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 3084956 7914236 2.333333 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 3086767 7916817 5.716667 0
Galaxy Server administration Galaxy Installation with Ansible https://training.galaxyproject.org//topics/admin/tutorials/ansible-galaxy/tutorial.html Database management, Informatics, Data management 2019-01-28 2025-11-28 108 True True True False 0 3110582 7961837 4.066667 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 3089053 7921280 5.583333 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 3085859 7915645 5.083333 0
Galaxy Server administration Reference Data with CVMFS https://training.galaxyproject.org//topics/admin/tutorials/cvmfs/tutorial.html 2019-01-27 2025-11-24 54 True True True False 0 3087128 7917438 5.466667 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 3087856 7919596 3.200000 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 3084956 7914238 2.333333 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 3086319 7916370 3.900000 0
Galaxy Server administration Galaxy Interactive Tools https://training.galaxyproject.org//topics/admin/tutorials/interactive-tools/tutorial.html 2020-02-27 2025-11-27 28 True True True False 0 3087292 7917741 4.966667 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 3084956 7914239 2.333333 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 3068798 7851151 4.350000 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 3085556 7915036 10.933333 0
Galaxy Server administration Running Jobs on Remote Resources with Pulsar https://training.galaxyproject.org//topics/admin/tutorials/pulsar/tutorial.html 2019-01-28 2025-11-25 58 True True True False 0 3087538 7918475 5.183333 0
Galaxy Server administration Ansible https://training.galaxyproject.org//topics/admin/tutorials/ansible/tutorial.html 2018-07-11 2024-08-08 48 True True True False 0 3091440 7925802 4.016667 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 3084956 7914239 2.333333 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 3084956 7914239 2.333333 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 3084956 7914239 2.333333 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 3084956 7914239 2.333333 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 3085667 7915352 3.116667 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 3084956 7914239 2.333333 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 3084956 7914239 2.333333 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 3084956 7914239 2.333333 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 1077991 2318324 1.950000 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 3084956 7914239 2.333333 0
Galaxy Server administration Reference Data with Data Managers https://training.galaxyproject.org//topics/admin/tutorials/reference-genomes/tutorial.html Genome indexing, Read mapping, Sequence alignment, Generation 2019-01-28 2023-04-21 7 True True False False bwa_mem_index_builder_data_manager, data_manager_fetch_genome_all_fasta_dbkey, bwa 0 3085540 7914998 6.516667 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 3084956 7914239 2.333333 0
Galaxy Server administration Setting up Celery Workers for Galaxy https://training.galaxyproject.org//topics/admin/tutorials/celery/tutorial.html 2022-07-16 2025-11-24 19 True True False False 0 2229773 5093745 3.716667 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 3084956 7914239 2.333333 0
Galaxy Server administration Deploying a Beacon v1 in Galaxy https://training.galaxyproject.org//topics/admin/tutorials/beacon/tutorial.html 2023-04-16 2025-11-22 7 True False False False 0 153 171 1.900000 0
Galaxy Server administration Configuring the Onedata connectors (remotes, Object Store, BYOS, BYOD) https://training.galaxyproject.org//topics/admin/tutorials/onedata-configuration/tutorial.html 2025-03-24 2025-04-08 2 True False False False 0 53 58 3.233333 0
Galaxy Server administration Enable upload via FTP https://training.galaxyproject.org//topics/admin/tutorials/ftp/tutorial.html 2021-06-18 2025-11-24 28 True False False False 0 1255 1716 1.616667 0
Galaxy Server administration Upgrading Galaxy https://training.galaxyproject.org//topics/admin/tutorials/upgrading/tutorial.html 2021-06-08 2024-11-25 10 True False True False 0 727 1107 2.883333 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 46 52 2.566667 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 0 885 1291 5.450000 0
Galaxy Server administration Monitoring Galaxy and Pulsar with Sentry https://training.galaxyproject.org//topics/admin/tutorials/sentry/tutorial.html 2023-04-19 2025-11-25 12 True False False False 0 231 279 1.416667 0
Galaxy Server administration Galaxy Monitoring with Reports https://training.galaxyproject.org//topics/admin/tutorials/reports/tutorial.html 2019-01-31 2025-11-24 47 True False False False 0 506 673 2.700000 0
Galaxy Server administration How I learned to stop worrying and love the systemd https://training.galaxyproject.org//topics/admin/tutorials/stop-worrying-love-systemd/tutorial.html 2022-07-06 2023-09-28 3 True False False False 0 689 792 0.616667 0
Galaxy Server administration Training Infrastructure as a Service (TIaaS) https://training.galaxyproject.org//topics/admin/tutorials/tiaas/tutorial.html 2020-02-12 2025-11-24 45 True False True False 0 557 742 3.183333 0
Galaxy Server administration Mapping Jobs to Destinations using TPV https://training.galaxyproject.org//topics/admin/tutorials/job-destinations/tutorial.html 2021-01-17 2025-11-24 43 True False True False 0 1705 2661 3.350000 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 0 205 244 2.033333 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 0 601 733 4.333333 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 67 73 2.583333 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 1098 1396 2.600000 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 3046 4973 1.066667 0
Galaxy Server administration Adding file-sources to Galaxy https://training.galaxyproject.org//topics/admin/tutorials/file_sources/tutorial.html 2025-01-20 2025-01-20 1 True False False False 0 59 77 2.666667 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 8325 16474 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 2023-11-23 9 True False False False 0 406 543 2.383333 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 1620 2671 2.266667 0
Galaxy Server administration Managing Galaxy on Kubernetes https://training.galaxyproject.org//topics/admin/tutorials/k8s-managing-galaxy/tutorial.html 2019-07-02 2024-12-19 7 True False False False 0 677 987 2.100000 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 80 99 1.633333 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 78 86 0.466667 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 1110 1264 0.333333 0
Galaxy Server administration Deploying Tailscale/Headscale for private mesh networking https://training.galaxyproject.org//topics/admin/tutorials/wireguard-headscale/tutorial.html Data security, Software engineering 2022-09-21 2024-12-19 4 True False False False 0 2379 3062 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 3101014 7944424 3.283333 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 1723771 3806092 2.116667 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 1738054 3838468 2.116667 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 1785004 3941864 2.116667 0
Assembly An Introduction to Genome Assembly https://training.galaxyproject.org//topics/assembly/tutorials/general-introduction/tutorial.html Visualisation, Sequence composition calculation, De-novo assembly, Formatting, Sequencing quality control, Sequence assembly validation, Statistical calculation, Validation 2017-05-23 2024-09-12 29 True True True True velvetg, quast, multiqc, fastqc, velveth, fastq_paired_end_interlacer Galaxy@AuBi, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 3120934 7973108 5.183333 0
Assembly Genome Assembly Quality Control https://training.galaxyproject.org//topics/assembly/tutorials/assembly-quality-control/tutorial.html Biodiversity, Sequence assembly, Data quality management Phasing, Visualisation, Sequence assembly validation, Scaffolding, Genome assembly, k-mer counting, De-novo assembly 2022-08-26 2025-06-04 6 True True False True busco, quast, meryl, merqury, chromeister UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au UseGalaxy.cz 0 2184411 4960582 4.383333 0
Assembly Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial resistance Sequence contamination filtering, Filtering, Mapping assembly, Visualisation, Scatter plot plotting, Genome assembly, Read mapping, Cross-assembly, Sequence composition calculation, De-novo assembly, Sequencing quality control, Sequence assembly validation, Sequence alignment, Box-Whisker plot plotting, Sequence assembly visualisation, Statistical calculation, Sequencing error detection 2021-03-24 2024-11-29 15 True False False True upload1, flye, filtlong, quast, nanoplot, bandage_image, polypolish, porechop, fastqc, CONVERTER_bz2_to_uncompressed, fastp, bwa_mem2 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr 0 10547 15790 3.400000 0
Assembly Large genome assembly and polishing https://training.galaxyproject.org//topics/assembly/tutorials/largegenome/tutorial.html Genomics, Sequence assembly, Biodiversity Base-calling, Mapping assembly, Genome assembly, Cross-assembly, De-novo assembly, Sequence assembly validation, Sequence assembly, Box-Whisker plot plotting, Sequence assembly visualisation, Variant calling, Pairwise sequence alignment, Sequence contamination filtering, Visualisation, Scatter plot plotting, Sequence composition calculation, Sequencing quality control, Statistical calculation, Validation 2023-03-06 2025-06-04 14 True False True True minimap2, flye, busco, barchart_gnuplot, fasta-stats, genomescope, quast, medaka_consensus_pipeline, nanoplot, bandage_image, meryl, multiqc, fastqc, fastp, racon UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 7524 9755 1.983333 0
Assembly Hybrid genome assembly - Nanopore and Illumina https://training.galaxyproject.org//topics/assembly/tutorials/hybrid_denovo_assembly/tutorial.html Read mapping, Mapping assembly, Visualisation, Generation, Genome assembly, Read alignment, Cross-assembly, De-novo assembly, Genome indexing, Sequencing quality control, Sequence assembly validation, Sequence alignment, Analysis, Aggregation, Sequence assembly, Validation 2025-11-03 2025-11-06 2 True False False True flye, busco, quast, bwa_mem, multiqc, pilon, unicycler UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.be, UseGalaxy.no 0 182 234 2.066667 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, Data deposition, Visualisation, Genome assembly, Pairwise sequence alignment, De-novo assembly, Sequence trimming, Phasing, Sequence assembly validation, Scaffolding, k-mer counting, Data parsing, Sequence alignment, Sequence assembly visualisation, Genotyping, Data handling 2023-06-23 2025-06-04 8 True False True True busco, samtools_stats, merqury, collapse_dataset, interactive_tool_blobtoolkit, smudgeplot, gfastats, CONVERTER_gz_to_uncompressed, minimap2, blobtoolkit, bellerophon, tp_find_and_replace, meryl, bwa_mem2, pretext_map, genomescope, __EXTRACT_DATASET__, bandage_image, bg_diamond, pretext_snapshot UseGalaxy.eu UseGalaxy.org (Main), UseGalaxy.org.au 0 2009 2606 2.050000 0
Assembly Chloroplast genome assembly https://training.galaxyproject.org//topics/assembly/tutorials/chloroplast-assembly/tutorial.html Read mapping, Mapping assembly, Generation, Genome assembly, Cross-assembly, De-novo assembly, Genome indexing, Sequence alignment, Sequence assembly, Box-Whisker plot plotting, Sequence assembly visualisation, Scatter plot plotting, Read alignment, Gene prediction, Genome visualisation, Genome annotation, Analysis, Coding region prediction 2020-12-04 2025-05-15 21 True False True True upload1, flye, fasta-stats, bwa_mem, jbrowse, bandage_image, nanoplot, pilon, prokka, bandage_info UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 8113 12618 2.800000 0
Assembly Assembly of the mitochondrial genome from PacBio HiFi reads https://training.galaxyproject.org//topics/assembly/tutorials/mitochondrion-assembly/tutorial.html Genomics, Sequence assembly, Biodiversity, Mitochondria 2024-09-03 2025-06-04 4 True False True True mitohifi, compress_file UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 906 1098 1.833333 0
Assembly Decontamination of a genome assembly https://training.galaxyproject.org//topics/assembly/tutorials/assembly-decontamination/tutorial.html Genomics, Sequence assembly, Biodiversity Data handling, Taxonomic classification 2024-09-04 2025-06-04 5 True False True True tp_cat, kraken2, ncbi_blastn_wrapper, Cut1, ncbi_dustmasker_wrapper, parse_mito_blast, tp_sed_tool, gfastats, Filter1 UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 1693 2093 2.433333 0
Assembly Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology Sequence contamination filtering, Read mapping, Visualisation, Genome assembly, Sequence composition calculation, Sequencing quality control, Sequence assembly validation, Sequence assembly visualisation, Statistical calculation 2021-03-24 2025-11-18 17 True False True True upload1, quast, bandage_image, fastqc, fastp, bandage_info, falco, shovill UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 10291 15797 3.550000 0
Assembly Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Sequence alignment analysis, Read mapping, Genome assembly, Sequence trimming, Sequence file editing, Sequence assembly validation, Sequence assembly visualisation, Variant calling, Statistical calculation, Sequence contamination filtering, Visualisation, Read pre-processing, Sequence composition calculation, Formatting, Sequencing quality control, Primer removal, Local alignment, Data handling 2025-12-07 2025-12-07 0 True False True True coverm_contig, random_lines1, bamtools, tp_cat, cutadapt, ngsutils_bam_filter, quast, megahit, bg_uniq, filter_tabular, bandage_image, collection_column_join, megahit_contig2fastg, metaspades, bowtie2, fastqc, bandage_info, seqtk_subseq UseGalaxy.cz, UseGalaxy.eu 0 1 1 0.000000 0
Assembly De Bruijn Graph Assembly https://training.galaxyproject.org//topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html Sequence assembly, Optimisation and refinement, Genome assembly 2017-05-24 2024-02-01 25 True True False True velvetoptimiser, spades, fasta-stats Galaxy@AuBi, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 3091565 7924727 5.016667 0
Assembly Unicycler Assembly https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html Sequence assembly, Genomics, Microbiology Visualisation, Genome assembly, Gene prediction, Sequence composition calculation, Sequencing quality control, Sequence assembly validation, Genome annotation, Aggregation, Coding region prediction, Statistical calculation, Validation 2017-10-11 2025-05-15 24 True True False True quast, multiqc, fastqc, prokka, unicycler UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3097980 7936496 4.400000 0
Assembly Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads https://training.galaxyproject.org//topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html Sequence contamination filtering, Read mapping, Data handling, Scatter plot plotting, Genome assembly, Sequence file editing, Sequencing quality control, Aggregation, Box-Whisker plot plotting, Sequence assembly visualisation, Pairwise sequence alignment, Validation 2020-04-21 2025-05-15 14 True True True True minimap2, samtools_stats, fasta_filter_by_length, seqtk_sample, nanoplot, bandage_image, collapse_dataset, samtools_view, multiqc, __ZIP_COLLECTION__, fasterq_dump, bowtie2, samtools_fastx, fastp, bandage_info, unicycler UseGalaxy.eu, UseGalaxy.org.au Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 3090975 7924278 5.533333 0
Assembly Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step https://training.galaxyproject.org//topics/assembly/tutorials/vgp_genome_assembly/tutorial.html Genomics, Sequence assembly, Biodiversity Visualisation, Genome assembly, Read pre-processing, Pairwise sequence alignment, De-novo assembly, Sequence trimming, Phasing, Sequence assembly validation, Scaffolding, k-mer counting, Read binning, Primer removal, Sequence alignment, Mapping, Data handling 2021-06-04 2025-06-04 57 True False True True busco, sort1, collection_column_join, merqury, hifiasm, salsa, collapse_dataset, cat1, gfastats, tp_cut_tool, purge_dups, minimap2, cutadapt, quast, bellerophon, tp_find_and_replace, meryl, yahs, gfa_to_fa, bwa_mem2, pretext_map, tp_grep_tool, genomescope, Add_a_column1, Convert characters1, pretext_snapshot, bedtools_bamtobed, bionano_scaffold UseGalaxy.cz 0 16063 24186 1.966667 0
Assembly Genome assembly using PacBio data https://training.galaxyproject.org//topics/assembly/tutorials/hifi-assembly/tutorial.html Genomics, Sequence assembly, Biodiversity Mapping assembly, Sequence assembly validation, Visualisation, Genome assembly, Cross-assembly, De-novo assembly 2021-11-29 2025-06-04 2 True False False True flye, busco, fasta-stats, quast, hifiasm, gfa_to_fa UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.no 0 885 1039 1.533333 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 3621 5005 2.633333 0
Assembly Making sense of a newly assembled genome https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html Sequence assembly, Genomics, Microbiology Read mapping, Sequence alignment, Mapping, Genome visualisation, Sequence visualisation 2018-06-14 2024-06-24 29 True False False True bedtools_complementbed, jbrowse, circos_aln_to_links, tp_sed_tool, Grep1, upload1, circos_interval_to_tiles, lastz_wrapper_2, collapse_dataset, cat1, bedtools_intersectbed, Filter1, mergeCols1, tp_sort_header_tool, tp_cat, addValue, random_lines1, tp_grep_tool, bedtools_sortbed, join1, fasta_filter_by_length, Cut1, circos, tp_replace_in_line, fasta_compute_length, tp_replace_in_column, datamash_ops 0 6769 13021 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 2025-04-23 2 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 625237 1205265 1.483333 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 3064237 7845709 2.333333 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 2603416 6289191 2.266667 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_panoply, interactive_tool_copernicus_notebook, interactive_tool_copernicus 0 316 363 0.516667 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 2478408 5889851 4.166667 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, argo_getdata, xarray_coords_info, xarray_metadata_info, timeseries_extraction UseGalaxy.eu 0 318 379 1.066667 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__, ggplot2_point, __EXTRACT_DATASET__, xarray_select, graphicsmagick_image_montage, xarray_coords_info, xarray_metadata_info, climate_stripes, xarray_mapplot, regexColumn1, xarray_netcdf2netcdf UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 2478179 5889331 5.050000 0
Climate Ocean's variables study https://training.galaxyproject.org//topics/climate/tutorials/ocean-variables/tutorial.html 2023-11-29 2025-05-10 5 True False False True interactive_tool_divand, divand_full_analysis, interactive_tool_odv UseGalaxy.eu 0 235 282 1.650000 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, interactive_tool_odv, harmonize_insitu_to_netcdf, tool_odv_history, tool_biogeochemical_calibration UseGalaxy.eu 0 48 59 1.716667 0
Climate Functionally Assembled Terrestrial Ecosystem Simulator (FATES) https://training.galaxyproject.org//topics/climate/tutorials/fates/tutorial.html Visualisation 2020-10-25 2025-05-10 18 True True True True interactive_tool_panoply, ggplot2_point, __EXTRACT_DATASET__, xarray_select, tp_find_and_replace, xarray_metadata_info, ctsm_fates UseGalaxy.eu, UseGalaxy.org (Main) 0 3086445 7916587 4.133333 0
Climate Getting your hands-on climate data https://training.galaxyproject.org//topics/climate/tutorials/climate-101/tutorial.html Visualisation 2020-04-30 2025-05-10 14 True False False True interactive_tool_panoply, cds_essential_variability, psy_maps, ggplot2_point, climate_stripes, tp_awk_tool, Grep1, datamash_ops UseGalaxy.eu 0 1085 1494 1.266667 0
Climate Introduction to climate data https://training.galaxyproject.org//topics/climate/tutorials/introduction/slides.html 2020-10-11 2025-05-10 2 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3084956 7914245 2.333333 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 0 421 507 1.133333 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 0 561 968 1.750000 0
Climate Getting your hands-on earth data https://training.galaxyproject.org//topics/climate/tutorials/earth_system/tutorial.html 2024-10-04 2025-05-10 2 True False False False argo_getdata, obis_data, spocc_occ, c3s UseGalaxy.eu 0 114 148 1.950000 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 0 188 234 0.866667 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 6365 10341 0.800000 0
Galaxy Community Building Creation of the labs in the different Galaxy instances for your community https://training.galaxyproject.org//topics/community/tutorials/community-lab/tutorial.html 2025-10-04 2025-11-04 3 True False False False 0 40 43 0.333333 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 64 78 0.516667 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 16 17 0.016667 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 47 62 7.516667 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 0 101 125 2.100000 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 22 24 2.000000 0
Galaxy Community Building What's a Special Interest Group? https://training.galaxyproject.org//topics/community/tutorials/sig_define/tutorial.html 2024-07-08 2024-12-20 3 True False False False 0 102 136 2.750000 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 0 133 146 1.750000 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, tp_cat, ctb_alignit, sort1, openbabel_addh, rdconf UseGalaxy.cz 0 1277 1838 2.366667 0
Computational chemistry Data management in Medicinal Chemistry https://training.galaxyproject.org//topics/computational-chemistry/tutorials/med-chem-data/tutorial.html 2024-01-08 2024-09-13 4 True False True True openbabel_compound_convert, openbabel_svg_depiction, chembl, md_converter, get_pdb, ctb_im_rxn_maker, ctb_silicos_qed UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 471 561 1.683333 0
Computational chemistry Protein-ligand docking https://training.galaxyproject.org//topics/computational-chemistry/tutorials/cheminformatics/tutorial.html 2019-10-19 2025-12-04 17 True False False True ctb_chemfp_nxn_clustering, ctb_online_data_fetch, sdf_to_tab, ctb_np-likeness-calculator, ctb_filter, ctb_remDuplicates, ctb_chemfp_mol2fps, collapse_dataset, fpocket, get_pdb, tp_cat, ctb_remIons, tp_find_and_replace, ctb_obgrep, prepare_receptor, ctb_change_title, ctb_chemfp_butina_clustering, tp_grep_tool, ctb_compound_convert, prepare_box, openbabel_svg_depiction, docking, chembl, openbabel_compound_convert UseGalaxy.org (Main) 0 19849 33796 1.600000 0
Computational chemistry Analysis of molecular dynamics simulations https://training.galaxyproject.org//topics/computational-chemistry/tutorials/analysis-md-simulations/tutorial.html 2019-06-03 2023-11-09 13 True False False True bio3d_rmsd, bio3d_pca, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_rdf, mdanalysis_cosine_analysis, mdanalysis_ramachandran_plot, bio3d_rmsf UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 32522 57595 1.233333 0
Computational chemistry Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring https://training.galaxyproject.org//topics/computational-chemistry/tutorials/covid19-docking/tutorial.html 2020-03-27 2023-11-09 10 True False False True enumerate_charges, split_file_to_collection, rxdock_rbdock, xchem_pose_scoring, rdock_rbcavity, collapse_dataset, rdock_rbdock, ctb_frankenstein_ligand, rxdock_rbcavity, xchem_transfs_scoring, openbabel_compound_convert, sucos_max_score 0 3203 5256 3.033333 0
Computational chemistry Running molecular dynamics simulations using GROMACS https://training.galaxyproject.org//topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.html 2019-06-03 2023-11-09 15 True False False True gmx_em, tp_grep_tool, gmx_solvate, gmx_setup, get_pdb, gmx_sim, gmx_editconf UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 26924 48071 1.433333 0
Computational chemistry High Throughput Molecular Dynamics and Analysis https://training.galaxyproject.org//topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html 2020-05-20 2025-04-08 19 True False True True openbabel_compound_convert, gmx_energy, gmx_em, bio3d_rmsd, bio3d_pca, tp_grep_tool, ambertools_acpype, gmx_solvate, gmx_setup, mdanalysis_cosine_analysis, md_converter, vmd_hbonds, get_pdb, bio3d_rmsf, gmx_sim, gmx_merge_topology_files, bio3d_pca_visualize, gmx_editconf UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 10932 19140 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, setup, namd_npt, minimizer 0 4259 7111 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 1818 2446 1.633333 0
Contributing to the Galaxy Training Material Contributing to the Galaxy Training Network with GitHub https://training.galaxyproject.org//topics/contributing/tutorials/github-contribution/tutorial.html 2017-06-12 2025-03-14 2 True True False False 0 3085068 7914373 3.816667 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 3084956 7914246 2.333333 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 5440 6478 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 0 329 635 0.933333 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 0 280 362 3.466667 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 0 687 1038 2.383333 0
Contributing to the Galaxy Training Material Generating PDF artefacts of the website https://training.galaxyproject.org//topics/contributing/tutorials/generating-pdf/tutorial.html 2018-06-04 2023-11-09 12 True False False False 0 80 97 2.300000 0
Contributing to the Galaxy Training Material Preview the GTN website as you edit your training material https://training.galaxyproject.org//topics/contributing/tutorials/rendering_gtn/tutorial.html 2025-03-14 2025-07-02 3 True False True False 0 407 553 4.450000 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 0 302 460 2.366667 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 0 272 359 2.716667 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 67 109 0.683333 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 0 560 751 1.650000 0
Contributing to the Galaxy Training Material Including a new topic https://training.galaxyproject.org//topics/contributing/tutorials/create-new-topic/tutorial.html 2018-06-04 2025-12-01 33 True False False False 0 1250 1708 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 0 603 794 2.683333 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 46 51 0.483333 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 0 114 128 0.283333 0
Contributing to the Galaxy Training Material Creating a new tutorial https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial/tutorial.html Sequence file editing, Read mapping, Primer removal, Read pre-processing, Data handling, Sequence trimming 2018-06-20 2025-11-20 33 True False True True random_lines1, cutadapt, tp_cat, fastq_to_tabular, Cut1, c3s, tp_sorted_uniq, tp_sed_tool, bowtie2, tp_cut_tool, Filter1, bam_to_sam, seqtk_subseq 0 1815 2676 4.966667 0
Contributing to the Galaxy Training Material FAIR Galaxy Training Material https://training.galaxyproject.org//topics/contributing/tutorials/fair-gtn/tutorial.html 2025-12-07 2025-12-07 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 50 52 0.516667 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 45 45 0.083333 0
Contributing to the Galaxy Training Material Creating content in Markdown https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-content/tutorial.html Sequencing quality control, Validation 2017-06-25 2025-04-08 85 True False False False multiqc, upload1 0 3758 9774 2.100000 0
Contributing to the Galaxy Training Material Creating Slides https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-slides/slides.html 2018-06-13 2024-11-08 17 False True True False 0 3084956 7914247 2.333333 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 0 108 126 3.766667 0
Using Galaxy and Managing your Data Automating Galaxy workflows using the command line https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-automation/tutorial.html Sequence contamination filtering, Sequencing quality control, Visualisation, Read mapping, Tree-based sequence alignment, Variant classification, Validation 2021-06-08 2025-11-21 10 True False True True collapse_dataset, bcftools_consensus, multiqc, pangolin, snpSift_filter, fastp, compose_text_param, falco UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 2910 3522 2.016667 0
Using Galaxy and Managing your Data Submitting sequence data to ENA https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-data-to-ena/tutorial.html 2021-08-10 2024-12-11 10 True True False True ena_consensus_submit, ena_upload 0 2764166 6823775 3.650000 0
Variant Analysis Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html Tree-based sequence alignment, Variant classification, Variant calling, Methylation analysis 2021-06-30 2025-03-28 18 True False True False upload1, nextclade, fasta_regex_finder, pangolin, Filter1, datamash_ops UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 7411 13248 3.433333 0
Variant Analysis From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2/tutorial.html Sequence contamination filtering, Read mapping, Generation, Formatting, SNP detection, Genome indexing, Sequencing quality control, Sequence alignment, Data handling, Validation 2020-06-24 2024-06-14 16 True False True True samtools_stats, lofreq_viterbi, bwa_mem, snpeff_sars_cov_2, picard_MarkDuplicates, multiqc, fasterq_dump, lofreq_indelqual, tp_cut_tool, snpSift_extractFields, Filter1, fastp, Grep1, lofreq_call UseGalaxy.eu, UseGalaxy.org (Main) MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 13753 20663 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, Genome indexing, Read mapping, Generation, Sequence alignment, Data handling 2021-08-04 2023-11-09 5 True False False True trimmomatic, seqtk_subseq, bwa_mem, __ZIP_COLLECTION__, __UNZIP_COLLECTION__, samtools_fastx, tp_replace_in_line, Grep1 UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 4085 5791 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 SNP detection, Data handling 2021-05-31 2024-06-14 12 True True True False tp_cat, fastq_dump, snpeff_sars_cov_2, fastq_to_fasta_python, fasterq_dump, jq, query_tabular UseGalaxy.be, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2865671 7159722 3.966667 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 indexing, Read mapping, Generation, Sequence alignment, Sequencing quality control, Genome visualisation, Sequence composition calculation, Statistical calculation 2023-07-10 2024-02-29 2 True False False False bwa_mem, fastqc, jbrowse UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz 0 1283 1663 3.983333 0
Foundations of Data Science Data Manipulation Olympics https://training.galaxyproject.org//topics/data-science/tutorials/data-manipulation-olympics/tutorial.html 2025-12-07 2025-12-07 0 True False False True {{version_sort}}, {{version_remove_beginning}}, {{version_split}}, {{version_join}}, tabular_to_csv, {{version_select_first}}, upload1, {{version_datamash}}, {{version_cut_columns}}, Remove beginning1, Grouping1, cat1, Filter1, {{version_cat}}, regexColumn1, {{version_compute}}, tp_sort_header_tool, {{version_cut_advanced}}, {{version_replace_text_line}}, wc_gnu, {{version_filter}}, tp_cat, tp_split_on_column, {{version_unique}}, Show beginning1, tp_sorted_uniq, {{version_remove_columns_by_header}}, {{version_replace_text_column}}, Count1, join1, {{version_paste}}, Cut1, Add_a_column1, {{version_count}}, {{version_wc}}, datamash_ops 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 1365876 3013221 2.566667 0
Foundations of Data Science Learning about one gene across biological resources and formats https://training.galaxyproject.org//topics/data-science/tutorials/online-resources-gene/tutorial.html 2023-09-07 2023-11-09 3 True True True False ncbi_blastp_wrapper Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, PepSimili, UseGalaxy.no 0 1521538 3363591 4.633333 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 0 301 532 0.583333 0
Foundations of Data Science Python - Warm-up for statistics and machine learning https://training.galaxyproject.org//topics/data-science/tutorials/python-warmup-stat-ml/tutorial.html 2025-03-11 2025-03-11 1 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 134 155 0.883333 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 0 512 694 0.466667 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 0 686 742 0.366667 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 9025 11789 2.033333 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 0 957 1216 2.350000 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 0 590 719 1.316667 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 1387 1811 1.883333 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 1153 1623 2.816667 0
Foundations of Data Science One protein along the UniProt page https://training.galaxyproject.org//topics/data-science/tutorials/online-resources-protein/tutorial.html 2023-09-07 2024-12-05 5 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 471 500 0.433333 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 0 978 1214 1.233333 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 3389 4370 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 2088 2370 0.550000 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 0 153 398 0.283333 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 2779 3760 2.150000 0
Foundations of Data Science Advanced SQL https://training.galaxyproject.org//topics/data-science/tutorials/sql-advanced/tutorial.html 2021-10-11 2024-12-13 9 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1427 1792 0.550000 0
Foundations of Data Science SQL with R https://training.galaxyproject.org//topics/data-science/tutorials/sql-r/tutorial.html 2021-10-11 2023-11-16 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 620 781 0.516667 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 0 634 715 0.966667 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 1618 2531 2.800000 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 0 983 1154 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 0 257 318 1.900000 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 0 539 718 1.216667 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 0 396 674 5.950000 0
Foundations of Data Science Introduction to sequencing with Python (part two) https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture3/tutorial.html 2024-01-23 2024-02-20 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 129 135 0.450000 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 0 626 815 0.833333 0
Foundations of Data Science Plotting in Python https://training.galaxyproject.org//topics/data-science/tutorials/python-plotting/tutorial.html 2021-11-08 2024-10-15 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 582 704 1.500000 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 0 811 906 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 0 364 415 0.850000 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 0 139 149 0.383333 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 2134 2516 0.550000 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 0 136 149 0.850000 0
Foundations of Data Science Python - Flow Control https://training.galaxyproject.org//topics/data-science/tutorials/python-flow/tutorial.html 2022-04-25 2023-02-13 3 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 274 325 0.766667 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 0 388 463 1.633333 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 56 62 0.800000 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 12 12 0.066667 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 0 549 638 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 0 596 682 0.366667 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 0 237 281 1.583333 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 0 696 749 0.533333 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 1331 1447 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 0 202 224 1.200000 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 0 628 665 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 0 228 251 0.366667 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 0 533 575 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 1164 1349 0.316667 0
Foundations of Data Science Python - Coding Style https://training.galaxyproject.org//topics/data-science/tutorials/python-linting/tutorial.html 2022-11-03 2023-05-18 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 187 200 0.516667 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 0 870 935 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 3084956 7914251 2.333333 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 3084956 7914251 2.333333 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 3085693 7915211 4.466667 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 3085673 7915105 3.283333 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 3084956 7914251 2.333333 0
Development in Galaxy Tool Dependencies and Containers https://training.galaxyproject.org//topics/dev/tutorials/containers/slides.html 2017-06-20 2022-10-18 14 False True False False 0 3084956 7914251 2.333333 0
Development in Galaxy Prerequisites for building software/conda packages https://training.galaxyproject.org//topics/dev/tutorials/conda_sys/slides.html 2018-02-15 2021-05-28 6 False True False False 0 3084956 7914251 2.333333 0
Development in Galaxy Generic plugins https://training.galaxyproject.org//topics/dev/tutorials/visualization-generic/tutorial.html 2016-09-30 2023-11-09 21 True True False False 0 3085312 7914758 4.116667 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 2873429 7185037 4.766667 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 3085152 7914511 3.633333 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 3084956 7914251 2.333333 0
Development in Galaxy Tool development and integration into Galaxy https://training.galaxyproject.org//topics/dev/tutorials/tool-integration/slides.html 2016-09-30 2025-04-08 30 external True False False 0 3084959 7914255 2.333333 0
Development in Galaxy Galaxy Interactive Tours https://training.galaxyproject.org//topics/dev/tutorials/interactive-tours/slides.html 2017-01-12 2021-07-27 14 False True False False 0 3084956 7914251 2.333333 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 1 1 0.200000 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 0 432 516 1.416667 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 0 233 342 2.833333 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 1227 1628 2.733333 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 0 246 336 2.783333 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 2760 4448 2.550000 0
Development in Galaxy Debugging Galaxy https://training.galaxyproject.org//topics/dev/tutorials/debugging/tutorial.html 2021-06-15 2025-11-05 15 True False False False 0 598 1202 2.816667 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 0 281 336 2.283333 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 0 734 1097 2.650000 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 0 281 709 2.000000 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 29 32 2.200000 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 wc_gnu, tp_grep_tool, wordcloud, tp_find_and_replace, Remove beginning1, diff, tp_replace_in_line UseGalaxy.cz, UseGalaxy.eu UseGalaxy.org.au 0 73 89 1.450000 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 wordcloud, sort1, Cut1, Add_a_column1, diff, tp_replace_in_line, Filter1, datamash_ops UseGalaxy.cz 0 161 188 1.466667 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 interactive_tool_openrefine, barchart_gnuplot, tp_grep_tool, wordcloud, tp_head_tool, datamash_ops, filter_tabular, Cut1, Remove beginning1, param_value_from_file, compose_text_param, regexColumn1, tp_sort_header_tool UseGalaxy.eu 0 32 36 0.016667 0
Ecology Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities https://training.galaxyproject.org//topics/ecology/tutorials/MetaShARK_tutorial/tutorial.html 2024-03-04 2024-09-10 7 True False False False interactive_tool_metashark UseGalaxy.eu, UseGalaxy.fr 0 208 253 1.800000 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 phylogenetic_occupancy_matcher, phylo_index, crsconverter, estimate_endem UseGalaxy.eu 0 92 117 0.833333 0
Ecology Sentinel 2 biodiversity https://training.galaxyproject.org//topics/ecology/tutorials/remote-sensing/tutorial.html 2023-04-13 2025-06-03 6 True False False True srs_process_data, srs_global_indices, srs_preprocess_s2, srs_spectral_indices, srs_pca, srs_diversity_maps UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 625 801 1.600000 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_glmcomm, datamash_transpose, tp_cat, Count1, pampa_communitymetrics, pampa_plotglm, regex1, tp_easyjoin_tool, tp_cut_tool, pampa_glmsp, Filter1, pampa_presabs, regexColumn1, mergeCols1, tp_sort_header_tool UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au 0 1116 1483 1.933333 0
Ecology RAD-Seq to construct genetic maps https://training.galaxyproject.org//topics/ecology/tutorials/genetic-map-rad-seq/tutorial.html Data handling 2017-02-14 2025-06-03 13 True False False True stacks_genotypes, stacks_denovomap UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 899 1261 1.333333 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_dissim, cb_ivr, cb_div, cb_eco, cb_qecb 0 181 331 1.816667 0
Ecology Species distribution modeling https://training.galaxyproject.org//topics/ecology/tutorials/species-distribution-modeling/tutorial.html 2019-07-04 2025-06-03 18 True False False True interactive_tool_wallace, tp_find_and_replace, tp_cut_tool, spocc_occ, Filter1, tabular_to_csv UseGalaxy.eu, UseGalaxy.fr 0 3212 4845 1.150000 0
Ecology Visualization of Climate Data using NetCDF xarray Map Plotting https://training.galaxyproject.org//topics/ecology/tutorials/x-array-map-plot/tutorial.html 2022-10-26 2024-06-27 9 True False False True graphicsmagick_image_montage, xarray_coords_info, xarray_metadata_info, xarray_mapplot, cdo_operations UseGalaxy.eu UseGalaxy.cz 0 2394 2769 0.466667 0
Ecology RAD-Seq de-novo data analysis https://training.galaxyproject.org//topics/ecology/tutorials/de-novo-rad-seq/tutorial.html Sequencing quality control, Sequence composition calculation, Data handling, Statistical calculation 2017-02-14 2025-06-03 14 True False False True stacks_denovomap, fastqc, stacks_populations, stacks_procrad UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 2707 4304 2.100000 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 tp_awk_tool, csv2tab_R, Count1, ggplot2_point, flight-curve, Remove beginning1, regionalgam_ab_index, tab2csv_R, regexColumn1, regionalgam_flight_curve, Filter1, Paste1, regionalgam_autocor_acf, regionalgam_gls, mergeCols1, regionalgam_glmmpql, regionalgam_plot_trend 0 351 469 3.400000 0
Ecology Metabarcoding/eDNA through Obitools https://training.galaxyproject.org//topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html Sequencing quality control, Sequence analysis, Sequence composition calculation, Statistical calculation 2022-02-28 2025-06-03 12 True False True True obi_uniq, unzip, fastq_groomer, obi_grep, wc_gnu, obi_stat, obi_clean, join1, ncbi_blastn_wrapper, obi_ngsfilter, Cut1, obi_annotate, fastqc, obi_illumina_pairend, Filter1, seq_filter_by_id, obi_tab UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 4557 6332 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 obisindicators, obis_data, tp_cut_tool UseGalaxy.eu 0 319 399 2.000000 0
Ecology Preparing genomic data for phylogeny reconstruction https://training.galaxyproject.org//topics/ecology/tutorials/phylogeny-data-prep/tutorial.html Genome annotation, Sequence assembly validation, Sequence analysis, Genetic variation analysis, Sequence clustering, Multiple sequence alignment 2022-10-21 2025-06-03 5 True False False True clustalw, clipkit, busco, phykit_alignment_based, repeatmasker_wrapper, collapse_dataset, regex1, funannotate_predict, proteinortho_grab_proteins, glimmer_gbk_to_orf, tp_replace_in_line, Filter1, proteinortho 0 2248 3093 2.750000 0
Ecology Ecoregionalization workflow tutorial https://training.galaxyproject.org//topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html 2024-09-16 2025-06-03 7 True False False True unzip, ecoregion_cluster_estimate, ecoregion_GeoNearestNeighbor, ecoregion_taxa_seeker, ecoregion_brt_analysis, interactive_tool_jupyter_notebook, filter_tabular, ecoregion_clara_cluster, tp_cut_tool, ecoregion_eco_map, regexColumn1, mergeCols1 UseGalaxy.eu 0 287 380 2.650000 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 unzip, ecoregion_taxa_seeker, ecoregion_GeoNearestNeighbor, column_remove_by_header, ecoregion_brt_analysis, WormsMeasurements, ClaraGuess, tp_cut_tool, Filter1, ecoregion_eco_map, regexColumn1 UseGalaxy.eu 0 46 49 2.100000 0
Ecology Checking expected species and contamination in bacterial isolate https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Cross-assembly, Taxonomic classification, Expression analysis, Statistical calculation 2024-03-04 2024-06-27 4 True False False True est_abundance, kraken2, recentrifuge, upload1 UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main) 0 886 1180 3.283333 0
Ecology RAD-Seq Reference-based data analysis https://training.galaxyproject.org//topics/ecology/tutorials/ref-based-rad-seq/tutorial.html Read mapping, Generation, Sequence composition calculation, Genome indexing, Sequencing quality control, Sequence alignment, Statistical calculation, Data handling, Validation 2017-02-14 2025-11-06 15 True False False True Summary_Statistics1, addValue, Count1, stacks_refmap, bwa, Cut1, bwa_wrapper, multiqc, Convert characters1, cat1, stacks_populations, fastqc, stacks_procrad, tp_replace_in_line, Filter1, regex_replace, Grep1, tp_sort_header_tool 0 3165 4927 1.800000 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 0 113 123 1.483333 0
Ecology Taxonomic Analysis of eDNA https://training.galaxyproject.org//topics/ecology/tutorials/eDNA-taxonomic-analysis/tutorial.html Sequence contamination filtering, Sequencing quality control 2025-06-02 2025-06-03 2 True False False True cshl_fastq_to_fasta, ncbi_blastn_wrapper, Count1, fastp UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.no 0 478 600 0.750000 0
Ecology Cleaning GBIF data for the use in Ecology https://training.galaxyproject.org//topics/ecology/tutorials/gbif_cleaning/tutorial.html 2022-10-28 2025-06-03 6 True False False True Summary_Statistics1, Count1, gdal_ogr2ogr, spocc_occ, Filter1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no 0 651 806 0.916667 0
Ecology From NDVI data with OpenEO to time series visualisation with Holoviews https://training.galaxyproject.org//topics/ecology/tutorials/ndvi_openeo/tutorial.html 2024-01-24 2024-06-29 3 True False False True interactive_tool_holoviz, interactive_tool_copernicus_notebook UseGalaxy.eu 0 211 250 1.016667 0
Ecology Marine Omics identifying biosynthetic gene clusters https://training.galaxyproject.org//topics/ecology/tutorials/marine_omics_bgc/tutorial.html Protein feature detection, Genome annotation, Sequence motif recognition 2024-08-19 2025-06-03 3 True False False True regex1, SanntiS_marine, sanntis_marine, interproscan, prodigal 0 192 226 2.350000 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, ecology_presence_abs_abund, Remove beginning1, tool_anonymization, ecology_homogeneity_normality, tp_cut_tool, ecology_link_between_var, regexColumn1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr 0 1635 2284 2.716667 0
Ecology Data submission using ENA upload Tool https://training.galaxyproject.org//topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html Sequencing quality control, Visualisation, Read mapping, Primer removal, Validation, Read pre-processing, Sequence trimming 2024-12-13 2025-03-20 2 True False False False fastq_groomer, cutadapt, __FILTER_EMPTY_DATASETS__, fastq_filter, __RELABEL_FROM_FILE__, ncbi_blastn_wrapper, bg_uniq, falco, regex1, fastq_to_fasta_python, collection_element_identifiers, multiqc, Paste1, ab1_fastq_converter UseGalaxy.eu UseGalaxy.cz 0 249 261 0.633333 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) 0 243 306 1.233333 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 17 20 0.000000 0
Ecology Cleaning GBIF data using OpenRefine https://training.galaxyproject.org//topics/ecology/tutorials/openrefine_gbif/tutorial.html 2025-01-21 2025-06-03 5 True False False False interactive_tool_openrefine, regex1 UseGalaxy.eu, UseGalaxy.fr 0 165 202 1.116667 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 0 282 325 1.616667 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 0 643 807 1.383333 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 0 981 1172 1.516667 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 1929 2286 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 98 113 1.200000 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 1623 1909 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 1274 1471 0.766667 0
Statistics and machine learning Fine-tuning a LLM for DNA Sequence Classification https://training.galaxyproject.org//topics/statistics/tutorials/genomic-llm-finetuning/tutorial.html 2025-04-17 2025-05-22 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 573 669 1.300000 0
Statistics and machine learning Neural networks using Python https://training.galaxyproject.org//topics/statistics/tutorials/neural-networks-with-python/tutorial.html 2025-03-11 2025-03-11 1 True True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 703452 1397375 1.583333 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 0 185 210 1.816667 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 703454 1397379 2.016667 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 0 151 169 0.683333 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 38 40 0.883333 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 703487 1397425 2.850000 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 Read mapping, Read pre-processing, Enrichment analysis, Sequence composition calculation, Genome visualisation, Sequence trimming, Pathway visualisation, Sequencing quality control, Primer removal, Mapping, Gene regulatory network analysis, Peak calling, Structure visualisation, Statistical calculation 2018-09-17 2025-04-08 14 True True False True bedtools_mergebed, deeptools_compute_matrix, trim_galore, samtools_idxstats, bedtools_sortbed, deeptools_bam_coverage, deeptools_multi_bam_summary, deeptools_plot_heatmap, cat1, deeptools_bam_compare, deeptools_plot_correlation, deeptools_plot_fingerprint, bowtie2, fastqc, jbrowse2, bbgtobigwig, Filter1, macs2_callpeak UseGalaxy.eu, UseGalaxy.org (Main) 0 3090952 7926066 5.966667 0
Epigenetics CUT&RUN data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/cut_and_run/tutorial.html Sequence alignment analysis, Read mapping, Visualisation, Read pre-processing, Enrichment analysis, Sequence trimming, Formatting, Sequencing quality control, Primer removal, Gene regulatory network analysis, Mapping, Peak calling, Data handling, Validation 2024-03-06 2025-03-19 5 True False False True datamash_transpose, deeptools_compute_matrix, trim_galore, deeptools_plot_heatmap, bowtie2, Grep1, macs2_callpeak, bedtools_intersectbed, bamFilter, pe_histogram, falco, idr, wig_to_bigWig, multiqc, meme_chip, Extract genomic DNA 1, deeptools_plot_fingerprint, __EXTRACT_DATASET__, __FLATTEN__, picard_MarkDuplicates, bedtools_bamtobed 0 6288 8020 1.366667 0
Epigenetics ATAC-Seq data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/atac-seq/tutorial.html Sequence alignment analysis, Read mapping, Visualisation, Read pre-processing, Enrichment analysis, Sequence composition calculation, Sequence trimming, Formatting, Sequencing quality control, Primer removal, Gene regulatory network analysis, Mapping, Peak calling, Statistical calculation, Data handling 2019-09-02 2024-08-08 23 True True True True pe_histogram, pygenomeTracks, cutadapt, deeptools_compute_matrix, samtools_idxstats, wig_to_bigWig, deeptools_plot_heatmap, Cut1, picard_MarkDuplicates, macs2_callpeak, bedtools_intersectbed, bowtie2, fastqc, bedtools_bamtobed, Filter1, bamFilter, Grep1, tp_sort_header_tool 0 3149401 8029936 4.116667 0
Epigenetics Hi-C analysis of Drosophila melanogaster cells using HiCExplorer https://training.galaxyproject.org//topics/epigenetics/tutorials/hicexplorer/tutorial.html Read mapping, Visualisation, Formatting 2018-02-23 2025-08-11 30 True False False True pygenomeTracks, hicexplorer_hicmergematrixbins, hicexplorer_hicplotmatrix, hicexplorer_hicdetectloops, hicexplorer_hicfindrestrictionsites, hicexplorer_hicinfo, hicexplorer_hicpca, bowtie2, hicexplorer_hicfindtads, hicexplorer_hicbuildmatrix, hicexplorer_hiccorrectmatrix UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no, UseGalaxy.org (Main) 0 7529 12608 1.500000 0
Epigenetics Identification of the binding sites of the Estrogen receptor https://training.galaxyproject.org//topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html Read mapping, Read pre-processing, Enrichment analysis, Sequence composition calculation, Sequence trimming, Sequencing quality control, Primer removal, Gene regulatory network analysis, Peak calling, Statistical calculation 2017-09-18 2025-04-08 10 True False False True deeptools_compute_matrix, trim_galore, samtools_idxstats, deeptools_bam_coverage, deeptools_multi_bam_summary, deeptools_plot_heatmap, deeptools_bam_compare, macs2_callpeak, deeptools_plot_correlation, deeptools_plot_fingerprint, bowtie2, fastqc, deeptools_compute_gc_bias, bam_to_sam UseGalaxy.be Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 1933 2847 2.766667 0
Epigenetics Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) https://training.galaxyproject.org//topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html ChIP-seq Read mapping, Generation, Enrichment analysis, Sequence composition calculation, Genome indexing, Sequencing quality control, Sequence alignment, Gene regulatory network analysis, Mapping, Peak calling, Statistical calculation 2016-12-20 2025-04-08 11 True False False True trimmomatic, deeptools_compute_matrix, samtools_idxstats, bwa, deeptools_correct_gc_bias, deeptools_plot_heatmap, deeptools_multi_bam_summary, deeptools_bam_compare, macs2_callpeak, deeptools_plot_correlation, deeptools_plot_fingerprint, fastqc, bedtools_intersectbed, deeptools_compute_gc_bias UseGalaxy.be, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 7334 13502 3.333333 0
Epigenetics Infinium Human Methylation BeadChip https://training.galaxyproject.org//topics/epigenetics/tutorials/ewas-suite/tutorial.html 2018-08-27 2024-10-15 21 True True False True clusterprofiler_bitr, chipeakanno_annopeaks, Cut1, Remove beginning1, minfi_analysis, clusterprofiler_go UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3087039 7917514 4.200000 0
Epigenetics DNA Methylation data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/methylation-seq/tutorial.html Epigenomics Sequencing quality control, Visualisation, Read mapping, Sequence composition calculation, Statistical calculation 2017-02-16 2025-04-03 24 True False False True deeptools_compute_matrix, replace_column_with_key_value_file, wig_to_bigWig, tp_tail_tool, bwameth, fastqc, metilene, deeptools_plot_profile, tp_awk_tool, falco, pileometh 0 15067 25026 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 3084956 7914253 2.333333 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 3084956 7914253 2.333333 0
Evolution Phylogenetics - Back to basics https://training.galaxyproject.org//topics/evolution/tutorials/abc_intro_phylo/tutorial.html Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree reconstruction, Phylogenetic tree generation (from molecular sequences), Sequence analysis, Phylogenetic analysis, Phylogenetic tree analysis, Multiple sequence alignment, Phylogenetic tree generation 2024-05-10 2024-05-10 1 True False False True newick_display, iqtree, fasttree, rbc_mafft UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 5101 6585 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 Variant calling, Phylogenetic tree generation, Antimicrobial resistance prediction, Phylogenetic tree visualisation 2022-03-16 2025-05-26 13 True False False True snippy, tb_profiler_profile, tp_sed_tool, clustering_from_distmat, Grep1, upload1, __MERGE_COLLECTION__, tb_variant_filter, collapse_dataset, bcftools_consensus, snp_dists, trimmomatic, tp_cat, tp_easyjoin_tool, addName, snp_sites, tp_grep_tool, samtools_view, tp_replace_in_line UseGalaxy.eu 0 2956 4250 2.666667 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 upload1, interactive_tool_rstudio, raxml UseGalaxy.eu 0 2271 3278 2.483333 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 1165323 2535556 2.000000 0
Evolution Phylogenetic analysis for bacterial comparative genomics https://training.galaxyproject.org//topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html Genomics, Microbiology, Phylogeny Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree generation (from molecular sequences) 2025-03-14 2025-03-14 1 True False False False upload1, fasttree Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) GalaxyTrakr 0 102 124 2.516667 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 1165323 2535556 2.000000 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 1165323 2535556 2.000000 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 1165323 2535556 2.000000 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 1165323 2535556 2.000000 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 1165323 2535556 2.000000 0
FAIR Data, Workflows, and Research Data management in Medicinal Chemistry https://training.galaxyproject.org//topics/fair/tutorials/med-chem-data/tutorial.html 2025-12-07 2025-12-07 0 True False True True openbabel_compound_convert, openbabel_svg_depiction, chembl, md_converter, get_pdb, ctb_im_rxn_maker, ctb_silicos_qed UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 0 0 0.000000 0
FAIR Data, Workflows, and Research An earth-system RO-Crate https://training.galaxyproject.org//topics/fair/tutorials/earth_system_rocrate/slides.html 2024-12-02 2024-12-02 1 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 852898 1765859 1.766667 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 15 17 0.750000 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 16 17 1.466667 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 0 604 794 1.666667 0
FAIR Data, Workflows, and Research FAIR in a nutshell https://training.galaxyproject.org//topics/fair/tutorials/fair-intro/tutorial.html 2023-05-30 2024-04-30 6 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 873 1121 1.683333 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 0 595 696 1.000000 0
FAIR Data, Workflows, and Research Introduction to Data Management Plan (DMP) for Peatland Research and PeatDataHub https://training.galaxyproject.org//topics/fair/tutorials/data-management-peatlands/tutorial.html 2024-09-13 2024-09-13 1 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 108 139 2.066667 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 0 343 435 1.366667 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 0 154 170 0.500000 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 0 338 441 1.616667 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 913612 1910252 3.183333 0
FAIR Data, Workflows, and Research FAIR data management solutions https://training.galaxyproject.org//topics/fair/tutorials/data-management/tutorial.html 2023-05-30 2025-01-16 5 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 379 468 2.566667 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 0 243 270 1.350000 0
FAIR Data, Workflows, and Research Exporting Workflow Run RO-Crates from Galaxy https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-in-galaxy/tutorial.html 2023-05-11 2024-08-26 8 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 277 336 2.316667 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 0 184 220 1.400000 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 0 156 190 2.233333 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 88 92 1.783333 0
FAIR Data, Workflows, and Research Best practices for workflows in GitHub repositories https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-galaxy-best-practices/tutorial.html 2023-05-11 2025-04-08 6 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 372 428 1.150000 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 0 293 351 2.400000 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 63 72 2.216667 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 49 57 3.750000 0
FAIR Data, Workflows, and Research REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data https://training.galaxyproject.org//topics/fair/tutorials/bioimage-REMBI/tutorial.html 2023-09-13 2025-11-27 9 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 286 327 2.216667 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 0 258 323 1.416667 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 0 263 321 1.233333 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 upload1, ggplot2_point, Cut1, Remove beginning1, Grouping1, tp_sorted_uniq, csv_to_tabular, datamash_ops UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz 0 879 1214 2.783333 0
Using Galaxy and Managing your Data Creating, Editing and Importing Galaxy Workflows https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-editor/tutorial.html 2020-07-17 2023-11-09 12 True False False True Paste1, Show beginning1, tp_tac Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au MISSISSIPPI 0 6004 7468 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 galaxy_intermine_exchange, intermine UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 186 243 2.850000 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 1987 2531 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 3084956 7914255 2.333333 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 2537177 6078275 2.250000 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 4795 6320 3.016667 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 2750 3710 3.283333 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 5159 7997 2.216667 0
Using Galaxy and Managing your Data Importing (uploading) data from Onedata https://training.galaxyproject.org//topics/galaxy-interface/tutorials/onedata-remote-import/tutorial.html 2025-03-24 2025-04-08 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 203 231 1.416667 0
Using Galaxy and Managing your Data Extracting Workflows from Histories https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history-to-workflow/tutorial.html 2017-10-18 2024-12-02 8 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3047 3941 3.516667 0
Using Galaxy and Managing your Data Use Jupyter notebooks in Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/galaxy-intro-jupyter/tutorial.html 2018-07-02 2025-05-11 10 True False True False interactive_tool_jupyter_notebook UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 2459 3248 2.383333 0
Using Galaxy and Managing your Data Downloading and Deleting Data in Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/download-delete-data/tutorial.html 2019-10-17 2023-11-09 6 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 7453 9870 1.616667 0
Using Galaxy and Managing your Data Rule Based Uploader: Advanced https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.html 2018-05-25 2024-06-14 11 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 801 1062 4.583333 0
Using Galaxy and Managing your Data Using dataset collections https://training.galaxyproject.org//topics/galaxy-interface/tutorials/collections/tutorial.html Genome indexing, Read mapping, Sequence alignment, Generation 2016-09-30 2024-12-05 20 True False True False collapse_dataset, bwa_mem, snpSift_extractFields, lofreq_call UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 16078 21960 2.983333 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 0 409 615 2.200000 0
Using Galaxy and Managing your Data Annotate, prepare tests and publish Galaxy workflows in workflow registries https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-fairification/tutorial.html Sequencing quality control, Visualisation, Read mapping, Validation 2025-05-26 2025-05-26 1 True False False False multiqc, falco UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr 0 227 264 2.100000 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 2139 3419 2.800000 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 88 103 3.083333 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 0 145 186 3.016667 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 40 42 0.083333 0
Using Galaxy and Managing your Data Name tags for following complex histories https://training.galaxyproject.org//topics/galaxy-interface/tutorials/name-tags/tutorial.html 2019-04-08 2023-11-09 8 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1690 2260 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 5542 7138 2.833333 0
Using Galaxy and Managing your Data Creating high resolution images of Galaxy Workflows https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-posters/tutorial.html 2024-02-05 2025-04-08 3 True False False False graphicsmagick_image_convert UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 274 329 2.316667 0
Genome Annotation Genome annotation with Prokka https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Genome annotation, Gene prediction, Genome visualisation, Coding region prediction 2018-03-06 2025-03-19 26 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 3103802 7946069 4.250000 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, gecko, tp_awk_tool, chromeister UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz 0 3040372 7753907 4.533333 0
Genome Annotation Identification of AMR genes in an assembled bacterial genome https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial resistance Read mapping, Antimicrobial resistance prediction, Genome visualisation, Genome annotation 2024-01-23 2025-06-10 9 True False True True upload1, staramr_search, jbrowse, bowtie2, tbl2gff3, bakta, Grep1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, UseGalaxy.org (Main) 0 3531 4879 3.016667 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 annotation, Sequence assembly validation, Sequence alignment, Sequence annotation, Gene prediction, Genome visualisation 2025-06-20 2025-06-25 2 True False False True omark, helixer, braker3, busco, gffread, rna_star, jbrowse 0 383 456 1.666667 0
Genome Annotation Masking repeats with RepeatMasker https://training.galaxyproject.org//topics/genome-annotation/tutorials/repeatmasker/tutorial.html Sequence composition, complexity and repeats, Genomics Editing, RNA-Seq analysis, Genome annotation, Mapping, Repeat sequence detection 2021-11-29 2025-06-03 22 True False True True red, bedtools_maskfastabed, repeatmasker_wrapper, repeatmodeler UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 10162 12933 1.383333 0
Genome Annotation Secondary metabolite discovery https://training.galaxyproject.org//topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html Service invocation, Differential gene expression analysis, Sequence clustering, Gene prediction, Data handling 2024-02-21 2024-09-27 2 True False False True tp_awk_tool, bp_genbank2gff3, collapse_dataset, openbabel_remDuplicates, ctb_np-likeness-calculator, ctb_simsearch, Remove beginning1, antismash, ctb_chemfp_mol2fps, edu.tamu.cpt.gff3.customGbkToGff, ncbi_acc_download, ctb_silicos_qed, interactive_tool_jupyter_notebook UseGalaxy.eu 0 681 855 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 jbrowse, iframe, create_or_update, list_organism, create_account UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2859955 7137749 5.100000 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 annotation, Sequence assembly validation, Sequence alignment, Sequence annotation, Gene prediction, Genome visualisation 2025-03-17 2025-06-20 4 True False False True omark, braker3, busco, gffread, rna_star, fasta-stats, jbrowse 0 1394 1721 1.866667 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 annotation, Sequence assembly validation, Sequence annotation, Gene prediction, Genome visualisation 2024-08-21 2025-06-04 8 True False False True omark, helixer, busco, gffread, jbrowse, jcvi_gff_stats 0 1243 1479 1.683333 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 Nucleic acid feature detection, Genome assembly, Protein feature detection, Genome visualisation, Structural variation detection, Multilocus sequence typing, Genome annotation, Scaffolding, Sequence motif recognition 2024-02-01 2024-10-15 6 True False True True upload1, tp_tail_tool, jbrowse, Grouping1, isescan, integron_finder, tbl2gff3, bakta, tp_replace_in_column, plasmidfinder UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main) 0 6578 8946 2.616667 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 3084956 7914258 2.333333 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 35116 63954 1.450000 0
Genome Annotation Creating an Official Gene Set https://training.galaxyproject.org//topics/genome-annotation/tutorials/official-gene-set/tutorial.html 2023-11-02 2024-02-29 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 43 49 1.500000 0
Genome Annotation Dataset construction for bacterial comparative genomics https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html Genomics, Microbiology Sequence database search, Data retrieval, Data handling 2025-03-14 2025-03-14 1 True False False False upload1, sort1, bg_uniq, Cut1, Remove beginning1, datasets_download_genome, cat1 UseGalaxy.fr UseGalaxy.cz 0 84 102 3.033333 0
Genome Annotation Bacterial genome quality control https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html Genomics, Microbiology Sequencing quality control, Sequence assembly validation, Validation, Genome comparison, Sequence composition calculation, Statistical calculation 2025-03-14 2025-03-14 1 True False False False upload1, checkm2, drep_dereplicate UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz 0 92 102 2.183333 0
Genome Annotation Bacterial pangenomics https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-pangenomics/tutorial.html Genomics, Microbiology Rarefaction, Essential dynamics, Genome annotation, Sequence assembly 2025-03-14 2025-03-14 1 True False False False upload1, ppanggolin_all, ppanggolin_msa UseGalaxy.eu, UseGalaxy.fr 0 93 107 0.900000 0
Genome Annotation Genome annotation with Funannotate https://training.galaxyproject.org//topics/genome-annotation/tutorials/funannotate/tutorial.html Gene and protein families Information extraction, Homology-based gene prediction, Protein feature detection, Genome visualisation, Formatting, Query and retrieval, Sequence assembly validation, Genome annotation, Sequence alignment, Sequence annotation, Fold recognition, Sequence motif recognition 2021-11-29 2025-06-10 26 True False True True picard_MergeSamFiles, busco, eggnog_mapper, rna_star, jbrowse, funannotate_predict, funannotate_annotate, aegean_parseval, interproscan, funannotate_compare UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org.au 0 10767 15231 1.950000 0
Genome Annotation Comparative gene analysis in unannotated genomes https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html Genomics, Gene and protein families, Sequence analysis, Phylogeny, Comparative genomics Database search, Sequence alignment analysis, Coding region prediction, Transcriptome assembly, Multiple sequence alignment, De-novo assembly, Phylogenetic tree generation 2022-09-08 2025-06-03 10 True False False True tab2fasta, tp_split_on_column, rbc_mafft, join1, collapse_dataset, rapidnj, Cut1, Add_a_column1, bg_diamond, cat1, bg_diamond_makedb, Filter1, gops_intersect_1, regexColumn1, bg_diamond_view, orfipy UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 1869 2620 3.033333 0
Genome Annotation Genome annotation with Maker (short) https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html Genome annotation, Sequence assembly validation, Sequence annotation, Genome visualisation 2021-01-12 2024-02-29 3 True False False True busco, maker, gffread, fasta-stats, jbrowse, maker_map_ids, jcvi_gff_stats UseGalaxy.be 0 4013 5631 2.916667 0
Genome Annotation Essential genes detection with Transposon insertion sequencing https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html Genomics, Microbiology, Sequence analysis, Mobile genetic elements Primer removal, Read pre-processing, Transposon prediction, Sequence trimming 2019-07-02 2024-03-18 12 True True False True cutadapt, transit_gumbel, bowtie_wrapper, __EXTRACT_DATASET__, deeptools_bam_coverage, Cut1, bg_find_subsequences, Add_a_column1, gff_to_prot, tp_easyjoin_tool, Filter1, tp_sort_header_tool UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.eu 0 3093269 7929187 4.066667 0
Genome Annotation Genome annotation with Maker https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html Ab-initio gene prediction, Operation, Homology-based gene prediction, Gene prediction, Genome visualisation, Genome annotation, Sequence assembly validation, Sequence annotation 2018-09-24 2024-02-29 14 True False False True busco, maker, gffread, fasta-stats, augustus_training, jbrowse, maker_map_ids, snap_training, jcvi_gff_stats UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.org.au 0 13837 24450 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, Information extraction, Homology-based gene prediction, Protein feature detection, Query and retrieval, Genome annotation, Fold recognition, Sequence motif recognition 2022-07-20 2025-06-03 12 True False False True bg_diamond, interproscan, ncbi_blastp_wrapper, eggnog_mapper UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 4309 5768 1.666667 0
Genome Annotation Refining Genome Annotations with Apollo (eukaryotes) https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo-euk/tutorial.html Genomics Genome visualisation 2022-08-22 2025-06-03 16 True False False False create_or_update, jbrowse, iframe UseGalaxy.no UseGalaxy.cz, UseGalaxy.eu 0 1462 2224 2.500000 0
Genome Annotation Long non-coding RNAs (lncRNAs) annotation with FEELnc https://training.galaxyproject.org//topics/genome-annotation/tutorials/lncrna/tutorial.html RNA-Seq analysis, Annotation, Classification, Sequence annotation, Transcriptome assembly 2022-09-23 2024-09-18 11 True False True True stringtie, tp_cat, gffread, feelnc, Extract_features1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 1912 2555 2.133333 0
Genome Annotation CRISPR screen analysis https://training.galaxyproject.org//topics/genome-annotation/tutorials/crispr-screen/tutorial.html Read pre-processing, Sequence composition calculation, Sequence trimming, Sequencing quality control, Primer removal, Genetic variation analysis, Statistical calculation, Validation 2021-10-15 2024-08-08 12 True True True True mageck_mle, cutadapt, mageck_count, volcanoplot, multiqc, fastqc, tp_awk_tool, mageck_test UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2692925 6550043 4.166667 0
Variant Analysis Microbial Variant Calling https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Phylogenetic tree visualisation, Variant calling, Genome visualisation, Phylogenetic tree generation 2018-02-26 2025-03-19 24 True False False True jbrowse, snippy UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 15187 24237 2.033333 0
Visualisation Genomic Data Visualisation with JBrowse https://training.galaxyproject.org//topics/visualisation/tutorials/jbrowse/tutorial.html Genome visualisation 2020-01-10 2024-10-15 17 True True False False jbrowse Galaxy@AuBi, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz 0 3090114 7921111 4.633333 0
Imaging Using BioImage.IO models for image analysis in Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/process-image-bioimageio/tutorial.html Image annotation, Image analysis, Visualisation, Data handling 2025-04-09 2025-11-26 8 True False False True ip_overlay_images, ip_split_image, __EXTRACT_DATASET__, bioimage_inference, ip_binary_to_labelimage, image_math, ip_threshold UseGalaxy.eu 0 185 222 3.166667 0
Imaging Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/omero-suite/tutorial.html Image analysis 2024-12-04 2025-11-26 6 True False False False omero_get_id, omero_filter, omero_import, omero_roi_import, omero_get_value, omero_metadata_import 0 197 249 2.716667 0
Imaging Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/parameter-tuning/tutorial.html Image annotation, Image analysis, Visualisation, Data handling 2025-04-28 2025-11-26 3 True False False True tp_split_on_column, ip_segmetrics, collapse_dataset, ip_filter_standard, ip_histogram_equalization, param_value_from_file, ip_threshold UseGalaxy.eu UseGalaxy.cz 0 96 109 1.766667 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 annotation, Image analysis, Visualisation, Data handling 2025-03-20 2025-11-26 5 True False False True unzip, ip_overlay_images, ip_points_to_label, __EXTRACT_DATASET__, idr_download_by_ids, ip_binary_to_labelimage, ip_histogram_equalization, ip_spot_detection_2d UseGalaxy.cz, UseGalaxy.eu 0 191 236 1.266667 0
Imaging Object tracking using CellProfiler https://training.galaxyproject.org//topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html Parsing, Image analysis, Quantification 2021-03-17 2025-11-26 11 True False False True cp_overlay_outlines, unzip, cp_color_to_gray, cp_common, cp_measure_object_size_shape, cp_track_objects, cp_save_images, cp_cellprofiler, cp_identify_primary_objects, cp_measure_object_intensity, cp_tile, cp_export_to_spreadsheet UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 2199 2739 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 annotation, Visualisation, Image analysis, Data handling 2025-08-11 2025-11-26 3 True False False True ip_2d_feature_extraction, ip_points_to_label, ip_split_image, __EXTRACT_DATASET__, graphicsmagick_image_convert, interactive_tool_qupath, ip_imageinfo UseGalaxy.eu 0 257 308 1.016667 0
Imaging Nucleoli segmentation and feature extraction using CellProfiler https://training.galaxyproject.org//topics/imaging/tutorials/tutorial-CP/tutorial.html Parsing, Image analysis, Quantification 2020-07-01 2025-11-26 12 True True False True cp_measure_granularity, cp_mask_image, cp_gray_to_color, cp_common, cp_identify_primary_objects, cp_measure_object_intensity, cp_export_to_spreadsheet, cp_convert_objects_to_image, cp_image_math, cp_save_images, cp_measure_image_area_occupied, cp_measure_image_quality, cp_relate_objects, cp_measure_object_size_shape, cp_cellprofiler, cp_display_data_on_image, cp_measure_image_intensity, idr_download_by_ids, cp_enhance_or_suppress_features, cp_measure_texture UseGalaxy.be, UseGalaxy.eu Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 3088904 7920036 3.550000 0
Imaging Voronoi segmentation https://training.galaxyproject.org//topics/imaging/tutorials/voronoi-segmentation/tutorial.html Image annotation, Image analysis, Visualisation, Data handling 2025-05-13 2025-11-26 7 True False False True unzip, ip_overlay_images, ip_2d_feature_extraction, colorize_labels, ip_count_objects, voronoi_tessellation, repeat_channels, ip_binary_to_labelimage, ip_filter_standard, ip_imageinfo, image_math, ip_convertimage, ip_threshold UseGalaxy.eu 0 289 430 3.516667 0
Imaging Tracking of mitochondria and capturing mitoflashes https://training.galaxyproject.org//topics/imaging/tutorials/detection-of-mitoflashes/tutorial.html Image analysis 2024-11-20 2025-11-26 5 True False False True ip_points_association_nn, ip_spot_detection_2d, ip_curve_fitting UseGalaxy.cz, UseGalaxy.eu 0 181 211 1.050000 0
Imaging Introduction to Image Analysis using Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/imaging-introduction/tutorial.html Image annotation, Image analysis, Visualisation, Data handling 2019-08-13 2025-11-26 17 True False False True unzip, ip_overlay_images, ip_count_objects, ip_binary_to_labelimage, ip_filter_standard, ip_imageinfo, ip_histogram_equalization, ip_threshold UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 2682 3743 1.716667 0
Imaging Training Custom YOLO Models for Segmentation of Bioimages https://training.galaxyproject.org//topics/imaging/tutorials/yolo-segmentation-training/tutorial.html Visualisation, Image annotation, Image analysis, Data handling 2025-07-25 2025-11-26 7 True False False True unzip, json2yolosegment, yolo_training, graphicsmagick_image_convert, interactive_tool_anylabeling, ip_histogram_equalization UseGalaxy.eu 0 235 293 1.150000 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 gate_finder, vitessce_spatial, unet_coreograph, celesta, mesmer, squidpy_spatial, ip_convertimage, palom, rename_tiff_channels, quantification, basic_illumination, scimap_phenotyping, scanpy_compute_graph, scimap_mcmicro_to_anndata, ashlar 0 1442 1936 1.800000 0
Imaging Analyse HeLa fluorescence siRNA screen https://training.galaxyproject.org//topics/imaging/tutorials/hela-screen-analysis/tutorial.html Image annotation, Visualisation, Image analysis, Data handling 2019-08-13 2025-11-26 15 True False False True unzip, ip_2d_feature_extraction, collapse_dataset, ip_2d_filter_segmentation_by_features, ip_binary_to_labelimage, ip_filter_standard, ip_threshold UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no 0 795 1022 1.950000 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 upload1, CONVERTER_interval_to_bed_0, tp_tail_tool, Cut1, Add_a_column1, Grouping1, get_flanks1, gops_intersect_1, tp_replace_in_column, tp_sort_header_tool UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no 0 20484 33680 3.300000 0
Introduction to Galaxy Analyses NGS data logistics https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html Sequence contamination filtering, Read mapping, Generation, Formatting, SNP detection, Genome indexing, Sequencing quality control, Sequence alignment, Data handling, Validation 2017-02-22 2025-07-24 38 True False True True samtools_stats, lofreq_viterbi, bwa, bwa_mem, snpEff_build_gb, picard_MarkDuplicates, snpeff_sars_cov_2, samtools_view, multiqc, collapse_dataset, fasterq_dump, lofreq_indelqual, snpEff, snpSift_extractFields, Filter1, fastp, bwa_mem2, lofreq_call UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au MISSISSIPPI, UseGalaxy.cz 0 20339 34691 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 upload1, ggplot2_point, Cut1, Remove beginning1, Grouping1, tp_sorted_uniq, csv_to_tabular, datamash_ops Galaxy@AuBi, UseGalaxy.eu, UseGalaxy.org (Main) MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2201 2930 4.033333 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_sort}}, {{version_remove_beginning}}, {{version_split}}, {{version_join}}, tabular_to_csv, {{version_select_first}}, upload1, {{version_datamash}}, {{version_cut_columns}}, Remove beginning1, Grouping1, cat1, Filter1, {{version_cat}}, regexColumn1, {{version_compute}}, tp_sort_header_tool, {{version_cut_advanced}}, {{version_replace_text_line}}, wc_gnu, {{version_filter}}, tp_cat, tp_split_on_column, {{version_unique}}, Show beginning1, tp_sorted_uniq, {{version_remove_columns_by_header}}, {{version_replace_text_column}}, Count1, join1, {{version_paste}}, Cut1, Add_a_column1, {{version_count}}, {{version_wc}}, datamash_ops 0 6063 8801 3.433333 0
Introduction to Galaxy Analyses Introduction to Genomics and Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-strands/tutorial.html 2017-10-18 2024-10-15 41 True False True True tp_cat, cat1, Filter1, gops_intersect_1, gene2exon1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au MISSISSIPPI 0 20274 31977 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 3085082 7914446 2.333333 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 3085082 7914446 2.333333 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 8139 11458 1.466667 0
Introduction to Galaxy Analyses Best Practices for Citing Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-cite/tutorial.html 2025-11-06 2025-11-06 1 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 40 43 0.083333 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 0 447 508 2.666667 0
Introduction to Galaxy Analyses A short introduction to Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-short/tutorial.html Sequencing quality control, Sequence composition calculation, Statistical calculation 2018-08-27 2025-11-17 43 True True True True cshl_fastq_quality_filter, fastqc UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@Pasteur, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 3139676 7999510 7.033333 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 upload1, ggplot2_point, Cut1, Remove beginning1, Grouping1, tp_sorted_uniq, csv_to_tabular, datamash_ops UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz 0 23478 37231 3.916667 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 upload1, comp1, tp_sort_header_tool, tp_head_tool, bedtools_intersectbed, datamash_ops UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.no 0 48840 78776 3.433333 0
Introduction to Galaxy Analyses Very Short Introductions: QC https://training.galaxyproject.org//topics/introduction/tutorials/vsi_qc/tutorial.html Sequence contamination filtering, Sequencing quality control, Validation 2024-03-26 2024-06-25 4 True False False False multiqc, fastp Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 329 396 2.833333 0
Materials Science Finding the muon stopping site with pymuon-suite in Galaxy https://training.galaxyproject.org//topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.html 2024-01-22 2024-06-14 2 True False True True pm_muairss_read, pm_uep_opt UseGalaxy.cz, UseGalaxy.eu 0 274 355 1.866667 0
Metabolomics Mass spectrometry: LC-MS analysis https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms/tutorial.html Chromatographic alignment, Peak detection, Label-free quantification, Data filtering, Chromatogram visualisation, Mass spectrum visualisation, Validation 2019-07-02 2025-09-21 13 True False False True abims_xcms_xcmsSet, generic_filter, xcms_plot_chromatogram, abims_CAMERA_annotateDiffreport, abims_xcms_fillPeaks, abims_xcms_retcor, Univariate, xcms_merge, msnbase_readmsdata, wsdl_hmdb, quality_metrics, xcms_export_samplemetadata, abims_xcms_group, Batch_correction UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 12796 20845 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 Clustering, Peak detection, Standardisation and normalisation, Data filtering, Correlation, Chromatographic alignment, Filtering, Spectral library search, Format validation, Label-free quantification, Formatting, Chromatogram visualisation, Mass spectrum visualisation, Validation, Imputation 2023-05-08 2023-11-09 5 True False False True abims_xcms_xcmsSet, riassigner, waveica, ramclustr_define_experiment, ramclustr, msconvert, abims_xcms_retcor, matchms_similarity, matchms_filtering, xcms_merge, msnbase_readmsdata, matchms_formatter, abims_xcms_fillPeaks, abims_xcms_group UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au 0 2725 3500 1.500000 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_mz_images, cardinal_filtering, cardinal_data_exporter, Filter1, cardinal_spectra_plots UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 3028 4295 1.733333 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 openbabel_compound_convert, split_file_to_collection, tp_cat, qcxms_neutral_run, qcxms_getres, ctb_im_conformers, qcxms_production_run, xtb_molecular_optimization, tp_cut_tool, __FILTER_FAILED_DATASETS__, param_value_from_file UseGalaxy.eu UseGalaxy.org.au 0 951378 2025549 2.833333 0
Metabolomics Molecular formula assignment and mass recalibration with MFAssignR package https://training.galaxyproject.org//topics/metabolomics/tutorials/mfassignr/tutorial.html Visualisation, Mass spectra calibration, Deisotoping, Annotation 2025-05-19 2025-05-19 1 True False False True mfassignr_recallist, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_findRecalSeries, mfassignr_isofiltr, mfassignr_snplot, mfassignr_histnoise, mfassignr_kmdnoise 0 126 148 1.816667 0
Metabolomics Mass spectrometry imaging: Finding differential analytes https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html 2019-04-13 2023-11-09 9 True False False True Summary_Statistics1, cardinal_classification, maldi_quant_peak_detection, cardinal_segmentations, cardinal_quality_report, cardinal_combine, cardinal_mz_images, join_files_on_column_fuzzy, cardinal_preprocessing, Filter1, maldi_quant_preprocessing, Grep1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 1985 2838 1.816667 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 3085082 7914447 2.333333 0
Metabolomics Mass spectrometry: LC-MS preprocessing with XCMS https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html Chromatographic alignment, Peak detection, Label-free quantification, Data filtering, Chromatogram visualisation, Mass spectrum visualisation, Validation 2020-02-04 2024-10-15 14 True True False False abims_xcms_xcmsSet, xcms_plot_chromatogram, abims_CAMERA_annotateDiffreport, abims_xcms_summary, abims_xcms_fillPeaks, abims_xcms_retcor, idchoice, intens_check, xcms_merge, msnbase_readmsdata, xcms_export_samplemetadata, abims_xcms_group UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 3091218 7924074 4.616667 0
Metabolomics Mass spectrometry: GC-MS analysis with the metaMS package https://training.galaxyproject.org//topics/metabolomics/tutorials/gcms/tutorial.html Chromatographic alignment, Peak detection, Label-free quantification, Data filtering, Chromatogram visualisation, Mass spectrum visualisation, Validation 2021-09-22 2025-10-01 8 True False False False abims_xcms_xcmsSet, metams_runGC, xcms_plot_chromatogram, abims_xcms_fillPeaks, xcms_merge, msnbase_readmsdata, xcms_export_samplemetadata, abims_xcms_group UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.no 0 1610 2544 1.650000 0
Metabolomics Mass spectrometry: LC-MS data processing https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html 2021-12-14 2024-10-15 8 True False False False generic_filter, Multivariate, normalization, intens_check, quality_metrics, Batch_correction UseGalaxy.fr UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2877 3870 1.900000 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 3085082 7914447 2.333333 0
Microbiome Analyses of metagenomics data - The global picture https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control, Sequence read processing, DNA barcoding, Sequence clustering 2017-06-22 2024-08-09 4 True False False True mothur_align_seqs, mothur_merge_files, krona-text, mothur_classify_otu, mothur_classify_seqs, taxonomy_krona_chart, mothur_count_seqs, mothur_pre_cluster, mothur_make_shared, metaphlan2, mothur_summary_seqs, mothur_filter_seqs, mothur_unique_seqs, mothur_screen_seqs, mothur_make_biom, metaphlan2krona, mothur_make_group, humann2_renorm_table, mothur_cluster_split, humann2_regroup_table, humann2 UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 8775 11972 2.683333 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 Antimicrobial resistance prediction, Scatter plot plotting, Mapping assembly, Genome assembly, Sequence analysis, De-novo assembly, Aggregation, Box-Whisker plot plotting, Sequence assembly visualisation, Pairwise sequence alignment 2019-06-25 2024-06-14 4 True False True True minimap2, unicycler, staramr_search, PlasFlow, nanoplot, bandage_image, miniasm, gfa_to_fa, racon UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 3257 4555 3.000000 0
Microbiome MGnify v5.0 Amplicon Pipeline https://training.galaxyproject.org//topics/microbiome/tutorials/mgnify-amplicon/tutorial.html Metagenomics, Taxonomy, Sequence analysis Comparison, Sequence trimming, Alignment, Nucleic acid design, k-mer counting, Mapping, Sequence contamination filtering, Visualisation, Nucleic acid feature detection, Read pre-processing, Sequence composition calculation, Formatting, Sequencing quality control, Analysis, DNA barcoding, Sequence feature detection, Statistical calculation, Validation 2025-07-30 2025-11-18 3 True False False True CONVERTER_uncompressed_to_gz, bedtools_getfastabed, filter_tabular, collection_column_join, mapseq, cmsearch_deoverlap, fastqc, cshl_fasta_formatter, prinseq, __MERGE_COLLECTION__, mgnify_seqprep, infernal_cmsearch, ampvis2_load, lotus2, taxonomy_krona_chart, collapse_dataset, Grouping1, __FILTER_FROM_FILE__, gops_concat_1, tp_awk_tool, CONVERTER_gz_to_uncompressed, ampvis2_heatmap, trimmomatic, wc_gnu, bedtools_maskfastabed, fastq_dl, seqprep, tp_find_and_replace, fastq_to_fasta_python, collection_element_identifiers, biom_convert, multiqc, __FILTER_EMPTY_DATASETS__, fastq_filter, fastp, Add_a_column1, __UNZIP_COLLECTION__, param_value_from_file, query_tabular 0 184 246 4.716667 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 Base-calling, Sequence alignment analysis, Mapping assembly, Taxonomic classification, Genome assembly, Cross-assembly, De-novo assembly, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Multilocus sequence typing, Aggregation, Mapping, Sequence assembly, Box-Whisker plot plotting, Variant calling, Sequence assembly visualisation, Pairwise sequence alignment, Phylogenetic tree generation, Sequence contamination filtering, Phylogenetic tree reconstruction, Antimicrobial resistance prediction, Visualisation, Scatter plot plotting, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Multiple sequence alignment, Sequence composition calculation, Sequencing quality control, Statistical calculation, Data handling, Validation 2023-01-26 2025-11-18 12 True False True True split_file_to_collection, flye, bcftools_norm, bedtools_getfastabed, fasta2tab, clair3, collection_column_join, fastqc, samtools_depth, Grep1, newick_display, fasttree, fasta_merge_files_and_filter_unique_sequences, abricate, samtools_coverage, tp_multijoin_tool, collapse_dataset, taxonomy_krona_chart, Remove beginning1, Grouping1, bcftools_consensus, porechop, ggplot2_heatmap, tp_cut_tool, samtools_fastx, __FILTER_FAILED_DATASETS__, compose_text_param, regexColumn1, CONVERTER_gz_to_uncompressed, minimap2, barchart_gnuplot, tp_split_on_column, Paste1, kraken2, medaka_consensus_pipeline, tp_find_and_replace, collection_element_identifiers, tp_sorted_uniq, multiqc, krakentools_extract_kraken_reads, snpSift_filter, clustalw, __BUILD_LIST__, tab2fasta, __FILTER_EMPTY_DATASETS__, Count1, tp_head_tool, fastp, krakentools_kreport2krona, mlst, Cut1, Add_a_column1, regex1, bamtools_split_mapped, bandage_image, nanoplot, table_compute, snpSift_extractFields, param_value_from_file, tp_replace_in_column, add_line_to_file UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org.au 0 4828 7227 3.366667 0
Microbiome Clinical Metaproteomics 2: Discovery https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html Principal component plotting, Filtering, Visualisation, Protein quantification, Clustering, Standardisation and normalisation, Formatting, Heat map generation, Statistical calculation, Imputation 2025-12-07 2025-12-07 0 True False True True tp_cat, ident_params, search_gui, fasta_merge_files_and_filter_unique_sequences, fasta2tab, filter_tabular, Cut1, Remove beginning1, maxquant, Grouping1, msconvert, peptide_shaker, dbbuilder, fasta_cli, Filter1, Grep1, query_tabular 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 Principal component plotting, Visualisation, Protein quantification, Clustering, Standardisation and normalisation, Heat map generation, Statistical calculation, Imputation 2025-12-07 2025-12-07 0 True False True True Grouping1, Cut1, Grep1, maxquant 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.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, GalaxyTrakr 0 6769 8144 1.233333 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, Genome annotation, Taxonomic classification, Aggregation, Statistical calculation 2023-05-03 2025-04-24 6 True False True True interactive_tool_phinch, kraken2, krakentools_kreport2krona, taxonomy_krona_chart, est_abundance, __UNZIP_COLLECTION__, metaphlan, kraken_biom, interactive_tool_pavian UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 12235 16305 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, Read mapping, Genome assembly, Sequence trimming, Sequence file editing, Sequence assembly validation, Sequence assembly visualisation, Variant calling, Statistical calculation, Sequence contamination filtering, Visualisation, Read pre-processing, Sequence composition calculation, Formatting, Sequencing quality control, Primer removal, Local alignment, Data handling 2022-12-05 2025-06-16 6 True False True True coverm_contig, random_lines1, bamtools, tp_cat, cutadapt, ngsutils_bam_filter, quast, megahit, bg_uniq, filter_tabular, bandage_image, collection_column_join, megahit_contig2fastg, metaspades, bowtie2, fastqc, bandage_info, seqtk_subseq UseGalaxy.cz, UseGalaxy.eu 0 4399 6128 3.000000 0
Microbiome Building an amplicon sequence variant (ASV) table from 16S data using DADA2 https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Visualisation, Analysis, DNA barcoding, Deposition, Variant calling 2024-06-05 2025-07-03 11 True False True True phyloseq_from_dada2, dada2_learnErrors, dada2_dada, dada2_makeSequenceTable, dada2_removeBimeraDenovo, dada2_seqCounts, Grouping1, __SORTLIST__, cat1, dada2_mergePairs, dada2_filterAndTrim, dada2_plotQualityProfile, dada2_assignTaxonomyAddspecies, collection_element_identifiers, interactive_tool_phyloseq, tp_head_tool, Add_a_column1, __UNZIP_COLLECTION__, tp_replace_in_line, tp_replace_in_column UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 7044 9924 2.333333 0
Microbiome Binning of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html Metagenomics, Sequence assembly Read mapping, Genome comparison, Sequence composition calculation, Sequencing quality control, Sequence assembly validation, Genome annotation, Read binning, Sequence assembly, Sequence clustering, Statistical calculation, Validation 2023-12-05 2025-12-02 7 True False True True concoct_coverage_table, checkm_lineage_wf, samtools_sort, concoct_extract_fasta_bins, drep_dereplicate, binette, concoct, maxbin2, concoct_merge_cut_up_clustering, bowtie2, Fasta_to_Contig2Bin, semibin, das_tool, concoct_cut_up_fasta, metabat2_jgi_summarize_bam_contig_depths, __BUILD_LIST__, metabat2 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.org (Main), UseGalaxy.org.au 0 5593 6834 1.466667 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 0 723 915 1.666667 0
Microbiome Clinical Metaproteomics 5: Data Interpretation https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-5-data-interpretation/tutorial.html Visualisation, Prediction and recognition 2025-12-07 2025-12-07 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 Statistical calculation, Sequence contamination filtering, Sequencing quality control, Visualisation, Taxonomic classification, Sequence composition calculation, Validation 2020-11-24 2024-07-31 5 True False False True kraken2, taxonomy_krona_chart, Remove beginning1, multiqc, datamash_reverse, porechop, fastqc, tp_replace_in_line, fastp UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr 0 8182 11295 2.616667 0
Microbiome Clinical Metaproteomics 3: Verification https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html 2025-12-07 2025-12-07 0 True False True True uniprotxml_downloader, pepquery2, tp_cat, fasta_merge_files_and_filter_unique_sequences, collapse_dataset, Cut1, Remove beginning1, Grouping1, Filter1, dbbuilder, query_tabular UseGalaxy.cz, UseGalaxy.eu UseGalaxy.org (Main), UseGalaxy.org.au 0 0 0 0.000000 0
Microbiome Identification of the micro-organisms in a beer using Nanopore sequencing https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Sequence contamination filtering, Sequencing quality control, Visualisation, Taxonomic classification, Aggregation, Sequence composition calculation, Statistical calculation 2022-09-29 2024-11-29 5 True False True True kraken2, krakentools_kreport2krona, taxonomy_krona_chart, porechop, fastqc, Filter1, fastp UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2666 3886 2.866667 0
Microbiome Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data https://training.galaxyproject.org//topics/microbiome/tutorials/metaplasmidome_query/tutorial.html Genomics, Microbiology, Sequence analysis, Mobile genetic elements Visualisation, Pairwise sequence alignment 2025-01-07 2025-01-07 1 True False False True minimap2, tab2fasta, ggplot2_histogram, histogram_rpy, MQoutputfilter, join1, sort1, tp_tail_tool, Cut1, Add_a_column1, CONVERTER_fasta_to_tabular, Grouping1, cat1, tp_sorted_uniq, count_gff_features, add_column_headers, Filter1, tp_replace_in_column UseGalaxy.fr 0 301 345 0.850000 0
Microbiome Metatranscriptomics analysis using microbiome RNA-seq data (short) https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis Sequence alignment analysis, Phylogenetic inference, Taxonomic classification, Phylogenetic analysis, Phylogenetic tree editing, Sequence trimming, Sequence similarity search, Sequence comparison, Visualisation, Read pre-processing, Sequence composition calculation, Species frequency estimation, Sequencing quality control, Primer removal, Conversion, Statistical calculation, Validation, Phylogenetic tree visualisation 2020-02-13 2025-06-16 6 True False True True humann_renorm_table, export2graphlan, metaphlan, fastqc, humann_split_stratified_table, fastq_paired_end_interlacer, Grep1, combine_metaphlan2_humann2, taxonomy_krona_chart, tp_sort_header_tool, cutadapt, tp_find_and_replace, multiqc, graphlan, graphlan_annotate, bg_sortmerna, Cut1, humann_regroup_table, humann, humann_unpack_pathways, humann_rename_table UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.no 0 785 1024 2.433333 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 alignment analysis, Phylogenetic inference, Taxonomic classification, Phylogenetic analysis, Phylogenetic tree editing, Sequence trimming, Sequence similarity search, Aggregation, Sequence comparison, Visualisation, Read pre-processing, Sequence composition calculation, Species frequency estimation, Sequencing quality control, Primer removal, Conversion, Statistical calculation, Validation, Phylogenetic tree visualisation 2019-11-21 2025-06-16 6 True True True True humann_renorm_table, export2graphlan, metaphlan, fastqc, humann_split_stratified_table, fastq_paired_end_interlacer, Grep1, taxonomy_krona_chart, Grouping1, tp_sort_header_tool, combine_metaphlan_humann, cutadapt, tp_find_and_replace, multiqc, graphlan, graphlan_annotate, bg_sortmerna, Cut1, humann_regroup_table, humann, humann_unpack_pathways, humann_rename_table UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.eu 0 3091750 7923137 4.300000 0
Microbiome Clinical Metaproteomics 1: Database-Generation https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-1-database-generation/tutorial.html Target-Decoy, Protein identification, de Novo sequencing, Expression analysis, Tag-based peptide identification 2025-12-07 2025-12-07 0 True False True True fasta_merge_files_and_filter_unique_sequences, metanovo, uniprotxml_downloader, dbbuilder UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.org (Main) 0 0 0 0.000000 0
Microbiome Indexing and profiling microbes with MetaSBT https://training.galaxyproject.org//topics/microbiome/tutorials/metasbt/tutorial.html Microbial ecology, Taxonomy 2025-08-25 2025-08-25 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 52 60 2.516667 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 0 412 664 3.150000 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 0 583 896 2.733333 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, Visualisation, Taxonomic classification, Phylogenetic analysis, Phylogenetic tree analysis, Sequencing quality control, Sequence read processing, DNA barcoding, Sequence clustering, Phylogenetic tree generation 2019-05-13 2024-06-14 5 True False True True mothur_count_groups, mothur_summary_single, XY_Plot_1, mothur_remove_lineage, newick_display, mothur_classify_otu, mothur_classify_seqs, collapse_dataset, mothur_count_seqs, mothur_pre_cluster, mothur_make_shared, mothur_remove_seqs, mothur_summary_seqs, mothur_filter_seqs, mothur_unique_seqs, mothur_remove_groups, mothur_sub_sample, mothur_chimera_vsearch, mothur_cluster, mothur_screen_seqs, mothur_dist_seqs, mothur_dist_shared, mothur_heatmap_sim, mothur_tree_shared, mothur_rarefaction_single, mothur_venn, mothur_cluster_split UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.fr 0 5460 9209 4.583333 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, Visualisation, Taxonomic classification, Phylogenetic analysis, Phylogenetic tree analysis, Sequencing quality control, Sequence read processing, DNA barcoding, Sequence clustering, Phylogenetic tree generation 2017-02-12 2024-03-14 4 True False False True mothur_count_groups, mothur_summary_single, XY_Plot_1, mothur_make_contigs, mothur_align_seqs, mothur_remove_lineage, mothur_seq_error, newick_display, mothur_classify_otu, mothur_classify_seqs, taxonomy_krona_chart, mothur_count_seqs, mothur_pre_cluster, mothur_make_shared, mothur_remove_seqs, mothur_summary_seqs, mothur_filter_seqs, mothur_unique_seqs, mothur_remove_groups, mothur_sub_sample, mothur_chimera_vsearch, mothur_cluster, mothur_screen_seqs, mothur_make_biom, mothur_dist_seqs, mothur_taxonomy_to_krona, mothur_dist_shared, mothur_heatmap_sim, mothur_tree_shared, mothur_rarefaction_single, mothur_venn, mothur_cluster_split, mothur_get_groups UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 12182 17924 2.783333 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, Read mapping, Generation, Sequence contamination filtering, Sequence analysis, Multiple sequence alignment, Genome indexing, Sequencing quality control, Sequence alignment, Primer removal, Local alignment, Global alignment 2023-05-15 2024-03-20 4 True False False True fasta_regex_finder, fatovcf, mimodd_info, Grep1, upload1, qualimap_bamqc, __ZIP_COLLECTION__, ivar_trim, compose_text_param, ivar_consensus, rbc_mafft, samtools_merge, __APPLY_RULES__, bwa_mem, param_value_from_file, Cut1, Add_a_column1, samtools_view, EMBOSS: maskseq51, fasta_compute_length, fastp, datamash_ops UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org (Main) 0 1053 1247 2.316667 0
Variant Analysis M. tuberculosis Variant Analysis https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease Sequence alignment analysis, Sequence contamination filtering, Antimicrobial resistance prediction, Taxonomic classification, Sequence analysis, Genome visualisation, Sequence composition calculation, Sequencing quality control, Sequence alignment, Phylogenetic tree generation, Validation, Variant calling, Local alignment, Global alignment, Statistical calculation, Phylogenetic tree visualisation 2020-07-25 2025-11-18 31 True False True True EMBOSS: seqret84, samtools_stats, snippy, tb_profiler_profile, jbrowse, tp_sed_tool, EMBOSS:%20seqret84, fastqc, mosdepth, upload1, tb_variant_filter, qualimap_bamqc, bcftools_consensus, tp_awk_tool, kraken2, multiqc, jvarkit_wgscoverageplotter, __FLATTEN__, tbvcfreport, fastp 0 7526 11623 3.000000 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, Read mapping, Generation, Sequence contamination filtering, Sequence analysis, Phylogenetic analysis, Data retrieval, Multiple sequence alignment, De-novo assembly, Sequence file editing, Genome indexing, Sequencing quality control, Sequence alignment, Primer removal, Data handling 2022-11-21 2024-10-04 10 True False False False upload1, ivar_consensus, __RELABEL_FROM_FILE__, qualimap_bamqc, seqtk_subseq, collapse_dataset, bwa_mem, Show beginning1, tp_find_and_replace, vapor, bamtools_split_ref, samtools_view, rbc_mafft, iqtree, fastp, Grep1 UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 2057 2992 3.000000 0
Transcriptomics Whole transcriptome analysis of Arabidopsis thaliana https://training.galaxyproject.org//topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html RNA-Seq quantification, Read mapping, Visualisation, Read pre-processing, Differential gene expression analysis, Sequence composition calculation, Sequence trimming, Gene expression analysis, Sequencing quality control, RNA-Seq analysis, Primer removal, Validation 2021-04-08 2025-08-10 18 True True True True __MERGE_COLLECTION__, trim_galore, filter_by_fasta_ids, sort1, rbc_mirdeep2_quantifier, Cut1, deseq2, multiqc, cat1, targetfinder, rbc_mirdeep2_mapper, Filter1, sample_seqs, falco, salmon UseGalaxy.cz 0 2945848 7411472 4.866667 0
Sequence analysis Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants https://training.galaxyproject.org//topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html Phylogenetic inference (from molecular sequences), Sequence analysis, Phylogenetic analysis, Multiple sequence alignment, Phylogenetic tree editing 2025-03-26 2025-04-27 2 True False True True ete_treeviewer, rbc_mafft, filter_by_fasta_ids, quicktree, Cut1, Remove beginning1, trimal, iqtree, Filter1, tapscan_classify UseGalaxy.eu 0 250 305 1.033333 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 bg_diamond, ncbi_blastp_wrapper, ncbi_blastx_wrapper Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 1678 2120 3.050000 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_cluster_reduce_dimension, anndata_manipulate, scanpy_plot, scanpy_filter, scanpy_normalize, scanpy_inspect, scanpy_remove_confounders UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2766 3456 1.616667 0
Proteomics Statistical analysis of DIA data https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.html Spectrum calculation, Differential protein expression profiling, Tag-based peptide identification 2020-12-02 2023-11-09 9 True False False True Filter1, histogram_rpy, msstats, Grep1 UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.org.au 0 1347 1882 2.583333 0
Proteomics Neoantigen 5b: IEDB binding Validated Neopeptides https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-hla-binding-novel-peptides/tutorial.html 2025-01-14 2025-12-03 5 True False False False iedb_api, table_compute, fasta_to_tabular, Filter1, query_tabular 0 63 66 0.533333 0
Proteomics Proteogenomics 2: Database Search https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html Conversion, Peptide database search 2018-11-20 2025-05-08 24 True False True True mz_to_sqlite, tab2fasta, ident_params, search_gui, peptide_shaker, query_tabular UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 1546 2294 4.716667 0
Proteomics Library Generation for DIA Analysis https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html Principal component plotting, Visualisation, Protein quantification, Clustering, Standardisation and normalisation, Heat map generation, Statistical calculation, Imputation 2020-12-02 2025-06-02 12 True False False True diapysef, OpenSwathAssayGenerator, OpenSwathDecoyGenerator, TargetedFileConverter, maxquant, Filter1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 4605 6022 1.366667 0
Proteomics Proteogenomics 3: Novel peptide analysis https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.html 2018-11-20 2025-05-15 20 True False True True ncbi_blastp_wrapper, peptide_genomic_coordinate, pep_pointer, query_tabular UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.no 0 1686 2430 2.583333 0
Proteomics metaQuantome 3: Taxonomy https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy Quantification, Heat map generation, Indexing, Filtering, Visualisation, Differential protein expression analysis, Principal component visualisation, Statistical inference, Query and retrieval, Functional clustering 2020-10-29 2024-03-15 14 True False False True metaquantome_filter, metaquantome_viz, metaquantome_sample, metaquantome_expand, metaquantome_db, metaquantome_stat UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 448 586 2.250000 0
Proteomics Neoantigen 1a: Fusion-Database-Generation https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-fusion-database-generation/tutorial.html Sequence alignment 2025-01-14 2025-12-03 4 True False False False CONVERTER_gz_to_uncompressed, tab2fasta, rna_star, arriba_get_filters, arriba, regex1, tp_awk_tool, query_tabular UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 156 185 1.166667 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 fasta_merge_files_and_filter_unique_sequences, fragpipe_manifest_generator, collapse_dataset, Remove beginning1, validate_fasta_database, fragpipe, Grep1, query_tabular UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 190 220 1.233333 0
Proteomics Clinical Metaproteomics 2: Discovery https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html Principal component plotting, Filtering, Visualisation, Protein quantification, Clustering, Standardisation and normalisation, Formatting, Heat map generation, Statistical calculation, Imputation 2024-02-06 2025-08-10 5 True False True True tp_cat, ident_params, search_gui, fasta_merge_files_and_filter_unique_sequences, fasta2tab, filter_tabular, Cut1, Remove beginning1, maxquant, Grouping1, msconvert, peptide_shaker, dbbuilder, fasta_cli, Filter1, Grep1, query_tabular UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 350 464 6.283333 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 PeptideIndexer, ConsensusID, IDConflictResolver, IDFilter, MSGFPlusAdapter, MzTabExporter, FeatureFinderMultiplex, FalseDiscoveryRate, FileMerger, IDMerger, FileFilter, HighResPrecursorMassCorrector, IDMapper 0 869 1194 1.416667 0
Proteomics Proteogenomics 1: Database Creation https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html RNA-Seq analysis, Sequence alignment, Sequence annotation, Transcriptome assembly, Variant calling, Statistical calculation 2018-11-20 2025-05-08 29 True False True True stringtie, tab2fasta, custom_pro_db, hisat2, fasta_merge_files_and_filter_unique_sequences, cat_multi_datasets, bed_to_protein_map, fasta2tab, gffcompare_to_bed, filter_tabular, sqlite_to_tabular, gffcompare, freebayes, regexColumn1, query_tabular, tp_replace_in_column, translate_bed UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 5884 9611 2.600000 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, optitype, tp_awk_tool, query_tabular UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 68 73 0.033333 0
Proteomics Clinical Metaproteomics 4: Quantitation https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.html Principal component plotting, Visualisation, Protein quantification, Clustering, Standardisation and normalisation, Heat map generation, Statistical calculation, Imputation 2024-02-06 2025-08-10 5 True False True True Grouping1, Cut1, Grep1, maxquant UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 182 248 2.750000 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_data_exporter, cardinal_quality_report, Grep1, tp_sort_header_tool UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2760 4256 1.683333 0
Proteomics Protein FASTA Database Handling https://training.galaxyproject.org//topics/proteomics/tutorials/database-handling/tutorial.html Proteomics 2017-02-14 2025-04-08 30 True False False True tab2fasta, addValue, fasta_merge_files_and_filter_unique_sequences, fasta2tab, DecoyDatabase, dbbuilder UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 4813 7641 2.166667 0
Proteomics Label-free data analysis using MaxQuant https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-label-free/tutorial.html Principal component plotting, Differential protein expression profiling, Visualisation, Protein quantification, Clustering, Standardisation and normalisation, Heat map generation, Spectrum calculation, Statistical calculation, Tag-based peptide identification, Imputation 2020-04-29 2025-05-21 14 True False False True msstats, Add_a_column1, Cut1, maxquant, Filter1, histogram_rpy, Grep1, tp_sort_header_tool UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.org.au 0 20023 29233 1.766667 0
Proteomics Machine Learning Modeling of Anticancer Peptides https://training.galaxyproject.org//topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.html 2021-01-22 2023-11-09 8 True False False True pdaug_basic_plots, pdaug_ml_models, pdaug_sequence_property_based_descriptors, pdaug_merge_dataframes, pdaug_addclasslabel UseGalaxy.be 0 1030 1532 2.200000 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 tab2fasta, column_regex_find_and_replace, pep_pointer, cut, Convert characters1, select, regexColumn1, query_tabular 0 81 96 1.183333 0
Proteomics Biomarker candidate identification https://training.galaxyproject.org//topics/proteomics/tutorials/biomarker_selection/tutorial.html 2019-06-13 2023-11-09 9 True False False True Jvenn, retrieve_from_hpa, IDconverter, MQoutputfilter, prot_features, rna_abbased_data, retr_pepatlas1, tp_cut_tool UseGalaxy.be, UseGalaxy.fr 0 1682 2282 2.483333 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 Principal component plotting, Differential protein expression profiling, Visualisation, Protein quantification, Clustering, Standardisation and normalisation, Heat map generation, Spectrum calculation, Statistical calculation, Tag-based peptide identification, Imputation 2021-02-17 2025-09-22 19 True False True True Summary_Statistics1, uniprot, msstats, ggplot2_heatmap2, fasta2tab, Cut1, maxquant, tp_easyjoin_tool, Filter1, tp_replace_in_column, Grep1, datamash_ops UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 8529 13712 2.650000 0
Proteomics Neoantigen 3: PepQuery2 Verification https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-peptide-verification/tutorial.html Filtering, Formatting 2025-01-14 2025-12-03 4 True False False False tab2fasta, msconvert, ncbi_blastp_wrapper, pepquery2, query_tabular UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 61 69 1.933333 0
Proteomics Annotating a protein list identified by LC-MS/MS experiments https://training.galaxyproject.org//topics/proteomics/tutorials/proteome_annotation/tutorial.html 2019-09-12 2024-06-14 11 True False True True Jvenn, cluter_profiler, IDconverter, retrieve_from_hpa, MQoutputfilter, reactome_analysis, rna_abbased_data UseGalaxy.be, UseGalaxy.fr 0 3090 4483 2.766667 0
Proteomics DIA Analysis using OpenSwathWorkflow https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html Filtering, Formatting 2020-12-02 2025-05-20 12 True False False True pyprophet_export, pyprophet_protein, msconvert, pyprophet_peptide, pyprophet_merge, pyprophet_score, OpenSwathWorkflow, Grep1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 3234 4602 2.533333 0
Proteomics EncyclopeDIA https://training.galaxyproject.org//topics/proteomics/tutorials/encyclopedia/tutorial.html Filtering, Formatting 2021-06-21 2025-05-19 12 True False True True msconvert, encyclopedia_searchtolib, encyclopedia_quantify UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 2002 2723 1.766667 0
Proteomics Peptide and Protein ID using SearchGUI and PeptideShaker https://training.galaxyproject.org//topics/proteomics/tutorials/protein-id-sg-ps/tutorial.html 2017-06-12 2025-04-08 28 True False False True search_gui, FileConverter, peptide_shaker, PeakPickerHiRes, Grep1 0 3158 5039 1.883333 0
Proteomics Peptide and Protein ID using OpenMS tools https://training.galaxyproject.org//topics/proteomics/tutorials/protein-id-oms/tutorial.html Filtering, Formatting 2017-10-16 2025-04-08 32 True False False True PeptideIndexer, ConsensusID, IDScoreSwitcher, FidoAdapter, IDFilter, MSGFPlusAdapter, FileInfo, FalseDiscoveryRate, msconvert, IDMerger, IDPosteriorErrorProbability, TextExporter, PeakPickerHiRes, Grep1, XTandemAdapter UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 3549 5957 2.883333 0
Proteomics Clinical Metaproteomics 5: Data Interpretation https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-5-data-interpretation/tutorial.html Visualisation, Prediction and recognition 2024-02-06 2025-08-10 4 True False True True unipept, msstatstmt, Grep1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 282 372 2.633333 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, Sequence alignment, Sequence annotation, Transcriptome assembly, Variant calling, Statistical calculation 2025-01-14 2025-12-03 6 True False False False CONVERTER_gz_to_uncompressed, stringtie, tab2fasta, custom_pro_db, column_regex_find_and_replace, fasta_merge_files_and_filter_unique_sequences, bed_to_protein_map, hisat2, fasta2tab, gffcompare_to_bed, sqlite_to_tabular, concatenate, gffcompare, freebayes, regexColumn1, translate_bed 0 88 98 0.433333 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 0 298 327 1.383333 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, peptide_shaker, query_tabular UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz 0 2916 4634 2.700000 0
Proteomics Clinical Metaproteomics 3: Verification https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html 2024-02-06 2025-08-10 7 True False True True uniprotxml_downloader, pepquery2, tp_cat, fasta_merge_files_and_filter_unique_sequences, collapse_dataset, Cut1, Remove beginning1, Grouping1, Filter1, dbbuilder, query_tabular UseGalaxy.cz, UseGalaxy.eu UseGalaxy.org (Main), UseGalaxy.org.au 0 207 273 3.700000 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 Summary_Statistics1, PeptideIndexer, IDConflictResolver, IDScoreSwitcher, FidoAdapter, FileInfo, TextExporter, FalseDiscoveryRate, tp_tail_tool, FeatureFinderMultiplex, IDPosteriorErrorProbability, ProteinQuantifier, IDMapper, MultiplexResolver, histogram_rpy, Grep1, XTandemAdapter UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 1366 1905 1.533333 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_basic_plots, pdaug_sequence_property_based_descriptors, pdaug_merge_dataframes, pdaug_tsvtofasta, pdaug_addclasslabel, pdaug_peptide_data_access, pdaug_peptide_sequence_analysis, pdaug_fishers_plot UseGalaxy.be 0 747 1012 2.316667 0
Proteomics MaxQuant and MSstats for the analysis of TMT data https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.html Principal component plotting, Visualisation, Protein quantification, Clustering, Standardisation and normalisation, Heat map generation, Statistical calculation, Imputation 2021-08-13 2025-01-08 11 True False False True msstatstmt, maxquant UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.org (Main) 0 4286 5722 1.633333 0
Proteomics Secretome Prediction https://training.galaxyproject.org//topics/proteomics/tutorials/secretome-prediction/tutorial.html 2017-04-13 2025-04-08 15 True False False True uniprot, comp1, bg_uniq, wolf_psort, term_id_vs_term_name, tp_sorted_uniq, Convert characters1, tp_easyjoin_tool, get_subontology_from, tp_cut_tool, Filter1, Grep1 0 652 971 1.466667 0
Proteomics metaQuantome 2: Function https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics Quantification, Heat map generation, Indexing, Filtering, Visualisation, Differential protein expression analysis, Principal component visualisation, Statistical inference, Query and retrieval, Functional clustering 2020-10-29 2024-03-15 14 True False False True metaquantome_filter, metaquantome_viz, metaquantome_sample, metaquantome_expand, metaquantome_db, metaquantome_stat UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 421 592 4.166667 0
Proteomics metaQuantome 1: Data creation https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Filtering, Visualisation, Label-free quantification, Prediction and recognition, Formatting 2020-10-16 2024-03-14 20 True False False True search_gui, unipept, Cut1, Remove beginning1, msconvert, regex1, peptide_shaker, tp_replace_in_line, Filter1, flashlfq, tp_replace_in_column, Grep1, query_tabular UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 892 1506 3.733333 0
Proteomics Single Cell Proteomics data analysis with bioconductor-scp https://training.galaxyproject.org//topics/proteomics/tutorials/bioconductor-scp/tutorial.html Visualisation, Expression analysis 2025-02-07 2025-02-10 2 True False False False Grouping1, bioconductor_scp UseGalaxy.eu, UseGalaxy.org.au 0 234 288 0.966667 0
Proteomics Clinical Metaproteomics 1: Database-Generation https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.html Target-Decoy, Protein identification, de Novo sequencing, Expression analysis, Tag-based peptide 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.org (Main) 0 593 893 3.866667 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 3085082 7914452 2.333333 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 7688 12403 0.900000 0
Sequence analysis Mapping https://training.galaxyproject.org//topics/sequence-analysis/tutorials/mapping/tutorial.html Mapping Sequence alignment analysis, Read mapping, Read pre-processing, Genome visualisation, Sequence composition calculation, Sequence trimming, Sequencing quality control, Primer removal, Statistical calculation, Data handling, Validation 2016-10-04 2025-03-31 43 True True True True samtools_stats, trim_galore, jbrowse, multiqc, fastqc, bowtie2, bamFilter UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 3150953 8024634 5.083333 0
Sequence analysis Clean and manage Sanger sequences from raw files to aligned consensus https://training.galaxyproject.org//topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html Visualisation, Taxonomic classification, Demultiplexing, Phylogenetic analysis, Sequence file editing, Sequencing quality control, Sequence read processing, DNA barcoding, Sequence clustering, Data handling 2024-01-08 2024-03-05 2 True False False True cshl_fastx_reverse_complement, fastq_to_tabular, mothur_merge_files, ab1_fastq_converter, filter_by_fasta_ids, __FILTER_FROM_FILE__, __SORTLIST__, unzip, seqtk_trimfq, collection_element_identifiers, qiime_align_seqs, mothur_degap_seqs, aligned_to_consensus, cshl_fastq_to_fasta, fastq_groomer, tab2fasta, ncbi_blastn_wrapper, regex1, seqtk_mergepe, fastq_masker_by_quality UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 3376 4225 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, Sequence alignment, PCR primer design, Sequence analysis, Multiple sequence alignment, Local alignment, Global alignment 2025-03-20 2025-11-20 3 True False False True split_file_to_collection, EMBOSS: degapseq20, rbc_mafft, ncbi_makeblastdb, varvamp, fasta_compute_length UseGalaxy.eu 0 614 711 1.000000 0
Sequence analysis Quality Control https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-control/tutorial.html Scatter plot plotting, Read pre-processing, Sequence composition calculation, Sequence trimming, Sequencing quality control, Primer removal, Box-Whisker plot plotting, Statistical calculation, Validation 2016-10-04 2025-03-29 48 True True True True cutadapt, fastqe, nanoplot, multiqc, fastqc, pycoqc UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr 0 3192486 8109620 5.350000 0
Sequence analysis Screening assembled genomes for contamination using NCBI FCS https://training.galaxyproject.org//topics/sequence-analysis/tutorials/ncbi-fcs/tutorial.html Sequence contamination filtering, Sequence assembly validation, Sequence trimming 2024-04-16 2024-04-16 2 True False False True ncbi_fcs_gx, ncbi_fcs_adaptor UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 1862 2526 2.300000 0
Sequence analysis Quality and contamination control in bacterial isolate using Illumina MiSeq Data https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Sequence contamination filtering, Read mapping, Visualisation, Taxonomic classification, Cross-assembly, Sequencing quality control, Expression analysis, Statistical calculation 2024-07-15 2025-03-20 4 True False True True upload1, kraken2, est_abundance, recentrifuge, fastp, falco UseGalaxy.eu, UseGalaxy.fr GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main) 0 1665 2226 2.783333 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_deconvolution, music_construct_eset UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 3985 5026 1.583333 0
Single Cell Generating a single cell matrix using Alevin https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin/tutorial.html RNA-Seq quantification, Gene expression analysis, Sequence composition calculation 2021-03-03 2025-11-18 25 True False True True _dropletBarcodePlot, anndata_inspect, _ensembl_gtf2gene_list, dropletutils_empty_drops, join1, Cut1, anndata_manipulate, _salmon_kallisto_mtx_to_10x, sceasy_convert, dropletutils_read_10x, alevin UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 3484 5283 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 Community profiling, Loading 2024-02-13 2025-03-11 4 True False False True anndata_inspect, datamash_transpose, dropletutils_read_10x, join1, dropletutils, tp_tail_tool, Cut1, fastq_to_tabular, monocle3_create, seurat_read10x, scanpy_filter_cells, sceasy_convert, tp_cut_tool, tabular_to_fastq, Filter1, anndata_ops, regexColumn1 UseGalaxy.org (Main) 0 2592 3074 1.283333 0
Single Cell Pre-processing of 10X Single-Cell RNA Datasets https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html Community profiling, Sequencing quality control, Sequence alignment, Loading, Validation 2019-09-11 2025-04-29 13 True False True True multiqc, dropletutils, rna_starsolo UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.fr, UseGalaxy.no 0 12616 16317 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, Sequencing quality control, Read summarisation, Sequence alignment, Sequence alignment analysis, Data handling, Validation 2019-02-22 2025-04-08 5 True True False True featurecounts, samtools_stats, rna_star, umi_tools_extract, umi_tools_count, __FLATTEN__, collection_column_join, multiqc, tp_sed_tool, bamFilter UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 3091508 7922819 4.600000 0
Single Cell Pseudobulk Analysis with Decoupler and EdgeR https://training.galaxyproject.org//topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html Differential gene expression analysis, Expression profile clustering, Principal component visualisation 2025-02-12 2025-05-09 8 True False True True anndata_inspect, column_remove_by_header, volcanoplot, __EXTRACT_DATASET__, anndata_manipulate, decoupler_pseudobulk, scanpy_filter, tp_replace_in_line, edger, tp_replace_in_column, tp_awk_tool UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 1589 1827 0.633333 0
Single Cell Single-cell quality control with scater https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scater-qc/tutorial.html Sequencing quality control, Read pre-processing, Sequence visualisation 2019-10-23 2025-02-14 6 True False False True scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_create_qcmetric_ready_sce UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz 0 711 802 0.716667 0
Single Cell GO Enrichment Analysis on Single-Cell RNA-Seq Data https://training.galaxyproject.org//topics/single-cell/tutorials/GO-enrichment/tutorial.html Gene-set enrichment analysis 2024-09-17 2025-04-08 8 True True False True goenrichment, gprofiler_gost, Cut1, tp_split_on_column UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) 0 976745 2088421 2.700000 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 Read mapping, Generation, Visualisation, Differential gene expression analysis, Enrichment analysis, Principal component visualisation, Sequence composition calculation, Genome indexing, Expression profile clustering, Sequencing quality control, Sequence alignment, Mapping, Gene regulatory network analysis, Peak calling, Statistical calculation, Imputation 2023-04-24 2025-10-16 10 True False False True anndata_inspect, episcanpy_build_matrix, bedtools_sortbed, episcanpy_preprocess, sinto_barcode, bwa_mem, sinto_fragments, tp_sorted_uniq, macs2_callpeak, scanpy_plot, fastqc, falco UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 6025 7085 1.083333 0
Single Cell An introduction to scRNA-seq data analysis https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-intro/slides.html 2021-01-29 2025-02-13 8 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3052681 7800413 2.333333 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 0 619 855 3.616667 0
Single Cell Removing the effects of the cell cycle https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html Expression profile clustering, Differential gene expression analysis, Principal component visualisation 2023-01-25 2025-03-11 14 True False False True anndata_inspect, addValue, scanpy_cluster_reduce_dimension, sort1, scanpy_regress_variable, anndata_manipulate, cat1, scanpy_plot, table_compute, tp_easyjoin_tool, scanpy_inspect 0 2115 2488 0.766667 0
Single Cell Importing files from public atlases https://training.galaxyproject.org//topics/single-cell/tutorials/EBI-retrieval/tutorial.html 2023-11-14 2025-03-11 8 True False True True retrieve_scxa, tp_grep_tool, tp_find_and_replace, seurat_read10x, sceasy_convert, scanpy_read_10x, hca_matrix_downloader, regexColumn1, anndata_ops 0 583 768 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 Read mapping, Generation, Essential dynamics, Differential gene expression analysis, Principal component visualisation, Genome indexing, Dimensionality reduction, Gene expression profiling, Sequence alignment, Expression profile clustering 2024-07-11 2025-07-02 5 True False False True anndata_inspect, snapatac2_preprocessing, replace_column_with_key_value_file, bwa_mem, snapatac2_clustering, Cut1, anndata_manipulate, snapatac2_peaks_and_motif, snapatac2_plotting, scanpy_plot, scanpy_filter, fasta_compute_length, anndata_ops, scanpy_normalize, scanpy_inspect 0 1573 1900 1.100000 0
Single Cell Clustering 3K PBMCs with Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html Expression profile clustering, Differential gene expression analysis, Principal component visualisation 2019-12-19 2025-04-29 16 True True True True anndata_inspect, anndata_import, scanpy_cluster_reduce_dimension, scanpy_remove_confounders, anndata_manipulate, scanpy_plot, scanpy_filter, scanpy_normalize, scanpy_inspect, datamash_ops UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.fr, UseGalaxy.no 0 3093180 7925989 4.333333 0
Single Cell Combining single cell datasets after pre-processing https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html 2022-09-08 2025-11-18 23 True False True True anndata_inspect, Cut1, anndata_manipulate, Paste1, tp_replace_in_column, anndata_ops UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org (Main) 0 2531 3548 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 3300 3761 0.950000 0
Single Cell Understanding Barcodes https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-umis/tutorial.html Sequencing quality control, Sequence composition calculation, Statistical calculation 2019-02-20 2025-02-14 11 True False True True umi_tools_extract, seq_filter_by_id, fastqc UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, UseGalaxy.no 0 6393 7955 1.233333 0
Single Cell Downstream Single-cell RNA analysis with RaceID https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-raceid/tutorial.html Expression profile clustering, Molecular dynamics, Expression analysis 2019-03-25 2025-02-14 7 True False False True datamash_transpose, raceid_clustering, raceid_filtnormconf, raceid_inspecttrajectory, tp_head_tool, raceid_trajectory, raceid_inspectclusters, tp_sed_tool, datamash_ops UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org.au 0 1091 1287 1.250000 0
Single Cell Comparing inferred cell compositions using MuSiC deconvolution https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music-4-compare/tutorial.html 2023-01-20 2025-02-13 10 True False False True music_compare UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 287 430 1.383333 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 3336 3959 1.500000 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_filter_genes, scanpy_plot_embed, anndata_manipulate, scanpy_run_umap, scanpy_compute_graph, scanpy_find_cluster, retrieve_scxa, scanpy_filter, interactive_tool_cellxgene_vip, scanpy_filter_cells, scanpy_normalise_data, scanpy_normalize, scanpy_scale_data, anndata_inspect, scanpy_cluster_reduce_dimension, join1, Cut1, scanpy_plot, scanpy_find_markers, scanpy_run_tsne, scanpy_find_variable_genes, anndata_ops, scanpy_inspect, scanpy_run_pca 0 5449 8576 2.683333 0
Single Cell Clustering 3K PBMCs with Seurat https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-seurat-pbmc3k/tutorial.html 2025-01-23 2025-05-09 5 True False True True seurat_data, Cut1, seurat_plot, seurat_clustering, seurat_reduce_dimension, seurat_preprocessing, Filter1, csv_to_tabular, seurat_create MISSISSIPPI, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 1333 1602 1.166667 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_run_umap, retrieve_scxa, seurat_normalise_data, seurat_find_variable_genes, seurat_find_neighbours, seurat_scale_data, seurat_plot, seurat_find_markers, seurat_read10x, seurat_run_pca, seurat_filter_cells, seurat_find_clusters UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 2015 2452 1.400000 0
Single Cell Scanpy Parameter Iterator https://training.galaxyproject.org//topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.html 2023-07-19 2025-02-13 8 True False False True scanpy_find_cluster, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_run_tsne, scanpy_run_umap, scanpy_compute_graph UseGalaxy.org (Main), UseGalaxy.org.au 0 292 326 1.050000 0
Single Cell Converting NCBI Data to the AnnData Format https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html 2023-12-13 2025-03-11 7 True False True True unzip, anndata_inspect, anndata_import, Cut1, anndata_manipulate, scanpy_filter_cells, Paste1, tp_replace_in_column, anndata_ops UseGalaxy.org.au UseGalaxy.cz 0 463 547 1.600000 0
Single Cell Evaluating Reference Data for Bulk RNA Deconvolution https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html Visualisation, Annotation 2025-02-02 2025-03-11 3 True False False True datamash_transpose, collection_column_join, tp_sed_tool, collapse_dataset, tp_multijoin_tool, Remove beginning1, music_construct_eset, tp_cut_tool, annotatemyids, music_deconvolution, tp_awk_tool, __DUPLICATE_FILE_TO_COLLECTION__, tp_easyjoin_tool, ggplot2_violin, Count1, ggplot2_point, join1, Cut1, Add_a_column1, table_compute, bg_column_arrange_by_header, Paste1 UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 111 132 0.866667 0
Single Cell Multi-sample batch correction with Harmony and SnapATAC2 https://training.galaxyproject.org//topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html Dimensionality reduction, Gene expression profiling, Essential dynamics 2025-02-28 2025-07-02 2 True False False True anndata_inspect, snapatac2_preprocessing, __EXTRACT_DATASET__, Show beginning1, snapatac2_clustering, anndata_manipulate, collection_element_identifiers, __FILTER_FROM_FILE__, snapatac2_peaks_and_motif, snapatac2_plotting, fasta_compute_length UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 495 553 0.816667 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 3085082 7914455 2.333333 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 4597 5421 1.266667 0
Single Cell Inferring single cell trajectories with Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_trajectories/tutorial.html 2023-12-08 2025-03-11 13 True False False True scanpy_find_cluster, scanpy_run_diffmap, scanpy_run_dpt, scanpy_plot_embed, anndata_manipulate, scanpy_plot_trajectory, scanpy_compute_graph, scanpy_run_fdg, scanpy_run_paga UseGalaxy.org (Main), UseGalaxy.org.au 0 1316 1653 2.100000 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 retrieve_scxa, anndata_inspect, datamash_transpose, music_manipulate_eset, join1, sort1, Cut1, music_construct_eset, regex1, tp_sed_tool, tp_easyjoin_tool, scanpy_read_10x, tp_cut_tool, table_compute, annotatemyids, tp_awk_tool, add_line_to_file UseGalaxy.cz 0 742 1240 2.166667 0
Single Cell Single-cell Formats and Resources https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-data-formats/slides.html 2024-07-26 2025-02-13 4 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 1045838 2259226 1.933333 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 6476 7347 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 anndata_inspect, monocle3_orderCells, monocle3_partition, datamash_transpose, monocle3_topmarkers, monocle3_reduceDim, join1, monocle3_learnGraph, monocle3_plotCells, Cut1, monocle3_create, tp_cut_tool, Filter1, regexColumn1, monocle3_preprocess, monocle3_diffExp UseGalaxy.eu, UseGalaxy.org (Main) 0 3947 4887 1.483333 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 column_remove_by_header, music_manipulate_eset, sort1, music_construct_eset, regex1, tp_sed_tool, tp_easyjoin_tool, table_compute, tp_cut_tool, annotatemyids, tp_awk_tool UseGalaxy.cz 0 744 1154 1.783333 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 2129825 4828139 2.150000 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 1528601 3380131 2.100000 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 5706 10245 0.783333 0
Statistics and machine learning Clustering in Machine Learning https://training.galaxyproject.org//topics/statistics/tutorials/clustering_machinelearning/tutorial.html Visualisation 2020-05-08 2025-04-08 14 True False False True ggplot2_point, csv_to_tabular, sklearn_numeric_clustering UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 8522 14097 0.933333 0
Statistics and machine learning Deep Learning (Part 3) - Convolutional neural networks (CNN) https://training.galaxyproject.org//topics/statistics/tutorials/CNN/tutorial.html 2021-04-19 2025-05-09 19 True True True True keras_model_builder, ml_visualization_ex, keras_train_and_eval, keras_model_config, model_prediction, sklearn_to_categorical UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 2943240 7382837 3.200000 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 3087881 7918225 5.333333 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 flexynesis_cbioportal_import, __EXTRACT_DATASET__, table_compute, tp_cut_tool, flexynesis_utils, tp_sort_header_tool UseGalaxy.eu 0 46 46 0.633333 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 0 230 292 2.116667 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_targene_summary_figures, pancancer_targene_cell_line_predictions, pancancer_pathway_count_heatmaps, pancancer_targene_pharmacology, pancancer_visualize_decisions, pancancer_alternative_genes_pathwaymapper, pancancer_apply_weights, pancancer_external_sample_status_prediction, pancancer_compare_within_models, pancancer_within_disease_analysis, pancancer_classifier, pancancer_map_mutation_class 0 800 1241 3.050000 0
Statistics and machine learning Text-mining with the SimText toolset https://training.galaxyproject.org//topics/statistics/tutorials/text-mining_simtext/tutorial.html 2021-04-05 2025-05-07 8 True False False True pmids_to_pubtator_matrix, interactive_tool_simtext_app, pubmed_by_queries UseGalaxy.eu 0 530 727 2.633333 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, sklearn_ensemble, sklearn_build_pipeline, plotly_parallel_coordinates_plot UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 13243 21345 0.683333 0
Statistics and machine learning Modeling Breast Cancer Subtypes with Flexynesis https://training.galaxyproject.org//topics/statistics/tutorials/flexynesis_classification/tutorial.html 2025-08-13 2025-09-02 3 True False False True flexynesis_plot, datamash_transpose, tabpfn, flexynesis, join1, __EXTRACT_DATASET__, Show beginning1, pick_value, table_compute, tp_easyjoin_tool, tp_cut_tool, tp_sort_header_tool UseGalaxy.eu 0 81 115 2.016667 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 plotly_regression_performance_plots, sklearn_searchcv, Remove beginning1, sklearn_generalized_linear, sklearn_ensemble, sklearn_build_pipeline UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 3088335 7918563 3.616667 0
Statistics and machine learning Building the LORIS LLR6 PanCancer Model Using PyCaret https://training.galaxyproject.org//topics/statistics/tutorials/loris_model/tutorial.html 2024-12-13 2025-05-08 2 True True True True PyCaret_Model_Comparison 0 834420 1718782 3.716667 0
Statistics and machine learning Deep Learning (Part 1) - Feedforward neural networks (FNN) https://training.galaxyproject.org//topics/statistics/tutorials/FNN/tutorial.html 2021-04-28 2024-06-14 12 True True True True keras_model_builder, plotly_regression_performance_plots, keras_train_and_eval, keras_model_config, model_prediction UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no 0 2947836 7371938 3.050000 0
Statistics and machine learning Image classification in Galaxy with fruit 360 dataset https://training.galaxyproject.org//topics/statistics/tutorials/fruit_360/tutorial.html 2021-12-01 2024-07-09 8 True True True True keras_model_builder, ml_visualization_ex, keras_train_and_eval, keras_model_config, tp_cut_tool, model_prediction, sklearn_to_categorical UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 2603850 6285624 2.966667 0
Statistics and machine learning Introduction to deep learning https://training.galaxyproject.org//topics/statistics/tutorials/intro_deep_learning/tutorial.html 2020-03-26 2025-04-08 9 True False False True keras_model_builder, ml_visualization_ex, keras_train_and_eval, keras_model_config, model_prediction UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 2495 3182 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 flexynesis_plot, flexynesis, __EXTRACT_DATASET__, Add_a_column1, tp_replace_in_column, datamash_ops UseGalaxy.eu 0 59 67 0.800000 0
Statistics and machine learning Classification in Machine Learning https://training.galaxyproject.org//topics/statistics/tutorials/classification_machinelearning/tutorial.html 2020-04-30 2025-05-14 18 True True True True sklearn_svm_classifier, sklearn_searchcv, Remove beginning1, sklearn_nn_classifier, sklearn_generalized_linear, sklearn_ensemble, sklearn_build_pipeline, plotly_ml_performance_plots UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 3087936 7918603 4.500000 0
Statistics and machine learning Deep Learning (Part 2) - Recurrent neural networks (RNN) https://training.galaxyproject.org//topics/statistics/tutorials/RNN/tutorial.html 2021-02-23 2025-05-10 15 True True True True keras_model_builder, ml_visualization_ex, keras_train_and_eval, keras_model_config, model_prediction UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no 0 3018262 7664184 3.116667 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.eu 0 36 41 3.516667 0
Statistics and machine learning A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy https://training.galaxyproject.org//topics/statistics/tutorials/gpu_jupyter_lab/tutorial.html 2022-04-06 2025-04-08 9 True False False True Filter1, interactive_tool_ml_jupyter_notebook, Cut1 UseGalaxy.eu 0 1215 1537 1.450000 0
Statistics and machine learning Interval-Wise Testing for omics data https://training.galaxyproject.org//topics/statistics/tutorials/iwtomics/tutorial.html Comparison, Differential gene expression analysis, Differentially-methylated region identification, Genome annotation, Peak calling 2018-06-14 2023-11-09 17 True False False True iwtomics_plotwithscale, iwtomics_testandplot, iwtomics_loadandplot UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 374 496 2.866667 0
Statistics and machine learning Fine tune large protein model (ProtTrans) using HuggingFace https://training.galaxyproject.org//topics/statistics/tutorials/fine_tuning_protTrans/tutorial.html 2024-06-17 2025-04-08 4 True True True False interactive_tool_ml_jupyter_notebook UseGalaxy.eu 0 1111603 2401096 3.016667 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) 0 446 553 0.766667 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 4162 6181 1.083333 0
Synthetic Biology Evaluating and ranking a set of pathways based on multiple metrics https://training.galaxyproject.org//topics/synthetic-biology/tutorials/pathway_analysis/tutorial.html 2022-09-26 2024-06-14 7 True False True True rpranker, rpfba, rpscore, rpthermo 0 651 963 2.966667 0
Synthetic Biology Designing plasmids encoding predicted pathways by using the BASIC assembly method https://training.galaxyproject.org//topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.html 2022-05-12 2024-06-14 8 True False True True rpbasicdesign, dnabot, selenzy-wrapper 0 1042 1608 2.616667 0
Synthetic Biology Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools https://training.galaxyproject.org//topics/synthetic-biology/tutorials/retrosynthesis_analysis/tutorial.html 2022-06-23 2024-06-14 8 True False True True retropath2, rp2paths, rpcompletion, rrparser, rpextractsink, get_sbml_model 0 595 863 2.433333 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 2140423 4855175 2.166667 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 3085082 7914459 2.333333 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 0 292 514 2.433333 0
Teaching and Hosting Galaxy training Teaching online https://training.galaxyproject.org//topics/teaching/tutorials/teaching-online/tutorial.html 2022-09-23 2023-10-23 4 True False False False 0 25 25 0.083333 0
Teaching and Hosting Galaxy training Galaxy Admin Training https://training.galaxyproject.org//topics/teaching/tutorials/galaxy-admin-training/tutorial.html 2020-11-04 2024-09-17 5 True False False False 0 161 174 2.466667 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 29 31 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 0 270 292 0.950000 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 13 13 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 0 231 423 5.883333 0
Teaching and Hosting Galaxy training Running a workshop as instructor https://training.galaxyproject.org//topics/teaching/tutorials/running-workshop/tutorial.html 2018-11-15 2025-04-08 6 True False False False 0 170 299 1.066667 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 0 324 371 3.966667 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 0 144 167 1.316667 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 89 93 0.266667 0
Transcriptomics RNA-RNA interactome data analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-interactome/tutorial.html Statistical calculation, Sequencing quality control, Primer removal, Read pre-processing, Sequence composition calculation, Sequence trimming 2020-03-23 2023-11-09 12 True False False True cutadapt, chira_collapse, chira_extract, chira_map, fastqc, chira_merge, chira_quantify, query_tabular UseGalaxy.be, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 1494 2250 2.766667 0
Transcriptomics CLIP-Seq data analysis from pre-processing to motif detection https://training.galaxyproject.org//topics/transcriptomics/tutorials/clipseq/tutorial.html Sequencing quality control, Sequence alignment, Primer removal, Mapping, Sequence trimming, Read pre-processing, Sequence composition calculation, Statistical calculation 2018-08-17 2023-11-09 23 True False False True umi_tools_dedup, bedtools_slopbed, rna_star, umi_tools_extract, peakachu, sort1, deeptools_plot_correlation, fastqc, bedtools_genomecoveragebed_bedgraph, __MERGE_COLLECTION__, rcas, __SORTLIST__, tp_awk_tool, cutadapt, wig_to_bigWig, meme_chip, Extract genomic DNA 1, deeptools_plot_fingerprint, bctools_extract_alignment_ends, deeptools_multi_bam_summary UseGalaxy.no 0 8352 16383 1.866667 0
Transcriptomics Genome-wide alternative splicing analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html Sequence contamination filtering, Visualisation, Sequence analysis, Transcriptome assembly, Sequence composition calculation, Protein sequence analysis, De-novo assembly, Formatting, Sequencing quality control, RNA-Seq analysis, Sequence alignment, Sequence comparison, Sequence assembly validation, Sequence annotation, Statistical calculation, Data handling, Validation 2023-05-17 2025-03-28 11 True True False True rseqc_inner_distance, rna_star, sort1, fastqc, rseqc_infer_experiment, rseqc_junction_annotation, Remove beginning1, __FILTER_FROM_FILE__, cat1, isoformswitchanalyzer, Filter1, gene2exon1, tp_awk_tool, cpat, pygenomeTracks, addValue, tp_cat, collection_element_identifiers, multiqc, stringtie, tp_grep_tool, tp_uniq_tool, gffread, rseqc_junction_saturation, Cut1, __FLATTEN__, pfamscan, Add_a_column1, gffcompare, rna_quast, stringtie_merge, rseqc_read_distribution, rseqc_geneBody_coverage, fastp, gtftobed12 UseGalaxy.cz, UseGalaxy.fr 0 1732725 3820608 3.966667 0
Transcriptomics 3: RNA-seq genes to pathways https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html Gene-set enrichment analysis, Gene set testing, Gene functional annotation 2018-12-31 2023-11-09 13 True False False True join1, Add_a_column1, Cut1, egsea, tp_cut_tool, fgsea, goseq, tp_sort_header_tool UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 26426 42317 1.933333 0
Transcriptomics De novo transcriptome assembly, annotation, and differential expression analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/full-de-novo/tutorial.html Gene functional annotation, de Novo sequencing, Transcriptome assembly, Sequence composition calculation, De-novo assembly, Sequencing quality control, Coding region prediction, Statistical calculation, Validation 2020-02-13 2023-11-09 8 True False False True trinity_define_clusters_by_cutting_tree, trimmomatic, trinity_contig_exn50_statistic, trinity_analyze_diff_expr, trinity_run_de_analysis, trinotate, transdecoder, trinity_align_and_estimate_abundance, trinity_filter_low_expr_transcripts, trinity_samples_qccheck, multiqc, trinity_abundance_estimates_to_matrix, trinity, fastqc, describe_samples UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no 0 14757 26616 2.433333 0
Transcriptomics Visualization of RNA-Seq results with heatmap2 https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html 2018-12-31 2025-11-24 14 True False False True datamash_transpose, join1, ggplot2_heatmap2, Show beginning1, Cut1, Show tail1, cat1, Filter1, tp_sort_header_tool GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 78051 128253 1.366667 0
Transcriptomics RNA-Seq data analysis, clustering and visualisation tutorial https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html Differential gene expression analysis, RNA-Seq analysis, Gene functional annotation 2025-05-28 2025-06-16 5 True False False True volcanoplot, Multivariate, ggplot2_heatmap2, Show beginning1, Cut1, Add_a_column1, deseq2, Grouping1, cat1, deg_annotate, length_and_gc_content, tp_easyjoin_tool, table_compute, Filter1, goseq, tp_sort_header_tool UseGalaxy.eu, UseGalaxy.fr UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 1087 1406 1.516667 0
Transcriptomics 1: RNA-Seq reads to counts https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html RNA-Seq quantification, Read pre-processing, Sequence composition calculation, Sequence trimming, Formatting, Sequencing quality control, Read summarisation, Sequence alignment, Primer removal, Statistical calculation, Data handling, Validation 2018-09-23 2024-08-09 33 True False False True featurecounts, cutadapt, samtools_idxstats, picard_MarkDuplicates, collection_column_join, multiqc, rseqc_read_distribution, fastqc, rseqc_geneBody_coverage, rseqc_infer_experiment, hisat2 UseGalaxy.eu MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 79305 143629 2.600000 0
Transcriptomics Small Non-coding RNA Clustering using BlockClust https://training.galaxyproject.org//topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.html 2018-12-14 2023-11-09 8 True False False True blockclust, samtools_sort, blockbuster, tp_sort_header_tool UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 1041 1414 2.916667 0
Transcriptomics Differential abundance testing of small RNAs https://training.galaxyproject.org//topics/transcriptomics/tutorials/srna/tutorial.html RNA-Seq quantification, Read pre-processing, Differential gene expression analysis, Sequence composition calculation, Sequence trimming, Gene expression analysis, Sequencing quality control, RNA-Seq analysis, Sequence alignment, Primer removal, Statistical calculation 2017-06-29 2023-11-09 26 True False False True trim_galore, hisat2, deseq2, samtool_filter2, fastq_manipulation, fastqc, Filter1, bedtools_bamtofastq, salmon UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 6995 12231 2.083333 0
Transcriptomics Network analysis with Heinz https://training.galaxyproject.org//topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html Differential gene expression analysis, Pathway or network analysis, RNA-Seq analysis 2018-10-11 2024-01-15 16 True True False True heinz, deseq2, Cut1, heinz_scoring, heinz_bum, heinz_visualization UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 3087136 7917650 5.566667 0
Transcriptomics 2: RNA-seq counts to genes https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html RNA-Seq analysis, Annotation 2018-12-31 2024-04-10 21 True False False True tp_cut_tool, tp_replace_in_line, annotatemyids, limma_voom, mergeCols1 UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au 0 44226 74622 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 Filter1, goenrichment, goslimmer Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 23283 37721 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 154510 252706 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 3085082 7914463 2.333333 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 3087679 7918362 4.050000 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 3086112 7915773 5.783333 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 4281 5478 1.966667 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 22119 34616 2.183333 0
Transcriptomics RNA-seq Alignment with STAR https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.html 2023-05-15 2023-11-09 6 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 10895 13346 1.450000 0
Transcriptomics Visualization of RNA-Seq results with Volcano Plot in R https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot-r/tutorial.html 2021-06-14 2024-06-14 8 True False True False interactive_tool_rstudio, volcanoplot UseGalaxy.eu, UseGalaxy.org.au 0 31052 42374 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, Read mapping, Gene functional annotation, Pathway visualisation, Sequence trimming, RNA-Seq analysis, Sequence alignment, Read summarisation, RNA-Seq quantification, Visualisation, Read pre-processing, Differential gene expression analysis, Enrichment analysis, Exonic splicing enhancer prediction, Structure visualisation, Genome visualisation, Formatting, Sequencing quality control, Primer removal, Pathway or network visualisation, Data handling, Validation 2016-10-05 2025-11-24 106 True False True True samtools_idxstats, rna_star, length_and_gc_content, deg_annotate, dexseq, rseqc_infer_experiment, pathview, __MERGE_COLLECTION__, Grouping1, __FILTER_FROM_FILE__, cat1, Filter1, dexseq_count, goseq, falco, tp_sort_header_tool, __TAG_FROM_FILE__, featurecounts, pygenomeTracks, cutadapt, tp_cat, deseq2, collection_element_identifiers, multiqc, jbrowse2, ggplot2_heatmap2, ChangeCase, tp_grep_tool, join1, __EXTRACT_DATASET__, tp_tail_tool, Cut1, __FLATTEN__, Add_a_column1, picard_MarkDuplicates, samtools_view, rseqc_read_distribution, table_compute, rseqc_geneBody_coverage, tp_replace_in_line, gtftobed12 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.org.au 0 189336 353441 2.783333 0
Transcriptomics Pathway analysis with the MINERVA Platform https://training.galaxyproject.org//topics/transcriptomics/tutorials/minerva-pathways/tutorial.html RNA-Seq quantification, Gene functional annotation, Read pre-processing, Sequence composition calculation, Sequence trimming, Sequencing quality control, Read summarisation, RNA-Seq analysis, Annotation, Primer removal, Sequence alignment, Statistical calculation, Data handling, Validation 2024-03-28 2024-07-26 3 True False False True collection_column_join, fastqc, Grep1, annotatemyids, goseq, tp_sort_header_tool, featurecounts, cutadapt, tp_sorted_uniq, multiqc, fasterq_dump, limma_voom, join1, __EXTRACT_DATASET__, Cut1, Add_a_column1, rseqc_read_distribution, rseqc_geneBody_coverage, tp_replace_in_line, hisat2 UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 641 758 1.516667 0
Transcriptomics De novo transcriptome reconstruction with RNA-Seq https://training.galaxyproject.org//topics/transcriptomics/tutorials/de-novo/tutorial.html RNA-Seq quantification, Differential gene expression analysis, Transcriptome assembly, Sequence composition calculation, Sequencing quality control, RNA-Seq analysis, Read summarisation, Sequence alignment, Sequence annotation, Statistical calculation 2017-02-19 2024-06-14 36 True False True True featurecounts, stringtie, trimmomatic, deeptools_bam_coverage, deseq2, gffcompare, stringtie_merge, fastqc, Filter1, hisat2 Galaxy@AuBi, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 16889 29004 2.650000 0
Variant Analysis Introduction to Variant analysis https://training.galaxyproject.org//topics/variant-analysis/tutorials/introduction/slides.html 2016-08-19 2023-03-05 2 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3085082 7914465 2.333333 0
Variant Analysis Calling very rare variants https://training.galaxyproject.org//topics/variant-analysis/tutorials/dunovo/tutorial.html Read mapping, Generation, Sequence composition calculation, Genome indexing, Sequencing quality control, Sequence alignment, Variant calling, Statistical calculation 2017-02-22 2024-12-09 21 True False False True allele_counts_1, sequence_content_trimmer, naive_variant_caller, dunovo, align_families, bwa_mem, make_families, fastqc, correct_barcodes, Filter1, bamleftalign UseGalaxy.org (Main) 0 2044 3160 1.733333 0
Variant Analysis Mapping and molecular identification of phenotype-causing mutations https://training.galaxyproject.org//topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html 2018-03-07 2023-11-09 16 True False False True snpEff_download, mimodd_vcf_filter, mimodd_varcall, tp_find_and_replace, mimodd_varreport, snpEff, mimodd_varextract, mimodd_map UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 4428 6489 2.683333 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 CONVERTER_gz_to_uncompressed, bcftools_merge, tp_grep_tool, CONVERTER_uncompressed_to_gz, bcftools_norm, gene_iobio_display_generation_iframe, pyega3, gemini_inheritance, snpEff, gemini_load, Filter1, regexColumn1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org.au 0 1965 3459 3.566667 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, Read mapping, Generation, Visualisation, Sequence composition calculation, Genome indexing, Sequencing quality control, Sequence alignment, Variant calling, Statistical calculation, Data handling, Validation 2019-03-13 2025-03-20 16 True False False True trimmomatic, samtools_calmd, gemini_query, varscan_somatic, bwa_mem, gemini_annotate, samtools_rmdup, multiqc, snpEff, tp_easyjoin_tool, fastqc, bg_column_arrange_by_header, gemini_load, bamFilter, falco, bamleftalign UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 14592 26214 2.500000 0
Variant Analysis Calling variants in diploid systems https://training.galaxyproject.org//topics/variant-analysis/tutorials/dip/tutorial.html Sequence analysis, Genetic variation analysis, Variant calling, Statistical calculation 2017-02-20 2025-04-28 17 True False False True gemini_db_info, gemini_query, vcfallelicprimitives, snpEff, freebayes, gemini_load UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au 0 15617 26811 3.233333 0
Variant Analysis Somatic Variant Discovery from WES Data Using Control-FREEC https://training.galaxyproject.org//topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html Read mapping, Generation, Visualisation, Sequence composition calculation, Genome alignment, Copy number estimation, Sequence visualisation, Genome indexing, Sequencing quality control, Sequence alignment, Variant calling, Statistical calculation, Validation 2022-10-05 2025-03-20 14 True False False True trimmomatic, samtools_calmd, control_freec, __RELABEL_FROM_FILE__, __EXTRACT_DATASET__, bwa_mem, falco, circos, samtools_view, samtools_rmdup, multiqc, tp_text_file_with_recurring_lines, fastqc, tp_replace_in_line, __BUILD_LIST__, Grep1, bamleftalign UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 1891 2418 2.050000 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 Sequence alignment analysis, Read mapping, Generation, Sequence composition calculation, Formatting, Genome indexing, Sequencing quality control, Sequence alignment, Variant calling, Statistical calculation, Data handling 2017-02-16 2024-03-15 23 True False False True picard_MergeSamFiles, vcffilter2, vcf2tsv, bwa_mem, Cut1, picard_MarkDuplicates, fastqc, freebayes, bamFilter, bamleftalign UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 8749 15635 2.100000 0
Variant Analysis Exome sequencing data analysis for diagnosing a genetic disease https://training.galaxyproject.org//topics/variant-analysis/tutorials/exome-seq/tutorial.html Read mapping, Generation, Sequence analysis, Sequence composition calculation, Genome indexing, Sequencing quality control, Sequence alignment, Genetic variation analysis, Variant calling, Statistical calculation, Validation 2016-08-19 2025-05-11 29 True False True True trimmomatic, bcftools_norm, snpEff_download, bwa_mem, gemini_inheritance, samtools_view, samtools_rmdup, multiqc, snpEff, fastqc, freebayes, gemini_load UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au 0 35770 64670 2.716667 0
Variant Analysis Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates https://training.galaxyproject.org//topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html Read mapping, Visualisation, Generation, Read pre-processing, Sequence trimming, Genome indexing, Sequence alignment, Primer removal, Data handling 2025-02-24 2025-02-24 1 True False False True trim_galore, ggplot2_point, vcf2tsv, bwa_mem, fastq_dump, collapse_dataset, bcftools_call, bcftools_mpileup, ncbi_acc_download, tp_replace_in_line, Filter1, tp_replace_in_column, tp_awk_tool UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 275 373 1.016667 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 Database search, Service discovery, Genetic variation analysis 2024-08-06 2024-09-27 3 True False False False beacon2_cnv UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 193 230 2.166667 0
Variant Analysis Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons https://training.galaxyproject.org//topics/variant-analysis/tutorials/beaconise_1000hg/tutorial.html Database search, Service discovery, Genetic variation analysis 2024-08-06 2024-09-27 3 True False False False beacon2_import, cnv_phenopacket, beacon2_cnv, cnv_vcf2json UseGalaxy.eu 0 333 373 0.500000 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 upload1, random_lines1, Cut1, Remove beginning1, circos, Grep1 Galaxy@AuBi, Galaxy@Pasteur, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.no 0 3115587 7963058 3.983333 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 gff2bed1, circos_interval_to_text, deeptools_bam_coverage, Cut1, circos, circos_interval_to_tile, circos_wiggle_to_scatter, circos_gc_skew UseGalaxy.cz, UseGalaxy.fr Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 1467 1854 1.900000 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 1444431 3196163 2.083333 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 3085082 7914468 2.333333 0