2767 1.750000 0
Proteomics Peptide and Protein ID using SearchGUI and PeptideShaker https://training.galaxyproject.org//topics/proteomics/tutorials/protein-id-sg-ps/tutorial.html 2017-06-12 2025-04-08 28 True False False True search_gui, PeakPickerHiRes, Grep1, FileConverter, peptide_shaker 0 3259 5148 1.833333 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 FalseDiscoveryRate, TextExporter, IDScoreSwitcher, PeptideIndexer, XTandemAdapter, MSGFPlusAdapter, msconvert, ConsensusID, IDFilter, IDMerger, IDPosteriorErrorProbability, FidoAdapter, FileInfo, PeakPickerHiRes, Grep1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 3621 6044 2.833333 0
Proteomics Clinical Metaproteomics 5: Data Interpretation https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-5-data-interpretation/tutorial.html Visualisation, Prediction and recognition 2024-02-06 2025-08-10 4 True False True True unipept, msstatstmt, Grep1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 317 407 2.116667 0
Proteomics Neoantigen 1b: Non-Reference-Database-Generation https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html RNA-Seq analysis, Transcriptome assembly, Statistical calculation, Sequence alignment, Sequence annotation, Variant calling 2025-01-14 2025-12-03 6 True False False False freebayes, custom_pro_db, fasta_merge_files_and_filter_unique_sequences, translate_bed, column_regex_find_and_replace, bed_to_protein_map, tab2fasta, sqlite_to_tabular, gffcompare_to_bed, gffcompare, hisat2, stringtie, regexColumn1, CONVERTER_gz_to_uncompressed, concatenate, fasta2tab 0 127 139 0.516667 0
Proteomics Multiomics data analysis using MultiGSEA https://training.galaxyproject.org//topics/proteomics/tutorials/multiGSEA-tutorial/tutorial.html Gene-set enrichment analysis, Pathway analysis, Aggregation 2025-03-10 2025-03-11 2 True False False True Filter1, multigsea, tp_grep_tool UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org.au 0 392 434 1.300000 0
Proteomics Metaproteomics tutorial https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Visualisation, Prediction and recognition 2017-06-28 2024-06-14 41 True False True True search_gui, unipept, sqlite_to_tabular, query_tabular, peptide_shaker UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz 0 2995 4731 2.666667 0
Proteomics Clinical Metaproteomics 3: Verification https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html 2024-02-06 2025-08-10 7 True False True True pepquery2, Cut1, collapse_dataset, fasta_merge_files_and_filter_unique_sequences, Remove beginning1, dbbuilder, Filter1, query_tabular, tp_cat, uniprotxml_downloader, Grouping1 UseGalaxy.cz, UseGalaxy.eu UseGalaxy.org (Main), UseGalaxy.org.au 0 218 284 3.216667 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 FalseDiscoveryRate, TextExporter, FeatureFinderMultiplex, IDConflictResolver, IDMapper, IDScoreSwitcher, PeptideIndexer, XTandemAdapter, histogram_rpy, Summary_Statistics1, tp_tail_tool, IDPosteriorErrorProbability, FidoAdapter, FileInfo, ProteinQuantifier, MultiplexResolver, Grep1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 1405 1945 1.500000 0
Proteomics Peptide Library Data Analysis https://training.galaxyproject.org//topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.html 2021-01-22 2023-11-09 5 True False False True pdaug_tsvtofasta, pdaug_fishers_plot, pdaug_addclasslabel, pdaug_merge_dataframes, pdaug_basic_plots, pdaug_sequence_property_based_descriptors, pdaug_peptide_data_access, pdaug_peptide_sequence_analysis UseGalaxy.be 0 773 1038 2.266667 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, Statistical calculation, Protein quantification, Visualisation, Principal component plotting, Imputation, Clustering, Standardisation and normalisation 2021-08-13 2025-01-08 11 True False False True maxquant, msstatstmt UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.org (Main) 0 4376 5851 1.683333 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 comp1, bg_uniq, tp_sorted_uniq, term_id_vs_term_name, get_subontology_from, Filter1, wolf_psort, Grep1, tp_easyjoin_tool, tp_cut_tool, uniprot, Convert characters1 0 663 982 1.450000 0
Proteomics metaQuantome 2: Function https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics Statistical inference, Functional clustering, Query and retrieval, Principal component visualisation, Heat map generation, Filtering, Visualisation, Indexing, Quantification, Differential protein expression analysis 2020-10-29 2024-03-15 14 True False False True metaquantome_viz, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_db, metaquantome_filter UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 437 608 4.033333 0
Proteomics metaQuantome 1: Data creation https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Formatting, Visualisation, Filtering, Label-free quantification, Prediction and recognition 2020-10-16 2024-03-14 20 True False False True tp_replace_in_column, Cut1, search_gui, Remove beginning1, msconvert, unipept, tp_replace_in_line, Filter1, flashlfq, regex1, query_tabular, Grep1, peptide_shaker UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 909 1526 3.750000 0
Proteomics Single Cell Proteomics data analysis with bioconductor-scp https://training.galaxyproject.org//topics/proteomics/tutorials/bioconductor-scp/tutorial.html Visualisation, Expression analysis 2025-02-07 2025-02-10 2 True False False False bioconductor_scp, Grouping1 UseGalaxy.eu, UseGalaxy.org.au 0 302 368 0.900000 0
Proteomics Clinical Metaproteomics 1: Database-Generation https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.html Tag-based peptide identification, Target-Decoy, de Novo sequencing, Expression analysis, 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 UseGalaxy.be, UseGalaxy.org (Main) 0 635 942 3.600000 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 3443591 8403509 2.166667 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 7742 12460 0.900000 0
Sequence analysis Mapping https://training.galaxyproject.org//topics/sequence-analysis/tutorials/mapping/tutorial.html Mapping Sequence alignment analysis, Genome visualisation, Statistical calculation, Sequence trimming, Data handling, Primer removal, Read pre-processing, Validation, Read mapping, Sequence composition calculation, Sequencing quality control 2016-10-04 2025-12-18 44 True True True True bowtie2, __FLATTEN__, fastqc, multiqc, jbrowse, samtools_stats, trim_galore, bamFilter UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3510797 8515548 4.916667 0
Sequence analysis Clean and manage Sanger sequences from raw files to aligned consensus https://training.galaxyproject.org//topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html Sequence file editing, Sequence clustering, Phylogenetic analysis, Data handling, Sequence read processing, Taxonomic classification, Visualisation, Demultiplexing, DNA barcoding, Sequencing quality control 2024-01-08 2024-03-05 2 True False False True tab2fasta, fastq_to_tabular, unzip, seqtk_trimfq, __SORTLIST__, qiime_align_seqs, ncbi_blastn_wrapper, ab1_fastq_converter, mothur_merge_files, aligned_to_consensus, mothur_degap_seqs, fastq_masker_by_quality, seqtk_mergepe, collection_element_identifiers, cshl_fastq_to_fasta, cshl_fastx_reverse_complement, regex1, __FILTER_FROM_FILE__, filter_by_fasta_ids, fastq_groomer UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 3590 4497 1.666667 0
Sequence analysis Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes https://training.galaxyproject.org//topics/sequence-analysis/tutorials/viral_primer_design/tutorial.html Sequence alignment analysis, PCR primer design, Sequence alignment, Global alignment, Sequence analysis, Multiple sequence alignment, Local alignment 2025-03-20 2025-11-20 3 True False False True rbc_mafft, split_file_to_collection, EMBOSS: degapseq20, ncbi_makeblastdb, varvamp, fasta_compute_length UseGalaxy.be, UseGalaxy.eu 0 729 839 0.933333 0
Sequence analysis Quality Control https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-control/tutorial.html Scatter plot plotting, Statistical calculation, Primer removal, Read pre-processing, Box-Whisker plot plotting, Validation, Sequence trimming, Sequence composition calculation, Sequencing quality control 2016-10-04 2025-03-29 48 True True True True fastqc, pycoqc, multiqc, cutadapt, fastqe, nanoplot UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr 0 3553729 8602521 5.183333 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 contamination filtering, Sequence assembly validation 2024-04-16 2024-04-16 2 True False False True ncbi_fcs_adaptor, ncbi_fcs_gx UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 2007 2716 2.250000 0
Sequence analysis Quality and contamination control in bacterial isolate using Illumina MiSeq Data https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Statistical calculation, Expression analysis, Taxonomic classification, Visualisation, Sequence contamination filtering, Read mapping, Cross-assembly, Sequencing quality control 2024-07-15 2025-12-18 5 True False True True est_abundance, recentrifuge, fastp, falco, kraken2, upload1 GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 1826 2467 2.700000 0
Single Cell Bulk RNA Deconvolution with MuSiC https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music/tutorial.html 2022-02-11 2025-02-14 10 True False True True music_inspect_eset, music_construct_eset, music_deconvolution UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 4158 5220 1.566667 0
Single Cell Generating a single cell matrix using Alevin https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin/tutorial.html RNA-Seq quantification, Sequence composition calculation, Gene expression analysis 2021-03-03 2025-11-18 25 True False True True Cut1, dropletutils_empty_drops, anndata_inspect, sceasy_convert, _ensembl_gtf2gene_list, anndata_manipulate, alevin, dropletutils_read_10x, _salmon_kallisto_mtx_to_10x, join1, _dropletBarcodePlot UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 3599 5440 3.450000 0
Single Cell Converting between common single cell data formats https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-data-ingest/tutorial.html Loading, Community profiling 2024-02-13 2025-03-11 4 True False False True tabular_to_fastq, Cut1, seurat_read10x, datamash_transpose, anndata_inspect, monocle3_create, sceasy_convert, anndata_ops, Filter1, tp_tail_tool, fastq_to_tabular, regexColumn1, tp_cut_tool, dropletutils, join1, dropletutils_read_10x, scanpy_filter_cells UseGalaxy.org (Main) 0 2784 3288 1.266667 0
Single Cell Pre-processing of 10X Single-Cell RNA Datasets https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html Community profiling, Sequence alignment, Validation, Loading, Sequencing quality control 2019-09-11 2025-04-29 13 True False True True dropletutils, multiqc, rna_starsolo UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.fr, UseGalaxy.no 0 13082 16905 1.866667 0
Single Cell Pre-processing of Single-Cell RNA Data https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing/tutorial.html RNA-Seq quantification, Read summarisation, Sequence alignment analysis, Sequence alignment, Validation, Data handling, Sequencing quality control 2019-02-22 2025-04-08 5 True True False True __FLATTEN__, rna_star, multiqc, tp_sed_tool, samtools_stats, collection_column_join, umi_tools_count, featurecounts, bamFilter, umi_tools_extract UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 3450173 8412064 4.400000 0
Single Cell Pseudobulk Analysis with Decoupler and EdgeR https://training.galaxyproject.org//topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html Expression profile clustering, Differential gene expression analysis, Principal component visualisation 2025-02-12 2025-05-09 8 True False True True tp_replace_in_column, anndata_inspect, decoupler_pseudobulk, column_remove_by_header, tp_awk_tool, __EXTRACT_DATASET__, volcanoplot, tp_replace_in_line, anndata_manipulate, edger, scanpy_filter UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 1859 2131 0.650000 0
Single Cell Single-cell quality control with scater https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scater-qc/tutorial.html Read pre-processing, Sequence visualisation, Sequencing quality control 2019-10-23 2025-02-14 6 True False False True scater_plot_dist_scatter, scater_plot_pca, scater_filter, scater_create_qcmetric_ready_sce UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz 0 729 821 0.733333 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, Cut1, gprofiler_gost, goenrichment UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) 0 1341835 2577605 2.433333 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 Expression profile clustering, Statistical calculation, Mapping, Genome indexing, Differential gene expression analysis, Peak calling, Gene regulatory network analysis, Visualisation, Generation, Principal component visualisation, Sequence alignment, Enrichment analysis, Imputation, Read mapping, Sequence composition calculation, Sequencing quality control 2023-04-24 2025-10-16 10 True False False True fastqc, episcanpy_preprocess, anndata_inspect, episcanpy_build_matrix, sinto_fragments, bwa_mem, falco, sinto_barcode, scanpy_plot, macs2_callpeak, tp_sorted_uniq, bedtools_sortbed UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz 0 6199 7287 1.066667 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 3411162 8289472 2.166667 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 0 676 920 3.333333 0
Single Cell Removing the effects of the cell cycle https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html Expression profile clustering, Differential gene expression analysis, Principal component visualisation 2023-01-25 2025-03-11 14 True False False True sort1, anndata_inspect, cat1, scanpy_regress_variable, addValue, table_compute, scanpy_plot, anndata_manipulate, tp_easyjoin_tool, scanpy_cluster_reduce_dimension, scanpy_inspect 0 2198 2589 0.750000 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, hca_matrix_downloader, retrieve_scxa, anndata_ops, scanpy_read_10x, regexColumn1, tp_grep_tool, seurat_read10x 0 617 808 3.600000 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 Expression profile clustering, Genome indexing, Dimensionality reduction, Essential dynamics, Principal component visualisation, Sequence alignment, Read mapping, Differential gene expression analysis, Generation, Gene expression profiling 2024-07-11 2025-07-02 5 True False False True Cut1, anndata_inspect, snapatac2_peaks_and_motif, bwa_mem, replace_column_with_key_value_file, snapatac2_preprocessing, scanpy_plot, anndata_manipulate, snapatac2_clustering, anndata_ops, scanpy_filter, fasta_compute_length, scanpy_normalize, snapatac2_plotting, scanpy_inspect 0 1814 2161 1.016667 0
Single Cell Clustering 3K PBMCs with Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html Expression profile clustering, Differential gene expression analysis, Principal component visualisation 2019-12-19 2025-04-29 16 True True True True datamash_ops, anndata_inspect, anndata_import, scanpy_remove_confounders, scanpy_plot, anndata_manipulate, scanpy_filter, scanpy_normalize, scanpy_cluster_reduce_dimension, scanpy_inspect UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.fr, UseGalaxy.no 0 3451955 8415397 4.166667 0
Single Cell Combining single cell datasets after pre-processing https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html 2022-09-08 2025-11-18 23 True False True True tp_replace_in_column, Cut1, anndata_inspect, anndata_manipulate, anndata_ops, Paste1 UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.org (Main) 0 2622 3670 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 3493 3964 0.950000 0
Single Cell Understanding Barcodes https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-umis/tutorial.html Statistical calculation, Sequence composition calculation, Sequencing quality control 2019-02-20 2025-02-14 11 True False True True fastqc, umi_tools_extract, seq_filter_by_id UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, UseGalaxy.no 0 6587 8201 1.250000 0
Single Cell Downstream Single-cell RNA analysis with RaceID https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-raceid/tutorial.html Molecular dynamics, Expression profile clustering, Expression analysis 2019-03-25 2025-02-14 7 True False False True datamash_ops, raceid_filtnormconf, raceid_inspecttrajectory, raceid_clustering, tp_sed_tool, tp_head_tool, raceid_inspectclusters, raceid_trajectory, datamash_transpose UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.org.au 0 1116 1314 1.216667 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.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 316 461 1.183333 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 3520 4163 1.466667 0
Single Cell Filter, plot and explore single-cell RNA-seq data with Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html Expression profile clustering, Differential gene expression analysis, Principal component visualisation 2021-03-24 2025-04-23 24 True False True True scanpy_run_tsne, scanpy_find_variable_genes, scanpy_filter_genes, retrieve_scxa, anndata_manipulate, join1, scanpy_find_cluster, scanpy_compute_graph, scanpy_scale_data, scanpy_plot_embed, scanpy_normalise_data, scanpy_inspect, anndata_inspect, interactive_tool_cellxgene_vip, scanpy_run_umap, scanpy_find_markers, scanpy_plot, anndata_ops, scanpy_normalize, Cut1, scanpy_run_pca, scanpy_filter, scanpy_cluster_reduce_dimension, scanpy_filter_cells 0 5679 8895 2.733333 0
Single Cell Clustering 3K PBMCs with Seurat https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-seurat-pbmc3k/tutorial.html 2025-01-23 2025-05-09 5 True False True True seurat_create, seurat_data, seurat_preprocessing, Cut1, seurat_reduce_dimension, csv_to_tabular, seurat_clustering, Filter1, seurat_plot MISSISSIPPI, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 1626 1962 1.100000 0
Single Cell Filter, plot, and explore single cell RNA-seq data with Seurat https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html 2024-04-09 2025-03-11 10 True False False True seurat_find_clusters, seurat_run_umap, seurat_read10x, seurat_normalise_data, seurat_run_pca, seurat_find_neighbours, seurat_scale_data, retrieve_scxa, seurat_find_variable_genes, seurat_find_markers, seurat_plot, seurat_filter_cells UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 2265 2737 1.333333 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_run_tsne, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_run_umap, scanpy_find_cluster, scanpy_compute_graph UseGalaxy.be, UseGalaxy.org (Main), UseGalaxy.org.au 0 324 359 0.966667 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 tp_replace_in_column, Cut1, anndata_inspect, anndata_import, anndata_manipulate, unzip, anndata_ops, Paste1, scanpy_filter_cells UseGalaxy.be, UseGalaxy.org.au UseGalaxy.cz 0 503 591 1.483333 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 ggplot2_violin, collapse_dataset, table_compute, Count1, tp_cut_tool, join1, __DUPLICATE_FILE_TO_COLLECTION__, Remove beginning1, tp_sed_tool, tp_awk_tool, music_construct_eset, Paste1, tp_multijoin_tool, collection_column_join, datamash_transpose, bg_column_arrange_by_header, Cut1, music_deconvolution, Add_a_column1, tp_easyjoin_tool, ggplot2_point, annotatemyids UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 133 156 0.766667 0
Single Cell Multi-sample batch correction with Harmony and SnapATAC2 https://training.galaxyproject.org//topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html Essential dynamics, Dimensionality reduction, Gene expression profiling 2025-02-28 2025-07-02 2 True False False True __FILTER_FROM_FILE__, anndata_inspect, collection_element_identifiers, snapatac2_peaks_and_motif, __EXTRACT_DATASET__, snapatac2_preprocessing, Show beginning1, anndata_manipulate, snapatac2_clustering, fasta_compute_length, snapatac2_plotting UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 580 643 0.833333 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 3443591 8403519 2.166667 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 4755 5592 1.233333 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_diffmap, scanpy_plot_embed, scanpy_run_paga, scanpy_plot_trajectory, scanpy_run_dpt, anndata_manipulate, scanpy_run_fdg, scanpy_find_cluster, scanpy_compute_graph UseGalaxy.be, UseGalaxy.org (Main), UseGalaxy.org.au 0 1385 1740 2.150000 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 Cut1, sort1, anndata_inspect, table_compute, tp_sed_tool, tp_awk_tool, retrieve_scxa, annotatemyids, scanpy_read_10x, music_construct_eset, add_line_to_file, tp_easyjoin_tool, regex1, tp_cut_tool, join1, music_manipulate_eset, datamash_transpose UseGalaxy.cz 0 766 1270 2.066667 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 1411748 2748291 1.650000 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 6757 7650 0.783333 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_learnGraph, Cut1, monocle3_diffExp, monocle3_plotCells, anndata_inspect, monocle3_reduceDim, monocle3_create, Filter1, regexColumn1, monocle3_preprocess, tp_cut_tool, monocle3_partition, monocle3_topmarkers, join1, monocle3_orderCells, datamash_transpose UseGalaxy.eu, UseGalaxy.org (Main) 0 4067 5037 1.466667 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, table_compute, tp_sed_tool, column_remove_by_header, tp_awk_tool, annotatemyids, music_construct_eset, tp_cut_tool, tp_easyjoin_tool, regex1, music_manipulate_eset UseGalaxy.cz 0 768 1187 1.733333 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 2488343 5317204 1.966667 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 1887239 3869196 1.850000 0
Statistics and machine learning Machine learning: classification and regression https://training.galaxyproject.org//topics/statistics/tutorials/classification_regression/tutorial.html 2019-03-07 2025-04-08 13 True False False True sklearn_ensemble, plotly_regression_performance_plots, sklearn_svm_classifier, plotly_ml_performance_plots UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 5773 10325 0.816667 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 (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 8596 14177 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 model_prediction, keras_train_and_eval, keras_model_config, ml_visualization_ex, keras_model_builder, sklearn_to_categorical UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 3301862 7872067 3.050000 0
Statistics and machine learning Basics of machine learning https://training.galaxyproject.org//topics/statistics/tutorials/machinelearning/tutorial.html 2018-11-05 2025-05-13 15 True True True True sklearn_svm_classifier UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.fr, UseGalaxy.no 0 3446452 8407360 5.183333 0
Statistics and machine learning Prepare Data from CbioPortal for Flexynesis Integration https://training.galaxyproject.org//topics/statistics/tutorials/flexynesis_cbio_import/tutorial.html 2025-08-10 2025-08-13 2 True False False True table_compute, __EXTRACT_DATASET__, tp_sort_header_tool, flexynesis_cbioportal_import, flexynesis_utils, tp_cut_tool UseGalaxy.eu UseGalaxy.be 0 72 77 0.733333 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 0 254 319 1.916667 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_pathway_count_heatmaps, pancancer_visualize_decisions, pancancer_targene_pharmacology, pancancer_targene_summary_figures, pancancer_alternative_genes_pathwaymapper, pancancer_map_mutation_class, pancancer_compare_within_models, pancancer_external_sample_status_prediction, pancancer_apply_weights, pancancer_classifier, pancancer_targene_cell_line_predictions, pancancer_within_disease_analysis 0 825 1273 2.950000 0
Statistics and machine learning Text-mining with the SimText toolset https://training.galaxyproject.org//topics/statistics/tutorials/text-mining_simtext/tutorial.html 2021-04-05 2025-05-07 8 True False False True pmids_to_pubtator_matrix, pubmed_by_queries, interactive_tool_simtext_app UseGalaxy.eu 0 543 740 2.533333 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 plotly_regression_performance_plots, sklearn_searchcv, plotly_parallel_coordinates_plot, sklearn_ensemble, sklearn_build_pipeline UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 13308 21419 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 2026-01-16 4 True False False True tabpfn, table_compute, pick_value, __EXTRACT_DATASET__, flexynesis, tp_sort_header_tool, Show beginning1, flexynesis_plot, tp_easyjoin_tool, tp_cut_tool, join1, datamash_transpose UseGalaxy.eu 0 112 155 2.400000 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_searchcv, Remove beginning1, sklearn_build_pipeline, sklearn_ensemble, plotly_regression_performance_plots, sklearn_generalized_linear UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 3446935 8407763 3.450000 0
Statistics and machine learning Galaxy Tabular Learner - Building a Model using Chowell clinical data https://training.galaxyproject.org//topics/statistics/tutorials/loris_model/tutorial.html 2024-12-13 2026-01-10 3 True True True True tabular_learner, PyCaret_Model_Comparison 0 1197954 2207882 3.183333 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 model_prediction, keras_train_and_eval, keras_model_config, plotly_regression_performance_plots, keras_model_builder UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 3306483 7861216 2.900000 0
Statistics and machine learning Image classification in Galaxy with fruit 360 dataset https://training.galaxyproject.org//topics/statistics/tutorials/fruit_360/tutorial.html 2021-12-01 2024-07-09 8 True True True True model_prediction, keras_train_and_eval, keras_model_config, tp_cut_tool, ml_visualization_ex, keras_model_builder, sklearn_to_categorical UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 2962423 6774794 2.750000 0
Statistics and machine learning Introduction to deep learning https://training.galaxyproject.org//topics/statistics/tutorials/intro_deep_learning/tutorial.html 2020-03-26 2025-04-08 9 True False False True model_prediction, keras_train_and_eval, keras_model_config, ml_visualization_ex, keras_model_builder UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 2539 3230 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 tp_replace_in_column, datamash_ops, Add_a_column1, __EXTRACT_DATASET__, flexynesis, flexynesis_plot UseGalaxy.be, UseGalaxy.eu 0 90 104 0.433333 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_searchcv, Remove beginning1, plotly_ml_performance_plots, sklearn_ensemble, sklearn_build_pipeline, sklearn_generalized_linear, sklearn_svm_classifier, sklearn_nn_classifier UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 3446493 8407729 4.316667 0
Statistics and machine learning GLEAM Image Learner - Validating Skin Lesion Classification on HAM10000 https://training.galaxyproject.org//topics/statistics/tutorials/image_learner/tutorial.html 2026-01-28 2026-01-28 1 True True False True image_learner UseGalaxy.org (Main) 0 164998 186828 1.616667 0
Statistics and machine learning Deep Learning (Part 2) - Recurrent neural networks (RNN) https://training.galaxyproject.org//topics/statistics/tutorials/RNN/tutorial.html 2021-02-23 2025-05-10 15 True True True True model_prediction, keras_train_and_eval, keras_model_config, ml_visualization_ex, keras_model_builder UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 3376783 8153321 2.950000 0
Statistics and machine learning Unsupervised Analysis of Bone Marrow Cells with Flexynesis https://training.galaxyproject.org//topics/statistics/tutorials/flexynesis_unsupervised/tutorial.html 2025-08-10 2025-08-13 2 True False False True flexynesis, flexynesis_plot, flexynesis_utils, __EXTRACT_DATASET__ UseGalaxy.be, UseGalaxy.eu 0 55 61 1.983333 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 1256 1580 1.466667 0
Statistics and machine learning Interval-Wise Testing for omics data https://training.galaxyproject.org//topics/statistics/tutorials/iwtomics/tutorial.html Peak calling, Comparison, Genome annotation, Differential gene expression analysis, Differentially-methylated region identification 2018-06-14 2023-11-09 17 True False False True iwtomics_testandplot, iwtomics_loadandplot, iwtomics_plotwithscale UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 384 506 2.700000 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 1470378 2890345 2.666667 0
Statistics and machine learning Supervised Learning with Hyperdimensional Computing https://training.galaxyproject.org//topics/statistics/tutorials/hyperdimensional_computing/tutorial.html 2023-04-28 2023-11-09 2 True False False False chopin2 UseGalaxy.org (Main) 0 460 567 0.750000 0
Statistics and machine learning Introduction to Machine Learning using R https://training.galaxyproject.org//topics/statistics/tutorials/intro-to-ml-with-r/tutorial.html 2021-05-21 2024-10-15 15 True False True False interactive_tool_rstudio UseGalaxy.eu, UseGalaxy.org.au 0 4429 6817 1.366667 0
Synthetic Biology Evaluating and ranking a set of pathways based on multiple metrics https://training.galaxyproject.org//topics/synthetic-biology/tutorials/pathway_analysis/tutorial.html 2022-09-26 2024-06-14 7 True False True True rpscore, rpranker, rpthermo, rpfba UseGalaxy.be 0 673 988 2.833333 0
Synthetic Biology Designing plasmids encoding predicted pathways by using the BASIC assembly method https://training.galaxyproject.org//topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.html 2022-05-12 2024-06-14 8 True False True True dnabot, rpbasicdesign, selenzy-wrapper UseGalaxy.be UseGalaxy.fr 0 1082 1655 2.516667 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 rpcompletion, rp2paths, retropath2, get_sbml_model, rpextractsink, rrparser UseGalaxy.be 0 618 886 2.333333 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 2498966 5344244 1.966667 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 3443591 8403528 2.166667 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 0 316 552 2.033333 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 28 28 0.066667 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 0 172 188 2.233333 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 32 34 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 0 290 318 1.016667 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 16 16 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 0 261 454 5.033333 0
Teaching and Hosting Galaxy training Running a workshop as an instructor https://training.galaxyproject.org//topics/teaching/tutorials/running-workshop/tutorial.html 2018-11-15 2025-12-18 7 True False False False 0 194 325 0.866667 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 0 356 407 3.633333 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 0 170 196 0.833333 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 98 102 0.250000 0
Transcriptomics RNA-RNA interactome data analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-interactome/tutorial.html Read pre-processing, Statistical calculation, Sequence trimming, Primer removal, Sequence composition calculation, Sequencing quality control 2020-03-23 2023-11-09 12 True False False True fastqc, chira_merge, chira_quantify, chira_map, chira_extract, chira_collapse, cutadapt, query_tabular UseGalaxy.be, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 1531 2290 2.716667 0
Transcriptomics CLIP-Seq data analysis from pre-processing to motif detection https://training.galaxyproject.org//topics/transcriptomics/tutorials/clipseq/tutorial.html Statistical calculation, Mapping, Primer removal, Read pre-processing, Sequence alignment, Sequence trimming, Sequence composition calculation, Sequencing quality control 2018-08-17 2023-11-09 23 True False False True rna_star, deeptools_plot_fingerprint, meme_chip, fastqc, __SORTLIST__, peakachu, tp_awk_tool, rcas, cutadapt, sort1, bedtools_slopbed, Extract genomic DNA 1, bctools_extract_alignment_ends, bedtools_genomecoveragebed_bedgraph, __MERGE_COLLECTION__, wig_to_bigWig, deeptools_multi_bam_summary, umi_tools_dedup, umi_tools_extract, deeptools_plot_correlation 0 8552 16607 1.833333 0
Transcriptomics Genome-wide alternative splicing analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html Formatting, Transcriptome assembly, Protein sequence analysis, Statistical calculation, Sequence comparison, Data handling, Sequence analysis, RNA-Seq analysis, Visualisation, De-novo assembly, Validation, Sequence alignment, Sequence contamination filtering, Sequence annotation, Sequence composition calculation, Sequencing quality control, Sequence assembly validation 2023-05-17 2025-12-17 12 True True False True rseqc_geneBody_coverage, rna_star, rseqc_junction_annotation, tp_grep_tool, tp_cat, fastqc, fastp, gtftobed12, multiqc, Remove beginning1, addValue, tp_awk_tool, Filter1, cpat, gffread, sort1, collection_element_identifiers, rseqc_infer_experiment, stringtie, regex1, pygenomeTracks, __FLATTEN__, __FILTER_FROM_FILE__, stringtie_merge, Cut1, rseqc_junction_saturation, cat1, Add_a_column1, tp_uniq_tool, rna_quast, rseqc_inner_distance, gffcompare, gene2exon1, rseqc_read_distribution, isoformswitchanalyzer, pfamscan UseGalaxy.cz, UseGalaxy.fr 0 2091695 4310117 3.700000 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 egsea, goseq, Cut1, Add_a_column1, tp_sort_header_tool, tp_cut_tool, fgsea, join1 UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 27180 43319 1.966667 0
Transcriptomics De novo transcriptome assembly, annotation, and differential expression analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/full-de-novo/tutorial.html Transcriptome assembly, Statistical calculation, Gene functional annotation, De-novo assembly, de Novo sequencing, Validation, Coding region prediction, Sequence composition calculation, Sequencing quality control 2020-02-13 2023-11-09 8 True False False True fastqc, trinity_filter_low_expr_transcripts, describe_samples, trinotate, multiqc, trinity_run_de_analysis, trinity_samples_qccheck, trinity_contig_exn50_statistic, trinity_abundance_estimates_to_matrix, trinity_analyze_diff_expr, trinity_define_clusters_by_cutting_tree, transdecoder, trimmomatic, trinity, trinity_align_and_estimate_abundance UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no 0 15031 26948 2.416667 0
Transcriptomics Visualization of RNA-Seq results with heatmap2 https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html 2018-12-31 2025-11-24 14 True False False True ggplot2_heatmap2, Cut1, cat1, tp_sort_header_tool, Show beginning1, Filter1, Show tail1, join1, datamash_transpose GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 78773 129053 1.350000 0
Transcriptomics RNA-Seq data analysis, clustering and visualisation tutorial https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html 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, goseq, ggplot2_heatmap2, Cut1, deg_annotate, cat1, Add_a_column1, table_compute, volcanoplot, tp_sort_header_tool, Show beginning1, Filter1, deseq2, tp_easyjoin_tool, Multivariate, Grouping1 UseGalaxy.eu, UseGalaxy.fr UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 1654 2054 1.183333 0
Transcriptomics 1: RNA-Seq reads to counts https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html Formatting, Read summarisation, Statistical calculation, Data handling, Primer removal, Read pre-processing, RNA-Seq quantification, Sequence alignment, Validation, Sequence trimming, Sequence composition calculation, Sequencing quality control 2018-09-23 2024-08-09 33 True False False True fastqc, rseqc_geneBody_coverage, multiqc, collection_column_join, picard_MarkDuplicates, hisat2, rseqc_infer_experiment, cutadapt, rseqc_read_distribution, featurecounts, samtools_idxstats UseGalaxy.eu MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 80956 145983 2.616667 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 tp_sort_header_tool, samtools_sort, blockclust, blockbuster UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 1059 1432 2.833333 0
Transcriptomics Differential abundance testing of small RNAs https://training.galaxyproject.org//topics/transcriptomics/tutorials/srna/tutorial.html Statistical calculation, Differential gene expression analysis, RNA-Seq analysis, Primer removal, Read pre-processing, RNA-Seq quantification, Sequence alignment, Sequence trimming, Sequence composition calculation, Gene expression analysis, Sequencing quality control 2017-06-29 2023-11-09 26 True False False True fastqc, fastq_manipulation, salmon, bedtools_bamtofastq, hisat2, Filter1, deseq2, trim_galore, samtool_filter2 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 7133 12384 2.066667 0
Transcriptomics Network analysis with Heinz https://training.galaxyproject.org//topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html Differential gene expression analysis, RNA-Seq analysis, Pathway or network analysis 2018-10-11 2024-01-15 16 True True False True Cut1, heinz_bum, heinz_scoring, deseq2, heinz_visualization, heinz UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 3445671 8406751 5.366667 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 limma_voom, mergeCols1, tp_replace_in_line, tp_cut_tool, annotatemyids UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au 0 45499 76317 2.283333 0
Transcriptomics GO Enrichment Analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/goenrichment/tutorial.html Gene-set enrichment analysis 2019-01-23 2024-03-05 12 True False False True goslimmer, Filter1, goenrichment Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 23556 38026 1.333333 0
Transcriptomics Visualization of RNA-Seq results with Volcano Plot https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.html 2018-12-31 2025-04-17 16 True False True True volcanoplot UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 156756 255279 1.316667 0
Transcriptomics Introduction to Transcriptomics https://training.galaxyproject.org//topics/transcriptomics/tutorials/introduction/slides.html 2016-10-05 2025-04-08 3 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3443591 8403537 2.166667 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 3446216 8407466 3.900000 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 3444648 8404877 5.433333 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 4333 5552 1.950000 0
Transcriptomics Reference-based RNAseq data analysis (long) https://training.galaxyproject.org//topics/transcriptomics/tutorials/rb-rnaseq/tutorial.html 2017-02-22 2023-02-17 12 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 22319 34845 2.166667 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 11351 13881 1.433333 0
Transcriptomics Visualization of RNA-Seq results with Volcano Plot in R https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot-r/tutorial.html 2021-06-14 2024-06-14 8 True False True False interactive_tool_rstudio, volcanoplot UseGalaxy.eu, UseGalaxy.org.au 0 31204 42554 1.683333 0
Transcriptomics Reference-based RNA-Seq data analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/ref-based/tutorial.html Pathway or network analysis, Pathway visualisation, Sequence alignment, Sequence trimming, Read mapping, Formatting, Pathway or network visualisation, Read summarisation, Genome visualisation, Structure visualisation, Data handling, RNA-Seq analysis, Primer removal, Exonic splicing enhancer prediction, Gene functional annotation, Read pre-processing, RNA-Seq quantification, Visualisation, Validation, Enrichment analysis, Differential gene expression analysis, Sequencing quality control 2016-10-05 2025-12-11 107 True False True True rseqc_geneBody_coverage, ggplot2_heatmap2, rna_star, table_compute, tp_grep_tool, dexseq_count, join1, tp_cat, length_and_gc_content, deg_annotate, gtftobed12, multiqc, Remove beginning1, pathview, picard_MarkDuplicates, __EXTRACT_DATASET__, Filter1, cutadapt, dexseq, featurecounts, jbrowse2, collection_element_identifiers, falco, tp_sort_header_tool, rseqc_infer_experiment, __TAG_FROM_FILE__, pygenomeTracks, __FILTER_FROM_FILE__, __FLATTEN__, goseq, Cut1, __MERGE_COLLECTION__, ChangeCase, cat1, Add_a_column1, tp_replace_in_line, deseq2, rseqc_read_distribution, samtools_view, samtools_idxstats, Grouping1 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.org.au 0 195050 361558 2.750000 0
Transcriptomics Pathway analysis with the MINERVA Platform https://training.galaxyproject.org//topics/transcriptomics/tutorials/minerva-pathways/tutorial.html Annotation, Read summarisation, Statistical calculation, Data handling, Primer removal, RNA-Seq analysis, Read pre-processing, RNA-Seq quantification, Gene functional annotation, Sequence alignment, Validation, Sequence trimming, Sequence composition calculation, Sequencing quality control 2024-03-28 2024-07-26 3 True False False True rseqc_geneBody_coverage, Grep1, join1, fastqc, multiqc, __EXTRACT_DATASET__, cutadapt, featurecounts, limma_voom, collection_column_join, tp_sort_header_tool, goseq, Cut1, fasterq_dump, Add_a_column1, hisat2, tp_replace_in_line, rseqc_read_distribution, annotatemyids, tp_sorted_uniq UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 697 819 1.516667 0
Transcriptomics De novo transcriptome reconstruction with RNA-Seq https://training.galaxyproject.org//topics/transcriptomics/tutorials/de-novo/tutorial.html Read summarisation, Transcriptome assembly, Statistical calculation, Differential gene expression analysis, RNA-Seq analysis, RNA-Seq quantification, Sequence alignment, Sequence annotation, Sequence composition calculation, Sequencing quality control 2017-02-19 2024-06-14 36 True False True True fastqc, stringtie_merge, hisat2, gffcompare, Filter1, stringtie, deseq2, trimmomatic, featurecounts, deeptools_bam_coverage Galaxy@AuBi, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 17196 29381 2.633333 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 3443591 8403541 2.166667 0
Variant Analysis Calling very rare variants https://training.galaxyproject.org//topics/variant-analysis/tutorials/dunovo/tutorial.html Statistical calculation, Sequencing quality control, Genome indexing, Sequence alignment, Read mapping, Variant calling, Sequence composition calculation, Generation 2017-02-22 2024-12-09 21 True False False True fastqc, naive_variant_caller, allele_counts_1, dunovo, make_families, bwa_mem, Filter1, correct_barcodes, sequence_content_trimmer, align_families, bamleftalign UseGalaxy.org (Main) 0 2260 3395 1.616667 0
Variant Analysis Mapping and molecular identification of phenotype-causing mutations https://training.galaxyproject.org//topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html 2018-03-07 2023-11-09 16 True False False True snpEff, tp_find_and_replace, mimodd_map, mimodd_varextract, mimodd_vcf_filter, mimodd_varreport, mimodd_varcall, snpEff_download UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 4548 6622 2.616667 0
Variant Analysis Trio Analysis using Synthetic Datasets from RD-Connect GPAP https://training.galaxyproject.org//topics/variant-analysis/tutorials/trio-analysis/tutorial.html Sequence analysis, Genetic variation analysis 2022-05-19 2024-09-17 13 True False True True snpEff, gemini_inheritance, gemini_load, gene_iobio_display_generation_iframe, CONVERTER_uncompressed_to_gz, Filter1, regexColumn1, tp_grep_tool, bcftools_merge, bcftools_norm, CONVERTER_gz_to_uncompressed, pyega3 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org.au 0 2090 3631 3.383333 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 Sequence alignment analysis, Statistical calculation, Sequencing quality control, Data handling, Genome indexing, Visualisation, Sequence alignment, Validation, Variant calling, Read mapping, Sequence composition calculation, Generation 2019-03-13 2025-03-20 16 True False False True fastqc, bg_column_arrange_by_header, gemini_annotate, snpEff, multiqc, gemini_load, bwa_mem, samtools_rmdup, falco, varscan_somatic, samtools_calmd, trimmomatic, tp_easyjoin_tool, bamFilter, gemini_query, bamleftalign UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 15091 26900 2.500000 0
Variant Analysis Calling variants in diploid systems https://training.galaxyproject.org//topics/variant-analysis/tutorials/dip/tutorial.html Sequence analysis, Variant calling, Statistical calculation, Genetic variation analysis 2017-02-20 2025-04-28 17 True False False True freebayes, snpEff, gemini_db_info, gemini_load, vcfallelicprimitives, gemini_query UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.no, UseGalaxy.org.au 0 16453 27990 3.316667 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 Genome alignment, Statistical calculation, Sequencing quality control, Genome indexing, Copy number estimation, Visualisation, Sequence alignment, Validation, Sequence visualisation, Variant calling, Read mapping, Sequence composition calculation, Generation 2022-10-05 2025-03-20 14 True False False True fastqc, __RELABEL_FROM_FILE__, multiqc, __EXTRACT_DATASET__, bwa_mem, samtools_rmdup, tp_replace_in_line, __BUILD_LIST__, samtools_calmd, tp_text_file_with_recurring_lines, control_freec, falco, trimmomatic, samtools_view, circos, Grep1, bamleftalign UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 1969 2503 2.000000 0
Variant Analysis Calling variants in non-diploid systems https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Formatting, Sequence alignment analysis, Statistical calculation, Data handling, Genome indexing, Generation, Sequence alignment, Read mapping, Variant calling, Sequence composition calculation, Sequencing quality control 2017-02-16 2024-03-15 23 True False False True fastqc, freebayes, Cut1, picard_MarkDuplicates, bwa_mem, vcffilter2, picard_MergeSamFiles, bamFilter, vcf2tsv, bamleftalign UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 9453 16432 2.000000 0
Variant Analysis Exome sequencing data analysis for diagnosing a genetic disease https://training.galaxyproject.org//topics/variant-analysis/tutorials/exome-seq/tutorial.html Statistical calculation, Genetic variation analysis, Sequence analysis, Genome indexing, Generation, Sequence alignment, Validation, Variant calling, Read mapping, Sequence composition calculation, Sequencing quality control 2016-08-19 2025-05-11 29 True False True True fastqc, freebayes, snpEff, multiqc, gemini_inheritance, gemini_load, bwa_mem, samtools_rmdup, trimmomatic, samtools_view, bcftools_norm, snpEff_download UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au 0 37390 67016 2.733333 0
Variant Analysis Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates https://training.galaxyproject.org//topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html Data handling, Genome indexing, Primer removal, Visualisation, Read pre-processing, Sequence alignment, Read mapping, Sequence trimming, Generation 2025-02-24 2025-02-24 1 True False False True tp_replace_in_column, collapse_dataset, fastq_dump, tp_awk_tool, bwa_mem, tp_replace_in_line, Filter1, bcftools_mpileup, ggplot2_point, ncbi_acc_download, trim_galore, vcf2tsv, bcftools_call UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 366 466 0.816667 0
Variant Analysis Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs) https://training.galaxyproject.org//topics/variant-analysis/tutorials/beacon_cnv_query/tutorial.html Genetic variation analysis, Service discovery, Database search 2024-08-06 2024-09-27 3 True False False False beacon2_cnv UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 220 257 1.833333 0
Variant Analysis Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons https://training.galaxyproject.org//topics/variant-analysis/tutorials/beaconise_1000hg/tutorial.html Service discovery, Genetic variation analysis, Database search 2024-08-06 2026-01-12 4 True False False False cnv_phenopacket, beacon2_import, cnv_vcf2json, beacon2_cnv UseGalaxy.eu 0 365 405 0.566667 0
Visualisation Visualisation with Circos https://training.galaxyproject.org//topics/visualisation/tutorials/circos/tutorial.html Sequence visualisation 2020-01-10 2024-10-15 22 True True True True Cut1, Remove beginning1, upload1, Grep1, random_lines1, circos Galaxy@AuBi, Galaxy@Pasteur, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.no 0 3474515 8452627 3.800000 0
Visualisation Ploting a Microbial Genome with Circos https://training.galaxyproject.org//topics/visualisation/tutorials/circos-microbial/tutorial.html Sequence visualisation 2023-11-08 2024-09-17 3 True False False True circos_interval_to_tile, circos_wiggle_to_scatter, Cut1, circos_interval_to_text, circos_gc_skew, gff2bed1, deeptools_bam_coverage, circos UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr Galaxy@AuBi, MISSISSIPPI, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 1557 1954 1.916667 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 1803049 3685241 1.833333 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 3443591 8403543 2.166667 0