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 2844954 7529722 2.450000 0
Galaxy Server administration Reference Data with Data Managers https://training.galaxyproject.org//topics/admin/tutorials/reference-genomes/tutorial.html Read mapping, Sequence alignment, Generation, Genome indexing 2019-01-28 2023-04-21 7 True True False False bwa, bwa_mem_index_builder_data_manager, data_manager_fetch_genome_all_fasta_dbkey 0 2845508 7530446 6.900000 0
Galaxy Server administration Advanced customisation of a Galaxy instance https://training.galaxyproject.org//topics/admin/tutorials/advanced-galaxy-customisation/slides.html 2017-06-27 2023-04-17 18 False True False False 0 2844954 7529722 2.450000 0
Galaxy Server administration Connecting Galaxy to a compute cluster https://training.galaxyproject.org//topics/admin/tutorials/connect-to-compute-cluster/tutorial.html 2018-01-07 2025-04-08 59 True True True False 0 2848976 7536676 5.716667 0
Galaxy Server administration Setting up Celery Workers for Galaxy https://training.galaxyproject.org//topics/admin/tutorials/celery/tutorial.html 2022-07-16 2025-04-08 12 True True False False 0 1990818 4709175 3.883333 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 2844954 7529722 2.450000 0
Galaxy Server administration Galaxy Monitoring with gxadmin https://training.galaxyproject.org//topics/admin/tutorials/gxadmin/tutorial.html 2019-01-28 2024-08-08 27 True True True False 0 2845823 7531085 5.166667 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 2844954 7529722 2.450000 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 2845650 7530820 3.250000 0
Galaxy Server administration Running Jobs on Remote Resources with Pulsar https://training.galaxyproject.org//topics/admin/tutorials/pulsar/tutorial.html 2019-01-28 2025-04-08 49 True True True False 0 2847466 7533865 5.283333 0
Galaxy Server administration Gearing towards production https://training.galaxyproject.org//topics/admin/tutorials/production/slides.html 2019-01-28 2025-04-08 10 False True True False 0 2844954 7529723 2.450000 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 2844954 7529723 2.450000 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 2846296 7531829 4.000000 0
Galaxy Server administration Galactic Database https://training.galaxyproject.org//topics/admin/tutorials/database/slides.html 2019-01-28 2022-06-16 5 False True True False 0 2844954 7529723 2.450000 0
Galaxy Server administration Server Maintenance: Cleanup, Backup, and Restoration https://training.galaxyproject.org//topics/admin/tutorials/backup-cleanup/tutorial.html Database management, Informatics, Data management 2019-01-31 2024-08-09 5 True True True False 0 2845513 7530470 11.633333 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 2844954 7529723 2.450000 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 2844954 7529723 2.450000 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 2851328 7541143 4.116667 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 2844954 7529723 2.450000 0
Galaxy Server administration Reference Data with CVMFS https://training.galaxyproject.org//topics/admin/tutorials/cvmfs/tutorial.html 2019-01-27 2025-04-03 50 True True True False 0 2847053 7532836 5.600000 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 2844954 7529723 2.450000 0
Galaxy Server administration Data Libraries https://training.galaxyproject.org//topics/admin/tutorials/data-library/tutorial.html 2021-01-14 2024-06-14 32 True True True False 0 2828550 7466343 4.500000 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 2846727 7532262 5.916667 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 2844954 7529723 2.450000 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 2844954 7529723 2.450000 0
Galaxy Server administration Galaxy Installation with Ansible https://training.galaxyproject.org//topics/admin/tutorials/ansible-galaxy/tutorial.html Database management, Informatics, Data management 2019-01-28 2025-04-08 102 True True True False 0 2870349 7577049 4.183333 0
Galaxy Server administration Galaxy Monitoring with Telegraf and Grafana https://training.galaxyproject.org//topics/admin/tutorials/monitoring/tutorial.html 2019-01-31 2024-12-18 47 True True True False 0 2847807 7535025 3.316667 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 833446 1933808 2.250000 0
Galaxy Server administration Galaxy Interactive Tools https://training.galaxyproject.org//topics/admin/tutorials/interactive-tools/tutorial.html 2020-02-27 2025-04-08 27 True True True False 0 2847210 7533129 5.166667 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 0 682 1061 3.000000 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 0 669 771 0.633333 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 3013 4938 1.066667 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 0 191 230 2.216667 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 0 389 525 2.466667 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 8218 16273 0.650000 0
Galaxy Server administration Performant Uploads with TUS https://training.galaxyproject.org//topics/admin/tutorials/tus/tutorial.html 2022-03-01 2024-06-14 17 True False True False 0 851 1247 5.333333 0
Galaxy Server administration Deploying a Beacon v1 in Galaxy https://training.galaxyproject.org//topics/admin/tutorials/beacon/tutorial.html 2023-04-16 2024-12-18 5 True False False False 0 141 159 2.133333 0
Galaxy Server administration Galaxy Monitoring with Reports https://training.galaxyproject.org//topics/admin/tutorials/reports/tutorial.html 2019-01-31 2025-04-08 43 True False False False 0 493 659 2.783333 0
Galaxy Server administration Enable upload via FTP https://training.galaxyproject.org//topics/admin/tutorials/ftp/tutorial.html 2021-06-18 2024-02-20 23 True False False False 0 1231 1692 1.650000 0
Galaxy Server administration Customizing the look of Galaxy https://training.galaxyproject.org//topics/admin/tutorials/customization/tutorial.html 2023-04-16 2025-04-08 5 True False False False 0 571 699 4.666667 0
Galaxy Server administration Training Infrastructure as a Service (TIaaS) https://training.galaxyproject.org//topics/admin/tutorials/tiaas/tutorial.html 2020-02-12 2024-12-18 38 True False True False 0 536 717 3.383333 0
Galaxy Server administration Use Apptainer containers for running Galaxy jobs https://training.galaxyproject.org//topics/admin/tutorials/apptainer/tutorial.html 2021-01-08 2025-04-08 13 True False True False 0 1050 1340 2.600000 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 40 45 4.900000 0
Galaxy Server administration Mapping Jobs to Destinations using TPV https://training.galaxyproject.org//topics/admin/tutorials/job-destinations/tutorial.html 2021-01-17 2024-06-14 36 True False True False 0 1653 2598 3.266667 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 49 67 3.316667 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 30 35 4.683333 0
Galaxy Server administration Monitoring Galaxy and Pulsar with Sentry https://training.galaxyproject.org//topics/admin/tutorials/sentry/tutorial.html 2023-04-19 2024-03-18 6 True False False False 0 211 256 1.083333 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 56 62 3.666667 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 1598 2648 2.283333 0
Galaxy Server administration Managing Galaxy on Kubernetes https://training.galaxyproject.org//topics/admin/tutorials/k8s-managing-galaxy/tutorial.html 2019-07-02 2024-12-19 7 True False False False 0 656 966 2.166667 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 63 82 2.116667 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 54 62 0.500000 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 2342 3025 0.433333 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 1097 1251 0.333333 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 2860781 7559499 3.366667 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 1483114 3421577 2.300000 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 1544330 3557349 2.300000 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 1497391 3453953 2.300000 0
Assembly An Introduction to Genome Assembly https://training.galaxyproject.org//topics/assembly/tutorials/general-introduction/tutorial.html Statistical calculation, Formatting, Sequence composition calculation, Validation, Visualisation, De-novo assembly, Sequencing quality control, Sequence assembly validation 2017-05-23 2024-09-12 29 True True True True fastq_paired_end_interlacer, velvetg, multiqc, fastqc, velveth, quast Galaxy@AuBi, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 2880158 7587603 5.300000 0
Assembly Decontamination of a genome assembly https://training.galaxyproject.org//topics/assembly/tutorials/assembly-decontamination/tutorial.html Genomics, Sequence assembly, Biodiversity Data handling, Taxonomic classification 2024-09-04 2025-06-04 5 True False True True ncbi_blastn_wrapper, tp_sed_tool, parse_mito_blast, Filter1, ncbi_dustmasker_wrapper, kraken2, Cut1, gfastats, tp_cat UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 1536 1921 2.533333 0
Assembly Unicycler Assembly https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html Sequence assembly, Genomics, Microbiology Statistical calculation, Genome assembly, Coding region prediction, Sequencing quality control, Genome annotation, Gene prediction, Aggregation, Sequence composition calculation, Validation, Visualisation, Sequence assembly validation 2017-10-11 2025-05-15 24 True True False True unicycler, multiqc, fastqc, prokka, quast UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2857850 7551800 4.516667 0
Assembly Chloroplast genome assembly https://training.galaxyproject.org//topics/assembly/tutorials/chloroplast-assembly/tutorial.html Generation, Analysis, Sequence assembly visualisation, Coding region prediction, Box-Whisker plot plotting, Read alignment, Genome indexing, Genome assembly, Mapping assembly, Genome visualisation, Cross-assembly, Genome annotation, Gene prediction, Sequence alignment, Scatter plot plotting, Read mapping, De-novo assembly, Sequence assembly 2020-12-04 2025-05-15 21 True False True True bandage_image, bwa_mem, jbrowse, upload1, prokka, fasta-stats, nanoplot, pilon, bandage_info, flye UseGalaxy.eu GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 7834 12151 2.800000 0
Assembly Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads https://training.galaxyproject.org//topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html Read mapping, Genome assembly, Sequence assembly visualisation, Sequence contamination filtering, Box-Whisker plot plotting, Data handling, Sequencing quality control, Scatter plot plotting, Aggregation, Validation, Pairwise sequence alignment, Sequence file editing 2020-04-21 2025-05-15 14 True True True True unicycler, multiqc, seqtk_sample, fasterq_dump, collapse_dataset, fasta_filter_by_length, samtools_view, nanoplot, minimap2, bandage_info, fastp, samtools_fastx, bandage_image, bowtie2, samtools_stats, __ZIP_COLLECTION__ UseGalaxy.eu, UseGalaxy.org.au Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 2850785 7539499 5.733333 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 Statistical calculation, Genome assembly, Sequence assembly visualisation, Sequencing quality control, Sequence composition calculation, Read mapping, Visualisation, Sequence contamination filtering, Sequence assembly validation 2021-03-24 2025-03-20 16 True False True True shovill, upload1, fastqc, falco, bandage_info, fastp, bandage_image, quast UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 9861 15245 3.633333 0
Assembly Making sense of a newly assembled genome https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html Sequence assembly, Genomics, Microbiology Sequence alignment, Mapping, Sequence visualisation, Read mapping, Genome visualisation 2018-06-14 2024-06-24 29 True False False True random_lines1, tp_sed_tool, tp_replace_in_line, circos_interval_to_tiles, collapse_dataset, bedtools_sortbed, tp_cat, circos, join1, tp_replace_in_column, bedtools_complementbed, circos_aln_to_links, tp_sort_header_tool, fasta_filter_by_length, lastz_wrapper_2, Grep1, mergeCols1, tp_grep_tool, datamash_ops, bedtools_intersectbed, jbrowse, upload1, addValue, Filter1, cat1, Cut1, fasta_compute_length 0 6714 12964 2.933333 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.org (Main), UseGalaxy.org.au UseGalaxy.no 0 3427 4757 2.716667 0
Assembly Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step https://training.galaxyproject.org//topics/assembly/tutorials/vgp_genome_assembly/tutorial.html Genomics, Sequence assembly, Biodiversity Genome assembly, k-mer counting, Read binning, Sequence trimming, Primer removal, Mapping, Data handling, De-novo assembly, Phasing, Sequence alignment, Read pre-processing, Scaffolding, Visualisation, Pairwise sequence alignment, Sequence assembly validation 2021-06-04 2025-06-04 57 True False True True purge_dups, pretext_snapshot, collapse_dataset, Add_a_column1, yahs, tp_find_and_replace, tp_cut_tool, busco, minimap2, genomescope, quast, pretext_map, bwa_mem2, merqury, tp_grep_tool, bellerophon, bionano_scaffold, cutadapt, bedtools_bamtobed, cat1, collection_column_join, Convert characters1, salsa, gfa_to_fa, sort1, gfastats, meryl, hifiasm UseGalaxy.cz 0 15552 23573 2.000000 0
Assembly ERGA post-assembly QC https://training.galaxyproject.org//topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html Genomics, Sequence assembly, Biodiversity Genome assembly, Sequence assembly visualisation, k-mer counting, Sequence alignment analysis, Sequence trimming, Data parsing, Data handling, De-novo assembly, Phasing, Data deposition, Sequence alignment, Genotyping, Scaffolding, Visualisation, Pairwise sequence alignment, Sequence assembly validation 2023-06-23 2025-06-04 8 True False True True pretext_snapshot, collapse_dataset, tp_find_and_replace, samtools_stats, bg_diamond, busco, minimap2, interactive_tool_blobtoolkit, genomescope, smudgeplot, pretext_map, bwa_mem2, merqury, __EXTRACT_DATASET__, blobtoolkit, bellerophon, CONVERTER_gz_to_uncompressed, bandage_image, gfastats, meryl UseGalaxy.eu UseGalaxy.org (Main), UseGalaxy.org.au 0 1868 2396 1.966667 0
Assembly Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Genome assembly, Sequence assembly visualisation, Data handling, Variant calling, Local alignment, Formatting, Read mapping, Visualisation, Sequence file editing, Read pre-processing, Statistical calculation, Sequence alignment analysis, Sequence trimming, Primer removal, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering, Sequence assembly validation 2025-10-19 2025-10-19 0 True False True True coverm_contig, filter_tabular, random_lines1, cutadapt, fastqc, megahit_contig2fastg, ngsutils_bam_filter, megahit, bg_uniq, bandage_info, collection_column_join, seqtk_subseq, bandage_image, metaspades, bowtie2, quast, bamtools, tp_cat UseGalaxy.cz, UseGalaxy.eu 0 1 2 0.000000 0
Assembly Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial resistance Statistical calculation, Sequence assembly validation, Genome assembly, Sequence assembly visualisation, Box-Whisker plot plotting, Sequencing error detection, Filtering, Sequencing quality control, Cross-assembly, Sequence alignment, Scatter plot plotting, Sequence composition calculation, Read mapping, Visualisation, De-novo assembly, Sequence contamination filtering, Mapping assembly 2021-03-24 2024-11-29 15 True False False True CONVERTER_bz2_to_uncompressed, bandage_image, bwa_mem2, upload1, fastqc, porechop, nanoplot, fastp, filtlong, polypolish, flye, quast UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr 0 10187 15281 3.416667 0
Assembly De Bruijn Graph Assembly https://training.galaxyproject.org//topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html Optimisation and refinement, Genome assembly, Sequence 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 2851324 7539810 5.050000 0
Assembly Genome Assembly Quality Control https://training.galaxyproject.org//topics/assembly/tutorials/assembly-quality-control/tutorial.html Biodiversity, Sequence assembly, Data quality management Genome assembly, Phasing, k-mer counting, Scaffolding, Visualisation, De-novo assembly, Sequence assembly validation 2022-08-26 2025-06-04 6 True True False True merqury, busco, chromeister, quast, meryl UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au UseGalaxy.cz 0 1943408 4575657 4.516667 0
Assembly Large genome assembly and polishing https://training.galaxyproject.org//topics/assembly/tutorials/largegenome/tutorial.html Genomics, Sequence assembly, Biodiversity Genome assembly, Sequence assembly visualisation, Box-Whisker plot plotting, Variant calling, Scatter plot plotting, Validation, Visualisation, De-novo assembly, Mapping assembly, Statistical calculation, Sequence assembly, Sequencing quality control, Cross-assembly, Sequence composition calculation, Base-calling, Pairwise sequence alignment, Sequence contamination filtering, Sequence assembly validation 2023-03-06 2025-06-04 14 True False True True bandage_image, barchart_gnuplot, medaka_consensus_pipeline, racon, busco, multiqc, fastqc, fasta-stats, nanoplot, minimap2, fastp, genomescope, flye, quast, meryl UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 7105 9251 2.033333 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 0 809 992 2.050000 0
Assembly Genome assembly using PacBio data https://training.galaxyproject.org//topics/assembly/tutorials/hifi-assembly/tutorial.html Genomics, Sequence assembly, Biodiversity Genome assembly, Mapping assembly, Cross-assembly, Visualisation, De-novo assembly, Sequence assembly validation 2021-11-29 2025-06-04 2 True False False True busco, fasta-stats, flye, gfa_to_fa, quast, hifiasm UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.cz 0 702 831 1.483333 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 385632 820746 1.816667 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 2363443 5904672 2.400000 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 2824191 7461190 2.450000 0
Climate Ocean's variables study https://training.galaxyproject.org//topics/climate/tutorials/ocean-variables/tutorial.html 2023-11-29 2025-05-10 5 True False False True interactive_tool_odv, divand_full_analysis, interactive_tool_divand UseGalaxy.eu 0 210 253 1.933333 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 interactive_tool_odv, tool_biogeochemical_calibration, harmonize_insitu_to_netcdf, tool_odv_history, tool_odv UseGalaxy.eu 0 31 42 2.650000 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 tp_awk_tool, climate_stripes, ggplot2_point, psy_maps, Grep1, interactive_tool_panoply, cds_essential_variability, datamash_ops UseGalaxy.eu 0 1040 1446 1.283333 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 2238295 5505288 4.400000 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 xarray_select, xarray_metadata_info, interactive_tool_panoply, ggplot2_point, tp_find_and_replace, ctsm_fates, __EXTRACT_DATASET__ UseGalaxy.eu, UseGalaxy.org (Main) 0 2846418 7532045 4.283333 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, timeseries_extraction, xarray_metadata_info, argo_getdata, xarray_coords_info UseGalaxy.eu 0 294 355 1.200000 0
Climate Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools https://training.galaxyproject.org//topics/climate/tutorials/pangeo/tutorial.html Visualisation 2022-02-18 2025-05-10 6 True True True True __MERGE_COLLECTION__, xarray_netcdf2netcdf, xarray_select, xarray_metadata_info, climate_stripes, ggplot2_point, regexColumn1, xarray_mapplot, xarray_coords_info, graphicsmagick_image_montage, __EXTRACT_DATASET__ UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 2238085 5504794 5.266667 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_copernicus, interactive_tool_panoply, interactive_tool_copernicus_notebook 0 288 334 0.533333 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 2844954 7529728 2.450000 0
Climate Collaboration with JupyterGIS https://training.galaxyproject.org//topics/climate/tutorials/jupytergis_collaboration/tutorial.html 2025-04-03 2025-05-10 4 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 169 211 0.866667 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 0 545 952 1.800000 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 0 392 474 1.166667 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 6271 10232 0.800000 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, spocc_occ, obis_data, c3s UseGalaxy.eu 0 94 128 2.700000 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 2025-10-04 4 True False False False 0 71 94 3.316667 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 2025-10-04 1 True False False False 0 5 5 0.000000 0
Galaxy Community Building What's a Special Interest Group? https://training.galaxyproject.org//topics/community/tutorials/sig_define/tutorial.html 2024-07-08 2024-12-20 3 True False False False 0 75 106 3.933333 0
Galaxy Community Building Creation of resources listing Galaxy workflow for your community https://training.galaxyproject.org//topics/community/tutorials/community-workflow-table/tutorial.html 2025-09-17 2025-09-17 1 True False False False 0 5 6 0.000000 0
Galaxy Community Building Creation of a Galaxy tutorial table for your community https://training.galaxyproject.org//topics/community/tutorials/community-tutorial-table/tutorial.html 2025-09-17 2025-09-17 1 True False False False 0 6 7 0.000000 0
Galaxy Community Building Make your tools available on your subdomain https://training.galaxyproject.org//topics/community/tutorials/tools_subdomains/tutorial.html 2024-12-03 2024-12-20 2 True False False False 0 40 55 10.416667 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 44 57 0.116667 0
Galaxy Community Building Creating a Special Interest Group https://training.galaxyproject.org//topics/community/tutorials/sig_create/tutorial.html 2024-07-08 2024-12-20 2 True False False False 0 99 109 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 ctb_silicos_qed, ctb_im_rxn_maker, openbabel_compound_convert, chembl, md_converter, get_pdb, openbabel_svg_depiction UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 431 518 1.750000 0
Computational chemistry Protein-ligand docking https://training.galaxyproject.org//topics/computational-chemistry/tutorials/cheminformatics/tutorial.html 2019-10-19 2023-11-09 16 True False False True sdf_to_tab, openbabel_compound_convert, collapse_dataset, ctb_chemfp_butina_clustering, tp_find_and_replace, openbabel_svg_depiction, tp_cat, ctb_np-likeness-calculator, ctb_chemfp_mol2fps, ctb_change_title, ctb_compound_convert, prepare_receptor, ctb_remIons, ctb_online_data_fetch, ctb_remDuplicates, ctb_chemfp_nxn_clustering, docking, fpocket, ctb_filter, tp_grep_tool, prepare_box, chembl, get_pdb, ctb_obgrep UseGalaxy.org (Main) 0 19080 32741 1.550000 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 sucos_max_score, xchem_pose_scoring, ctb_frankenstein_ligand, openbabel_compound_convert, rxdock_rbdock, collapse_dataset, xchem_transfs_scoring, rdock_rbcavity, split_file_to_collection, rdock_rbdock, rxdock_rbcavity, enumerate_charges 0 3160 5211 3.050000 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, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_ramachandran_plot, mdanalysis_rdf, bio3d_pca, bio3d_rmsf, mdanalysis_cosine_analysis UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 32255 57257 1.233333 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 ctb_alignit, openbabel_addh, rdconf, split_file_to_collection, sort1, tp_cat UseGalaxy.cz 0 1212 1764 2.450000 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, gmx_editconf, gmx_solvate, gmx_sim, gmx_setup, get_pdb, tp_grep_tool UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 26370 47375 1.416667 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 setup, namd_nvt, namd_npt, minimizer 0 4185 7031 1.216667 0
Computational chemistry High Throughput Molecular Dynamics and Analysis https://training.galaxyproject.org//topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html 2020-05-20 2025-04-08 19 True False True True bio3d_rmsd, ambertools_acpype, gmx_em, openbabel_compound_convert, gmx_merge_topology_files, vmd_hbonds, gmx_editconf, bio3d_pca_visualize, gmx_energy, gmx_solvate, bio3d_pca, gmx_sim, md_converter, gmx_setup, get_pdb, bio3d_rmsf, mdanalysis_cosine_analysis, tp_grep_tool UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 10647 18768 2.433333 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 1775 2395 1.666667 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 2845040 7529828 3.616667 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 2844954 7529729 2.450000 0
Contributing to the Galaxy Training Material Adding auto-generated video to your slides https://training.galaxyproject.org//topics/contributing/tutorials/slides-with-video/tutorial.html 2020-10-20 2023-11-09 12 True False False False 0 264 346 3.866667 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 0 262 349 2.866667 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 0 244 537 1.166667 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 75 92 2.733333 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 33 38 0.716667 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 0 678 1029 2.366667 0
Contributing to the Galaxy Training Material Including a new topic https://training.galaxyproject.org//topics/contributing/tutorials/create-new-topic/tutorial.html 2018-06-04 2025-03-14 32 True False False False 0 1219 1677 0.566667 0
Contributing to the Galaxy Training Material Creating Interactive Galaxy Tours https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-tours/tutorial.html 2017-06-25 2025-04-08 13 True False False False 0 289 447 2.500000 0
Contributing to the Galaxy Training Material 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 0 571 761 2.883333 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 0 101 115 0.316667 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 0 318 443 5.150000 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 56 98 0.816667 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 5367 6398 0.783333 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 0 550 741 1.650000 0
Contributing to the Galaxy Training Material Creating a new tutorial https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial/tutorial.html Data handling, Sequence trimming, Primer removal, Read mapping, Sequence file editing, Read pre-processing 2018-06-20 2025-03-14 32 True False True True tp_cut_tool, random_lines1, tp_sed_tool, cutadapt, tp_sorted_uniq, bam_to_sam, Filter1, Cut1, seqtk_subseq, bowtie2, fastq_to_tabular, tp_cat, c3s 0 1768 2623 5.016667 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 38 38 0.116667 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 39 41 0.833333 0
Contributing to the Galaxy Training Material FAIR Galaxy Training Material https://training.galaxyproject.org//topics/contributing/tutorials/fair-gtn/tutorial.html 2025-10-19 2025-10-19 0 True False False False 0 1 1 0.000000 0
Contributing to the Galaxy Training Material Creating content in Markdown https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-content/tutorial.html Validation, Sequencing quality control 2017-06-25 2025-04-08 85 True False False False upload1, multiqc 0 3685 9683 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 2844954 7529730 2.450000 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 90 109 4.766667 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 Generation, Sequence alignment, Data handling, Genome indexing, Read mapping, Sequence file editing 2021-08-04 2023-11-09 5 True False False True bwa_mem, trimmomatic, tp_replace_in_line, seqtk_subseq, samtools_fastx, Grep1, __UNZIP_COLLECTION__, __ZIP_COLLECTION__ UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 4025 5635 2.300000 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 2524059 6439180 3.833333 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 Tree-based sequence alignment, Variant classification 2021-06-08 2025-04-08 9 True False True True pangolin, compose_text_param, bcftools_consensus, snpSift_filter, collapse_dataset UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr 0 2834 3440 2.083333 0
Variant Analysis Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html Tree-based sequence alignment, Methylation analysis, Variant classification, Variant calling 2021-06-30 2025-03-28 18 True False True False pangolin, fasta_regex_finder, nextclade, upload1, Filter1, datamash_ops UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main) 0 7292 13084 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 Generation, Data handling, Genome indexing, Validation, Sequencing quality control, Formatting, Sequence alignment, SNP detection, Read mapping, Sequence contamination filtering 2020-06-24 2024-06-14 16 True False True True tp_cut_tool, picard_MarkDuplicates, bwa_mem, multiqc, lofreq_call, lofreq_indelqual, snpeff_sars_cov_2, fasterq_dump, Filter1, snpSift_extractFields, fastp, lofreq_viterbi, Grep1, samtools_stats UseGalaxy.eu, UseGalaxy.org (Main) MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 13610 20501 2.883333 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 fastq_dump, snpeff_sars_cov_2, query_tabular, fasterq_dump, jq, tp_cat, fastq_to_fasta_python UseGalaxy.be, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2625549 6775155 4.166667 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 Statistical calculation, Generation, Genome visualisation, Sequence alignment, Genome indexing, Sequence composition calculation, Read mapping, Sequencing quality control 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 1219 1580 4.200000 0
Foundations of Data Science Data Manipulation Olympics https://training.galaxyproject.org//topics/data-science/tutorials/data-manipulation-olympics/tutorial.html 2025-10-19 2025-10-19 0 True False False True Grouping1, {{version_join}}, tp_sorted_uniq, {{version_count}}, {{version_select_first}}, {{version_cut_advanced}}, {{version_cat}}, Add_a_column1, {{version_sort}}, Count1, {{version_remove_beginning}}, {{version_split}}, tp_cat, {{version_unique}}, join1, {{version_wc}}, {{version_replace_text_line}}, Remove beginning1, tp_sort_header_tool, regexColumn1, {{version_remove_columns_by_header}}, wc_gnu, {{version_paste}}, datamash_ops, tp_split_on_column, upload1, {{version_datamash}}, {{version_replace_text_column}}, Filter1, tabular_to_csv, Show beginning1, Cut1, cat1, {{version_cut_columns}}, {{version_filter}}, {{version_compute}} 0 0 0 0.000000 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 1280868 2979056 5.266667 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 1125216 2628698 3.400000 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 0 668 723 0.383333 0
Foundations of Data Science Introduction to SQL https://training.galaxyproject.org//topics/data-science/tutorials/sql-basic/tutorial.html 2021-10-11 2024-12-13 8 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 558 685 1.383333 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 0 280 511 0.633333 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 2011 2290 0.566667 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 0 503 685 0.483333 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 0 928 1163 1.266667 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 1126 1594 2.816667 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 1415 1779 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 0 135 380 0.350000 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 3323 4299 0.916667 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 0 108 126 0.883333 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 1293 1687 1.900000 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 2656 3587 2.133333 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 0 933 1191 2.366667 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 0 423 449 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 8734 11408 2.016667 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 0 597 758 0.533333 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 0 229 290 2.116667 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 1510 2364 2.616667 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 0 962 1130 0.750000 0
Foundations of Data Science Advanced Python https://training.galaxyproject.org//topics/data-science/tutorials/python-advanced-np-pd/tutorial.html 2021-11-08 2024-10-15 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 518 697 1.316667 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 0 606 686 1.016667 0
Foundations of Data Science Data Manipulation Olympics - SQL https://training.galaxyproject.org//topics/data-science/tutorials/data-manipulation-olympics-sql/tutorial.html 2023-06-16 2024-05-07 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 779 872 0.550000 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 0 595 781 0.850000 0
Foundations of Data Science Plotting in Python https://training.galaxyproject.org//topics/data-science/tutorials/python-plotting/tutorial.html 2021-11-08 2024-10-15 7 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 558 680 1.583333 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 0 106 112 0.550000 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 0 389 667 6.033333 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 2069 2449 0.533333 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 0 115 124 0.383333 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 0 322 366 0.783333 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 0 117 128 0.816667 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 0 261 312 0.816667 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 0 371 446 1.716667 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 40 46 1.216667 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 10 10 0.083333 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 0 531 620 0.650000 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 0 573 657 0.316667 0
Foundations of Data Science Python - Introductory Graduation https://training.galaxyproject.org//topics/data-science/tutorials/python-basics-recap/tutorial.html 2022-04-25 2023-02-13 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 226 270 1.683333 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 0 637 687 0.566667 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 0 219 242 0.400000 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 0 609 645 0.183333 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 1313 1429 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 0 176 198 1.416667 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 0 519 561 0.450000 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 1148 1333 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 0 176 189 0.566667 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 0 849 913 0.300000 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 2844954 7529732 2.450000 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 2844954 7529732 2.450000 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 2844954 7529732 2.450000 0
Development in Galaxy JavaScript plugins https://training.galaxyproject.org//topics/dev/tutorials/visualization-charts/tutorial.html 2017-06-22 2025-04-08 20 True True False False 0 2845651 7530565 3.400000 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 2845292 7530222 4.383333 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 2844954 7529733 2.450000 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 2633316 6800438 4.850000 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 2845140 7529984 3.850000 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 2844954 7529734 2.450000 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 2844954 7529734 2.450000 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 2844954 7529734 2.450000 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 2845656 7530655 4.666667 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 2844957 7529738 2.450000 0
Development in Galaxy Writing Automated Tests for Galaxy https://training.galaxyproject.org//topics/dev/tutorials/writing_tests/tutorial.html 2022-07-15 2024-06-25 5 True False False False 0 255 683 2.366667 0
Development in Galaxy Contributing a New Feature to Galaxy Core https://training.galaxyproject.org//topics/dev/tutorials/core-contributing/tutorial.html 2021-06-08 2025-03-14 9 True False False False 0 706 1062 2.666667 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 2720 4402 2.566667 0
Development in Galaxy Setting up a dev Onedata instance https://training.galaxyproject.org//topics/dev/tutorials/onedata-dev-instance/tutorial.html 2025-03-24 2025-04-08 2 True False False False 0 18 21 3.900000 0
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 0 224 333 3.050000 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 0 401 485 1.633333 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 0 240 287 2.700000 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 0 220 310 3.300000 0
Development in Galaxy Debugging Galaxy https://training.galaxyproject.org//topics/dev/tutorials/debugging/tutorial.html 2021-06-15 2024-06-14 14 True False False False 0 582 1186 2.916667 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 1150 1536 2.816667 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 tp_replace_in_line, Filter1, Add_a_column1, Cut1, diff, sort1, wordcloud, datamash_ops 0 138 165 1.766667 0
Digital Humanities Introduction to Digital Humanities in Galaxy https://training.galaxyproject.org//topics/digital-humanities/tutorials/introduction_to_dh/tutorial.html 2025-09-11 2025-09-16 3 True False False True tp_replace_in_line, Remove beginning1, wc_gnu, tp_find_and_replace, diff, wordcloud, tp_grep_tool UseGalaxy.eu, UseGalaxy.org.au 0 44 56 1.800000 0
Digital Humanities OpenRefine Tutorial for researching cultural data https://training.galaxyproject.org//topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html 2025-09-24 2025-09-24 1 True False False True filter_tabular, barchart_gnuplot, compose_text_param, param_value_from_file, tp_head_tool, Remove beginning1, interactive_tool_openrefine, regexColumn1, Cut1, tp_sort_header_tool, wordcloud, datamash_ops, tp_grep_tool UseGalaxy.eu 0 12 15 0.016667 0
Ecology Checking expected species and contamination in bacterial isolate https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Statistical calculation, Expression analysis, Cross-assembly, Taxonomic classification 2024-03-04 2024-06-27 4 True False False True recentrifuge, upload1, kraken2, est_abundance UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main) 0 813 1091 3.350000 0
Ecology RAD-Seq to construct genetic maps https://training.galaxyproject.org//topics/ecology/tutorials/genetic-map-rad-seq/tutorial.html Data handling 2017-02-14 2025-06-03 13 True False False True stacks_denovomap, stacks_genotypes UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 872 1229 1.333333 0
Ecology Regional GAM https://training.galaxyproject.org//topics/ecology/tutorials/regionalGAM/tutorial.html Ecology Visualisation 2019-07-04 2025-06-03 18 True False False True regionalgam_glmmpql, regionalgam_flight_curve, tp_awk_tool, csv2tab_R, ggplot2_point, Remove beginning1, regionalgam_gls, Filter1, regexColumn1, regionalgam_plot_trend, flight-curve, Paste1, regionalgam_ab_index, Count1, regionalgam_autocor_acf, mergeCols1, tab2csv_R 0 335 449 3.516667 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 0 176 217 2.066667 0
Ecology Data submission using ENA upload Tool https://training.galaxyproject.org//topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html Read mapping, Sequence trimming, Primer removal, Validation, Visualisation, Sequencing quality control, Read pre-processing 2024-12-13 2025-03-20 2 True False False False fastq_groomer, ncbi_blastn_wrapper, multiqc, cutadapt, collection_element_identifiers, regex1, __RELABEL_FROM_FILE__, fastq_filter, falco, ab1_fastq_converter, bg_uniq, Paste1, __FILTER_EMPTY_DATASETS__, fastq_to_fasta_python UseGalaxy.eu UseGalaxy.cz 0 186 193 0.666667 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 tp_cut_tool, obisindicators, obis_data UseGalaxy.eu 0 306 385 2.100000 0
Ecology Champs blocs indicators https://training.galaxyproject.org//topics/ecology/tutorials/champs-blocs/tutorial.html 2023-01-04 2025-06-03 11 True False False True cb_div, cb_dissim, cb_qecb, cb_eco, cb_ivr 0 167 316 2.033333 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 tp_cut_tool, ecoregion_brt_analysis, ecoregion_taxa_seeker, interactive_tool_jupyter_notebook, ecoregion_clara_cluster, regexColumn1, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, filter_tabular, unzip, ecoregion_eco_map, mergeCols1 UseGalaxy.eu 0 234 321 3.266667 0
Ecology RAD-Seq Reference-based data analysis https://training.galaxyproject.org//topics/ecology/tutorials/ref-based-rad-seq/tutorial.html Statistical calculation, Generation, Data handling, Genome indexing, Validation, Sequencing quality control, Sequence alignment, Sequence composition calculation, Read mapping 2017-02-14 2025-06-03 14 True False False True Summary_Statistics1, bwa, multiqc, stacks_refmap, stacks_populations, fastqc, tp_replace_in_line, addValue, stacks_procrad, bwa_wrapper, Filter1, tp_sort_header_tool, cat1, Cut1, Grep1, Convert characters1, Count1, regex_replace 0 2987 4693 1.766667 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 98 105 1.983333 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 tp_cut_tool, ecology_beta_diversity, ecology_link_between_var, ecology_homogeneity_normality, ecology_stat_presence_abs, ecology_presence_abs_abund, Remove beginning1, tool_anonymization, regexColumn1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr 0 1582 2219 2.750000 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 ncbi_blastn_wrapper, Count1, cshl_fastq_to_fasta, fastp UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.no 0 389 494 0.800000 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_pca, srs_global_indices, srs_diversity_maps, srs_process_data, srs_preprocess_s2, srs_spectral_indices UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 589 759 1.550000 0
Ecology Metabarcoding/eDNA through Obitools https://training.galaxyproject.org//topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html Statistical calculation, Sequence analysis, Sequence composition calculation, Sequencing quality control 2022-02-28 2025-06-03 12 True False True True join1, ncbi_blastn_wrapper, obi_annotate, fastqc, unzip, obi_grep, obi_ngsfilter, obi_clean, obi_illumina_pairend, obi_uniq, Filter1, Cut1, wc_gnu, fastq_groomer, obi_stat, obi_tab, seq_filter_by_id UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 4406 6121 1.933333 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, estimate_endem, crsconverter UseGalaxy.eu 0 66 91 1.116667 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 tp_cut_tool, spocc_occ, interactive_tool_wallace, Filter1, tabular_to_csv, tp_find_and_replace UseGalaxy.eu, UseGalaxy.fr 0 3127 4746 1.150000 0
Ecology Compute and analyze biodiversity metrics with PAMPA toolsuite https://training.galaxyproject.org//topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html 2020-11-19 2025-09-03 23 True False True True tp_cut_tool, mergeCols1, pampa_glmcomm, tp_easyjoin_tool, pampa_presabs, regex1, datamash_transpose, regexColumn1, Filter1, pampa_plotglm, pampa_communitymetrics, tp_sort_header_tool, Count1, tp_cat, pampa_glmsp UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au 0 1078 1425 1.850000 0
Ecology From NDVI data with OpenEO to time series visualisation with Holoviews https://training.galaxyproject.org//topics/ecology/tutorials/ndvi_openeo/tutorial.html 2024-01-24 2024-06-29 3 True False False True interactive_tool_copernicus_notebook, interactive_tool_holoviz UseGalaxy.eu 0 186 224 1.183333 0
Ecology RAD-Seq de-novo data analysis https://training.galaxyproject.org//topics/ecology/tutorials/de-novo-rad-seq/tutorial.html Statistical calculation, Data handling, Sequence composition calculation, Sequencing quality control 2017-02-14 2025-06-03 14 True False False True stacks_denovomap, fastqc, stacks_populations, stacks_procrad UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 2626 4207 2.083333 0
Ecology Marine Omics identifying biosynthetic gene clusters https://training.galaxyproject.org//topics/ecology/tutorials/marine_omics_bgc/tutorial.html Sequence motif recognition, Genome annotation, Protein feature detection 2024-08-19 2025-06-03 3 True False False True interproscan, regex1, prodigal, SanntiS_marine, sanntis_marine 0 156 182 2.583333 0
Ecology Preparing genomic data for phylogeny reconstruction https://training.galaxyproject.org//topics/ecology/tutorials/phylogeny-data-prep/tutorial.html Genome annotation, Multiple sequence alignment, Sequence clustering, Genetic variation analysis, Sequence analysis, Sequence assembly validation 2022-10-21 2025-06-03 5 True False False True phykit_alignment_based, repeatmasker_wrapper, busco, tp_replace_in_line, regex1, funannotate_predict, proteinortho_grab_proteins, collapse_dataset, Filter1, clipkit, glimmer_gbk_to_orf, clustalw, proteinortho 0 2139 2929 2.700000 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 tp_cut_tool, ecoregion_brt_analysis, ecoregion_taxa_seeker, column_remove_by_header, regexColumn1, Filter1, ecoregion_GeoNearestNeighbor, ClaraGuess, unzip, ecoregion_eco_map, WormsMeasurements UseGalaxy.eu 0 24 26 4.366667 0
Ecology Visualization of Climate Data using NetCDF xarray Map Plotting https://training.galaxyproject.org//topics/ecology/tutorials/x-array-map-plot/tutorial.html 2022-10-26 2024-06-27 9 True False False True xarray_metadata_info, cdo_operations, xarray_mapplot, xarray_coords_info, graphicsmagick_image_montage UseGalaxy.eu UseGalaxy.cz 0 2343 2714 0.466667 0
Ecology Cleaning GBIF data for the use in Ecology https://training.galaxyproject.org//topics/ecology/tutorials/gbif_cleaning/tutorial.html 2022-10-28 2025-06-03 6 True False False True Summary_Statistics1, spocc_occ, Filter1, gdal_ogr2ogr, Count1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no 0 618 768 0.900000 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 0 135 162 0.883333 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) 0 222 285 1.350000 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 2025-10-15 2 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 3 6 0.000000 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 0 266 307 1.633333 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 0 418 506 1.100000 0
Statistics and machine learning Pretraining a Large Language Model (LLM) from Scratch on DNA Sequences https://training.galaxyproject.org//topics/statistics/tutorials/genomic-llm-pretraining/tutorial.html 2025-04-17 2025-05-22 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 710 837 1.750000 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 1898 2252 0.666667 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 1582 1866 0.750000 0
Teaching and Hosting Galaxy training Assessment and feedback in training and teachings https://training.galaxyproject.org//topics/teaching/tutorials/assessment/tutorial.html 2022-09-23 2025-03-11 11 True False False False 0 1237 1433 0.783333 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 84 98 0.616667 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 0 420 489 1.366667 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 465113 1012841 1.933333 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 0 101 105 2.600000 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 465114 1012845 2.050000 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 0 102 113 0.900000 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 21 23 0.033333 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 465138 1012881 3.750000 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 Statistical calculation, Pathway visualisation, Mapping, Sequence trimming, Primer removal, Peak calling, Structure visualisation, Enrichment analysis, Sequencing quality control, Genome visualisation, Sequence composition calculation, Read pre-processing, Read mapping, Gene regulatory network analysis 2018-09-17 2025-04-08 14 True True False True deeptools_bam_compare, deeptools_plot_fingerprint, deeptools_plot_heatmap, bbgtobigwig, fastqc, Filter1, deeptools_compute_matrix, deeptools_plot_correlation, trim_galore, cat1, bedtools_mergebed, macs2_callpeak, deeptools_bam_coverage, bedtools_sortbed, bowtie2, jbrowse2, deeptools_multi_bam_summary, samtools_idxstats UseGalaxy.eu, UseGalaxy.org (Main) 0 2850855 7541432 6.116667 0
Epigenetics DNA Methylation data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/methylation-seq/tutorial.html Epigenomics Statistical calculation, Sequence composition calculation, Read mapping, Visualisation, Sequencing quality control 2017-02-16 2025-04-03 24 True False False True bwameth, tp_awk_tool, fastqc, tp_tail_tool, wig_to_bigWig, pileometh, deeptools_compute_matrix, falco, replace_column_with_key_value_file, deeptools_plot_profile, metilene 0 14704 24574 2.050000 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 hicexplorer_hiccorrectmatrix, hicexplorer_hicfindrestrictionsites, hicexplorer_hicdetectloops, hicexplorer_hicbuildmatrix, hicexplorer_hicpca, pygenomeTracks, hicexplorer_hicfindtads, hicexplorer_hicmergematrixbins, bowtie2, hicexplorer_hicplotmatrix, hicexplorer_hicinfo UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no, UseGalaxy.org (Main) 0 7343 12398 1.516667 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, clusterprofiler_go, minfi_analysis, Remove beginning1, Cut1, chipeakanno_annopeaks UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2846994 7532948 4.350000 0
Epigenetics Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) https://training.galaxyproject.org//topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html ChIP-seq Statistical calculation, Generation, Mapping, Genome indexing, Peak calling, Enrichment analysis, Sequencing quality control, Sequence alignment, Sequence composition calculation, Read mapping, Gene regulatory network analysis 2016-12-20 2025-04-08 11 True False False True deeptools_bam_compare, deeptools_plot_fingerprint, bedtools_intersectbed, deeptools_plot_heatmap, bwa, deeptools_compute_gc_bias, trimmomatic, fastqc, deeptools_compute_matrix, macs2_callpeak, deeptools_plot_correlation, deeptools_correct_gc_bias, deeptools_multi_bam_summary, samtools_idxstats UseGalaxy.be, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 7123 13060 3.300000 0
Epigenetics Identification of the binding sites of the Estrogen receptor https://training.galaxyproject.org//topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html Statistical calculation, Sequence trimming, Primer removal, Peak calling, Enrichment analysis, Sequencing quality control, Sequence composition calculation, Read pre-processing, Read mapping, Gene regulatory network analysis 2017-09-18 2025-04-08 10 True False False True deeptools_bam_compare, deeptools_plot_fingerprint, deeptools_plot_heatmap, deeptools_compute_gc_bias, fastqc, bam_to_sam, deeptools_compute_matrix, deeptools_plot_correlation, trim_galore, macs2_callpeak, deeptools_bam_coverage, bowtie2, deeptools_multi_bam_summary, samtools_idxstats UseGalaxy.be Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 1905 2816 2.766667 0
Epigenetics CUT&RUN data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/cut_and_run/tutorial.html Sequence alignment analysis, Data handling, Primer removal, Sequence trimming, Validation, Mapping, Peak calling, Sequencing quality control, Enrichment analysis, Formatting, Read pre-processing, Read mapping, Visualisation, Gene regulatory network analysis 2024-03-06 2025-03-19 5 True False False True Extract genomic DNA 1, deeptools_compute_matrix, bowtie2, deeptools_plot_heatmap, multiqc, meme_chip, wig_to_bigWig, bamFilter, falco, pe_histogram, trim_galore, Grep1, picard_MarkDuplicates, deeptools_plot_fingerprint, bedtools_intersectbed, idr, datamash_transpose, bedtools_bamtobed, macs2_callpeak, __FLATTEN__, __EXTRACT_DATASET__ 0 5725 7267 1.383333 0
Epigenetics ATAC-Seq data analysis https://training.galaxyproject.org//topics/epigenetics/tutorials/atac-seq/tutorial.html Statistical calculation, Gene regulatory network analysis, Mapping, Sequence trimming, Primer removal, Sequence alignment analysis, Data handling, Peak calling, Enrichment analysis, Sequencing quality control, Formatting, Sequence composition calculation, Read mapping, Visualisation, Read pre-processing 2019-09-02 2024-08-08 23 True True True True picard_MarkDuplicates, bedtools_intersectbed, deeptools_plot_heatmap, cutadapt, fastqc, wig_to_bigWig, bedtools_bamtobed, bamFilter, pygenomeTracks, Filter1, deeptools_compute_matrix, pe_histogram, Cut1, tp_sort_header_tool, Grep1, macs2_callpeak, bowtie2, samtools_idxstats 0 2908122 7643703 4.250000 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 2844954 7529736 2.450000 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 2844954 7529736 2.450000 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 analysis, Phylogenetic analysis, Phylogenetic tree reconstruction, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation, Sequence analysis, Multiple sequence alignment 2024-05-10 2024-05-10 1 True False False True rbc_mafft, newick_display, fasttree, iqtree UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 4521 5834 1.950000 0
Evolution Tree thinking for tuberculosis evolution and epidemiology https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html Genomics, Microbiology, Phylogeny, Infectious disease Sequence analysis, Phylogenetic tree analysis 2022-03-16 2025-06-04 12 True False False True interactive_tool_rstudio, raxml, upload1 UseGalaxy.eu 0 2167 3129 2.266667 0
Evolution Identifying tuberculosis transmission links: from SNPs to transmission clusters https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html Genomics, Microbiology, Infectious disease, DNA polymorphism Antimicrobial resistance prediction, Phylogenetic tree generation, Phylogenetic tree visualisation, Variant calling 2022-03-16 2025-05-26 13 True False False True tb_variant_filter, tp_sed_tool, tp_replace_in_line, clustering_from_distmat, collapse_dataset, tp_cat, trimmomatic, snp_dists, samtools_view, snippy, snp_sites, bcftools_consensus, tp_easyjoin_tool, Grep1, tp_grep_tool, __MERGE_COLLECTION__, upload1, tb_profiler_profile, addName UseGalaxy.eu 0 2657 3823 2.833333 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 920649 2151039 2.283333 0
Evolution Phylogenetic analysis for bacterial comparative genomics https://training.galaxyproject.org//topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html Genomics, Microbiology, Phylogeny Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) 2025-03-14 2025-03-14 1 True False False False fasttree, upload1 GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@AuBi 0 81 102 3.966667 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 920649 2151039 2.283333 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 920649 2151039 2.283333 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 920649 2151039 2.283333 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 920649 2151039 2.283333 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 920649 2151039 2.283333 0
FAIR Data, Workflows, and Research Data management in Medicinal Chemistry https://training.galaxyproject.org//topics/fair/tutorials/med-chem-data/tutorial.html 2025-10-19 2025-10-19 0 True False True True ctb_silicos_qed, ctb_im_rxn_maker, openbabel_compound_convert, chembl, md_converter, get_pdb, openbabel_svg_depiction 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 615064 1381342 2.083333 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 0 133 149 0.600000 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 0 299 396 1.750000 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 0 508 598 0.933333 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 0 819 1058 1.783333 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 0 571 759 1.733333 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 88 117 2.316667 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 0 329 421 1.433333 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 675732 1525674 4.166667 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 0 232 258 1.383333 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 0 354 439 2.766667 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 0 262 319 2.400000 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 0 161 196 1.400000 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 69 73 1.600000 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 0 135 161 2.383333 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 0 354 410 1.250000 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 44 52 4.516667 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 54 63 2.783333 0
FAIR Data, Workflows, and Research FAIR Bioimage Metadata https://training.galaxyproject.org//topics/fair/tutorials/bioimage-metadata/tutorial.html 2023-09-13 2024-10-15 4 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 269 322 2.266667 0
FAIR Data, Workflows, and Research REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data https://training.galaxyproject.org//topics/fair/tutorials/bioimage-REMBI/tutorial.html 2023-09-13 2024-10-15 6 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 263 298 2.283333 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 0 150 168 0.600000 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 0 231 285 1.466667 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, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au MISSISSIPPI 0 5822 7252 3.000000 0
Using Galaxy and Managing your Data Workflow Reports https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-reports/tutorial.html Visualisation 2022-06-02 2024-06-14 9 True False True True csv_to_tabular, Grouping1, upload1, tp_sorted_uniq, ggplot2_point, Remove beginning1, Cut1, datamash_ops UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz 0 844 1174 2.916667 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 0 176 233 3.133333 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 1940 2481 2.316667 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 2844954 7529738 2.450000 0
Using Galaxy and Managing your Data Galaxy workflows in Dockstore https://training.galaxyproject.org//topics/galaxy-interface/tutorials/galaxy-on-dockstore/slides.html 2022-01-14 2022-10-27 4 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 2297076 5693758 2.383333 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 1598 2147 2.750000 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 5018 7805 2.166667 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 0 765 1024 4.800000 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 69 83 4.966667 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 2703 3660 3.300000 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 0 254 308 2.550000 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 0 153 176 2.616667 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 0 400 606 2.300000 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 2968 3835 3.583333 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 0 114 155 4.166667 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 4446 5883 3.116667 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 30 32 0.016667 0
Using Galaxy and Managing your Data JupyterLab in Galaxy https://training.galaxyproject.org//topics/galaxy-interface/tutorials/jupyterlab/tutorial.html 2020-03-05 2025-04-25 9 True False False False interactive_tool_jupyter_notebook UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 2092 3360 2.816667 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 7324 9729 1.633333 0
Using Galaxy and Managing your Data Using dataset collections https://training.galaxyproject.org//topics/galaxy-interface/tutorials/collections/tutorial.html Read mapping, Sequence alignment, Generation, Genome indexing 2016-09-30 2024-12-05 20 True False True False bwa_mem, snpSift_extractFields, lofreq_call, collapse_dataset UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 15621 21415 3.000000 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 2347 3114 2.433333 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 Validation, Read mapping, Visualisation, Sequencing quality control 2025-05-26 2025-05-26 1 True False False False falco, multiqc UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 173 206 1.733333 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 5445 7021 2.833333 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, Coding region prediction, Genome visualisation 2018-03-06 2025-03-19 26 True True True True prokka, jbrowse UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2863372 7560948 4.366667 0
Genome Annotation From small to large-scale genome comparison https://training.galaxyproject.org//topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.html Multiple sequence alignment 2021-02-08 2024-07-31 8 True True False True tp_awk_tool, gecko, chromeister, clustalw UseGalaxy.eu, UseGalaxy.org.au GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz 0 2800247 7369288 4.633333 0
Genome Annotation Comparison of two annotation tools - Helixer and Braker3 https://training.galaxyproject.org//topics/genome-annotation/tutorials/comparison-braker-helixer-annotation/tutorial.html Sequence assembly, Genomics Sequence annotation, Genome visualisation, Genome annotation, Gene prediction, Sequence alignment, Differential protein expression profiling, Sequence assembly validation 2025-06-20 2025-06-25 2 True False False True gffread, jbrowse, busco, rna_star, omark, braker3, helixer 0 266 324 2.000000 0
Genome Annotation Secondary metabolite discovery https://training.galaxyproject.org//topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html Gene prediction, Service invocation, Sequence clustering, Data handling, Differential gene expression analysis 2024-02-21 2024-09-27 2 True False False True ctb_silicos_qed, ncbi_acc_download, edu.tamu.cpt.gff3.customGbkToGff, openbabel_remDuplicates, ctb_simsearch, tp_awk_tool, ctb_np-likeness-calculator, interactive_tool_jupyter_notebook, antismash, Remove beginning1, bp_genbank2gff3, collapse_dataset, ctb_chemfp_mol2fps UseGalaxy.eu 0 618 783 1.316667 0
Genome Annotation Refining Genome Annotations with Apollo (prokaryotes) https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis Genome visualisation 2021-06-04 2025-05-15 22 True True True True create_or_update, jbrowse, iframe, create_account, list_organism UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2619764 6752999 5.116667 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 Genome annotation, Gene prediction, Sequence alignment, Differential protein expression profiling, Sequence annotation, Genome visualisation, Sequence assembly validation 2025-03-17 2025-06-20 4 True False False True gffread, jbrowse, busco, rna_star, fasta-stats, omark, braker3 0 1167 1453 2.033333 0
Genome Annotation Masking repeats with RepeatMasker https://training.galaxyproject.org//topics/genome-annotation/tutorials/repeatmasker/tutorial.html Sequence composition, complexity and repeats, Genomics Genome annotation, Mapping, RNA-Seq analysis, Repeat sequence detection, Editing 2021-11-29 2025-06-03 22 True False True True bedtools_maskfastabed, red, repeatmodeler, repeatmasker_wrapper UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 9830 12553 1.383333 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 Antimicrobial resistance prediction, Read mapping, Genome annotation, Genome visualisation 2024-01-23 2025-06-10 9 True False True True jbrowse, upload1, tbl2gff3, staramr_search, Grep1, bakta, bowtie2 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, UseGalaxy.org (Main) 0 3221 4425 2.950000 0
Genome Annotation Bacterial Genome Annotation https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements Sequence motif recognition, Genome assembly, Genome visualisation, Protein feature detection, Genome annotation, Nucleic acid feature detection, Multilocus sequence typing, Scaffolding, Structural variation detection 2024-02-01 2024-10-15 6 True False True True Grouping1, jbrowse, upload1, tp_replace_in_column, isescan, tp_tail_tool, tbl2gff3, bakta, integron_finder, plasmidfinder UseGalaxy.eu, UseGalaxy.fr Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main) 0 5939 7985 2.550000 0
Genome Annotation Genome annotation with Helixer https://training.galaxyproject.org//topics/genome-annotation/tutorials/helixer/tutorial.html Biodiversity, Genomics, Zoology, Plant biology Genome annotation, Gene prediction, Differential protein expression profiling, Sequence annotation, Genome visualisation, Sequence assembly validation 2024-08-21 2025-06-04 8 True False False True gffread, jbrowse, busco, jcvi_gff_stats, omark, helixer 0 1111 1331 1.666667 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 2844954 7529740 2.450000 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 39 45 1.683333 0
Genome Annotation Bacterial pangenomics https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-pangenomics/tutorial.html Genomics, Microbiology Essential dynamics, Rarefaction, Genome annotation, Sequence assembly 2025-03-14 2025-03-14 1 True False False False ppanggolin_msa, ppanggolin_all, upload1 UseGalaxy.eu, UseGalaxy.fr 0 78 91 1.116667 0
Genome Annotation Bacterial genome quality control https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html Genomics, Microbiology Statistical calculation, Sequence composition calculation, Genome comparison, Validation, Sequencing quality control, Sequence assembly validation 2025-03-14 2025-03-14 1 True False False False drep_dereplicate, checkm2, upload1 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) 0 67 74 2.916667 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, Remove beginning1, bg_uniq, cat1, Cut1, datasets_download_genome, sort1 UseGalaxy.fr UseGalaxy.cz 0 67 80 3.366667 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 34887 63639 1.450000 0
Genome Annotation Comparative gene analysis in unannotated genomes https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html Genomics, Gene and protein families, Sequence analysis, Phylogeny, Comparative genomics De-novo assembly, Database search, Coding region prediction, Sequence alignment analysis, Transcriptome assembly, Phylogenetic tree generation, Multiple sequence alignment 2022-09-08 2025-06-03 10 True False False True join1, bg_diamond, tp_split_on_column, collapse_dataset, tab2fasta, Filter1, Add_a_column1, regexColumn1, rapidnj, cat1, Cut1, orfipy, gops_intersect_1, rbc_mafft, bg_diamond_makedb, bg_diamond_view UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 1792 2538 3.100000 0
Genome Annotation Genome annotation with Funannotate https://training.galaxyproject.org//topics/genome-annotation/tutorials/funannotate/tutorial.html Gene and protein families Sequence motif recognition, Information extraction, Sequence annotation, Genome visualisation, Protein feature detection, Genome annotation, Formatting, Homology-based gene prediction, Sequence alignment, Fold recognition, Query and retrieval, Sequence assembly validation 2021-11-29 2025-06-10 26 True False True True aegean_parseval, interproscan, eggnog_mapper, busco, funannotate_compare, jbrowse, funannotate_predict, rna_star, picard_MergeSamFiles, funannotate_annotate UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org.au 0 10413 14798 1.966667 0
Genome Annotation Genome annotation with Maker (short) https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html Genome annotation, Sequence annotation, Genome visualisation, Sequence assembly validation 2021-01-12 2024-02-29 3 True False False True gffread, maker, jbrowse, busco, maker_map_ids, jcvi_gff_stats, fasta-stats UseGalaxy.be 0 3878 5471 2.983333 0
Genome Annotation Essential genes detection with Transposon insertion sequencing https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html Genomics, Microbiology, Sequence analysis, Mobile genetic elements Transposon prediction, Sequence trimming, Primer removal, Read pre-processing 2019-07-02 2024-03-18 12 True True False True cutadapt, tp_easyjoin_tool, gff_to_prot, bowtie_wrapper, Filter1, Add_a_column1, transit_gumbel, Cut1, tp_sort_header_tool, deeptools_bam_coverage, bg_find_subsequences, __EXTRACT_DATASET__ UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.eu 0 2852966 7544276 4.200000 0
Genome Annotation Genome annotation with Maker https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html Sequence annotation, Genome visualisation, Genome annotation, Gene prediction, Homology-based gene prediction, Ab-initio gene prediction, Operation, Sequence assembly validation 2018-09-24 2024-02-29 14 True False False True gffread, maker, jbrowse, busco, maker_map_ids, jcvi_gff_stats, snap_training, fasta-stats, augustus_training UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.org.au 0 13652 24222 1.866667 0
Genome Annotation Functional annotation of protein sequences https://training.galaxyproject.org//topics/genome-annotation/tutorials/functional/tutorial.html Function analysis, Protein sites, features and motifs Sequence motif recognition, Genome annotation, Homology-based gene prediction, Sequence alignment analysis, Information extraction, Fold recognition, Query and retrieval, Protein feature detection 2022-07-20 2025-06-03 12 True False False True interproscan, ncbi_blastp_wrapper, eggnog_mapper, bg_diamond UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 4033 5440 1.683333 0
Genome Annotation Refining Genome Annotations with Apollo (eukaryotes) https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo-euk/tutorial.html Genomics Genome visualisation 2022-08-22 2025-06-03 16 True False False False iframe, create_or_update, jbrowse UseGalaxy.no UseGalaxy.cz, UseGalaxy.eu 0 1404 2162 2.450000 0
Genome Annotation Long non-coding RNAs (lncRNAs) annotation with FEELnc https://training.galaxyproject.org//topics/genome-annotation/tutorials/lncrna/tutorial.html Annotation, Transcriptome assembly, RNA-Seq analysis, Sequence annotation, Classification 2022-09-23 2024-09-18 11 True False True True gffread, Extract_features1, stringtie, feelnc, tp_cat UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 1847 2475 2.166667 0
Genome Annotation CRISPR screen analysis https://training.galaxyproject.org//topics/genome-annotation/tutorials/crispr-screen/tutorial.html Statistical calculation, Sequence trimming, Primer removal, Genetic variation analysis, Sequencing quality control, Sequence composition calculation, Read pre-processing, Validation 2021-10-15 2024-08-08 12 True True True True mageck_test, multiqc, cutadapt, tp_awk_tool, fastqc, mageck_count, volcanoplot, mageck_mle UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2452680 6164845 4.316667 0
Variant Analysis Microbial Variant Calling https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation Genome visualisation, Phylogenetic tree generation, Phylogenetic tree visualisation, Variant calling 2018-02-26 2025-03-19 24 True False False True snippy, jbrowse UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 14933 23903 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 2850261 7536539 4.783333 0
Imaging Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/omero-suite/tutorial.html Image analysis 2024-12-04 2025-04-08 3 True False False False omero_get_id, omero_metadata_import, omero_roi_import, omero_get_value, omero_filter, omero_import 0 163 210 3.283333 0
Imaging Training Custom YOLO Models for Segmentation of Bioimages https://training.galaxyproject.org//topics/imaging/tutorials/yolo-segmentation-training/tutorial.html Image annotation, Visualisation, Image analysis, Data handling 2025-07-25 2025-10-14 4 True False False True graphicsmagick_image_convert, interactive_tool_anylabeling, json2yolosegment, yolo_training, unzip, ip_histogram_equalization UseGalaxy.eu 0 178 231 1.083333 0
Imaging Introduction to Image Analysis using Galaxy https://training.galaxyproject.org//topics/imaging/tutorials/imaging-introduction/tutorial.html Image annotation, Image analysis, Data handling, Visualisation 2019-08-13 2025-03-20 14 True False False True ip_binary_to_labelimage, ip_threshold, ip_filter_standard, ip_imageinfo, ip_count_objects, unzip, ip_overlay_images, ip_histogram_equalization UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 2610 3658 1.766667 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, Data handling, Visualisation 2025-04-09 2025-04-16 5 True False False True bioimage_inference, ip_binary_to_labelimage, ip_threshold, image_math, ip_overlay_images, ip_split_image, __EXTRACT_DATASET__ UseGalaxy.eu 0 157 188 3.600000 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, Data handling, Visualisation 2025-03-20 2025-03-20 2 True False False True ip_spot_detection_2d, ip_binary_to_labelimage, idr_download_by_ids, ip_points_to_label, unzip, ip_overlay_images, ip_histogram_equalization UseGalaxy.cz, UseGalaxy.eu 0 144 183 1.583333 0
Imaging Voronoi segmentation https://training.galaxyproject.org//topics/imaging/tutorials/voronoi-segmentation/tutorial.html Image annotation, Image analysis, Data handling, Visualisation 2025-05-13 2025-07-11 4 True False False True colorize_labels, ip_count_objects, ip_binary_to_labelimage, voronoi_tessellation, ip_2d_feature_extraction, ip_threshold, ip_filter_standard, ip_imageinfo, ip_convertimage, unzip, ip_overlay_images, image_math, repeat_channels UseGalaxy.eu 0 231 367 4.250000 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, Data handling, Visualisation 2025-04-28 2025-04-28 1 True False False True ip_segmetrics, tp_split_on_column, param_value_from_file, collapse_dataset, ip_threshold, ip_filter_standard, ip_histogram_equalization UseGalaxy.eu UseGalaxy.cz 0 66 78 2.616667 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, Image analysis, Data handling, Visualisation 2025-08-11 2025-08-11 1 True False False True graphicsmagick_image_convert, ip_2d_feature_extraction, ip_points_to_label, ip_imageinfo, ip_split_image, interactive_tool_qupath, __EXTRACT_DATASET__ UseGalaxy.eu 0 155 191 1.466667 0
Imaging Analyse HeLa fluorescence siRNA screen https://training.galaxyproject.org//topics/imaging/tutorials/hela-screen-analysis/tutorial.html Image annotation, Image analysis, Data handling, Visualisation 2019-08-13 2024-11-07 12 True False False True ip_2d_filter_segmentation_by_features, ip_binary_to_labelimage, ip_2d_feature_extraction, collapse_dataset, ip_threshold, ip_filter_standard, unzip UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no 0 755 974 2.216667 0
Imaging End-to-End Tissue Microarray Image Analysis with Galaxy-ME https://training.galaxyproject.org//topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html 2023-02-14 2025-03-14 6 True False False True scanpy_compute_graph, vitessce_spatial, squidpy_spatial, unet_coreograph, mesmer, gate_finder, basic_illumination, scimap_mcmicro_to_anndata, palom, scimap_phenotyping, ashlar, ip_convertimage, rename_tiff_channels, celesta, quantification 0 1343 1825 1.900000 0
Imaging Object tracking using CellProfiler https://training.galaxyproject.org//topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html Image analysis, Quantification, Parsing 2021-03-17 2024-10-15 8 True False False True cp_export_to_spreadsheet, cp_measure_object_intensity, cp_track_objects, unzip, cp_measure_object_size_shape, cp_color_to_gray, cp_common, cp_overlay_outlines, cp_cellprofiler, cp_identify_primary_objects, cp_tile, cp_save_images UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz 0 2128 2660 1.066667 0
Imaging Nucleoli segmentation and feature extraction using CellProfiler https://training.galaxyproject.org//topics/imaging/tutorials/tutorial-CP/tutorial.html Image analysis, Quantification, Parsing 2020-07-01 2024-10-15 9 True True False True cp_measure_object_intensity, cp_gray_to_color, cp_display_data_on_image, cp_enhance_or_suppress_features, idr_download_by_ids, cp_identify_primary_objects, cp_save_images, cp_measure_image_intensity, cp_cellprofiler, cp_measure_granularity, cp_measure_texture, cp_export_to_spreadsheet, cp_convert_objects_to_image, cp_measure_object_size_shape, cp_common, cp_measure_image_area_occupied, cp_mask_image, cp_relate_objects, cp_image_math, cp_measure_image_quality UseGalaxy.be, UseGalaxy.eu Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2849125 7535552 3.683333 0
Imaging Tracking of mitochondria and capturing mitoflashes https://training.galaxyproject.org//topics/imaging/tutorials/detection-of-mitoflashes/tutorial.html Image analysis 2024-11-20 2024-11-20 2 True False False True ip_points_association_nn, ip_curve_fitting, ip_spot_detection_2d UseGalaxy.cz, UseGalaxy.eu 0 137 161 0.900000 0
Imaging FAIR Bioimage Metadata https://training.galaxyproject.org//topics/imaging/tutorials/bioimage-metadata/tutorial.html 2025-10-19 2025-10-19 0 True False False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 0 0 0.000000 0
Imaging REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data https://training.galaxyproject.org//topics/imaging/tutorials/bioimage-REMBI/tutorial.html 2025-10-19 2025-10-19 0 True False True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 0 0 0.000000 0
Introduction to Galaxy Analyses From peaks to genes https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html 2016-03-29 2025-10-04 65 True False False True CONVERTER_interval_to_bed_0, get_flanks1, Grouping1, upload1, tp_replace_in_column, tp_tail_tool, Add_a_column1, Cut1, tp_sort_header_tool, gops_intersect_1 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no 0 20244 33346 3.316667 0
Introduction to Galaxy Analyses How to reproduce published Galaxy analyses https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-reproduce/tutorial.html Visualisation 2021-08-25 2024-10-15 12 True False False True csv_to_tabular, Grouping1, upload1, tp_sorted_uniq, ggplot2_point, Remove beginning1, Cut1, datamash_ops Galaxy@AuBi, UseGalaxy.eu, UseGalaxy.org (Main) MISSISSIPPI, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2156 2883 4.116667 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 Grouping1, {{version_join}}, tp_sorted_uniq, {{version_count}}, {{version_select_first}}, {{version_cut_advanced}}, {{version_cat}}, Add_a_column1, {{version_sort}}, Count1, {{version_remove_beginning}}, {{version_split}}, tp_cat, {{version_unique}}, join1, {{version_wc}}, {{version_replace_text_line}}, Remove beginning1, tp_sort_header_tool, regexColumn1, {{version_remove_columns_by_header}}, wc_gnu, {{version_paste}}, datamash_ops, tp_split_on_column, upload1, {{version_datamash}}, {{version_replace_text_column}}, Filter1, tabular_to_csv, Show beginning1, Cut1, cat1, {{version_cut_columns}}, {{version_filter}}, {{version_compute}} 0 5825 8494 3.450000 0
Introduction to Galaxy Analyses NGS data logistics https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html Generation, Data handling, Genome indexing, Validation, Sequencing quality control, Formatting, Sequence alignment, SNP detection, Read mapping, Sequence contamination filtering 2017-02-22 2025-07-24 38 True False True True picard_MarkDuplicates, bwa_mem, bwa_mem2, snpEff, multiqc, snpEff_build_gb, lofreq_call, lofreq_indelqual, snpeff_sars_cov_2, samtools_view, Filter1, fasterq_dump, collapse_dataset, snpSift_extractFields, fastp, lofreq_viterbi, bwa, samtools_stats UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au MISSISSIPPI, UseGalaxy.cz 0 19674 33660 3.400000 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 gene2exon1, Filter1, cat1, gops_intersect_1, tp_cat UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au MISSISSIPPI 0 19825 31386 3.566667 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 2845375 7530050 2.450000 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 2845375 7530050 2.450000 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 0 427 488 2.750000 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 7970 11274 1.483333 0
Introduction to Galaxy Analyses A short introduction to Galaxy https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-short/tutorial.html Sequence composition calculation, Statistical calculation, Sequencing quality control 2018-08-27 2025-09-23 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 2897722 7611515 7.050000 0
Introduction to Galaxy Analyses Galaxy Basics for everyone https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html Visualisation 2019-11-14 2024-12-02 34 True False True True csv_to_tabular, Grouping1, upload1, tp_sorted_uniq, ggplot2_point, Remove beginning1, Cut1, datamash_ops UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) Galaxy@AuBi, MISSISSIPPI, UseGalaxy.cz 0 22174 35199 3.983333 0
Introduction to Galaxy Analyses Galaxy Basics for genomics https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-101/tutorial.html Mapping 2016-12-19 2025-04-22 68 True False True True bedtools_intersectbed, upload1, tp_head_tool, tp_sort_header_tool, datamash_ops, comp1 UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.no 0 46700 75543 3.433333 0
Introduction to Galaxy Analyses Very Short Introductions: QC https://training.galaxyproject.org//topics/introduction/tutorials/vsi_qc/tutorial.html Validation, Sequence contamination filtering, Sequencing quality control 2024-03-26 2024-06-25 4 True False False False fastp, multiqc Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au MISSISSIPPI, UseGalaxy.no 0 294 357 3.166667 0
Materials Science Finding the muon stopping site with pymuon-suite in Galaxy https://training.galaxyproject.org//topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.html 2024-01-22 2024-06-14 2 True False True True pm_muairss_read, pm_uep_opt UseGalaxy.cz, UseGalaxy.eu 0 241 321 2.166667 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_mz_images, cardinal_quality_report, Filter1, cardinal_filtering, cardinal_data_exporter, cardinal_spectra_plots UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2971 4231 1.783333 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 Chromatographic alignment, Chromatogram visualisation, Filtering, Format validation, Spectral library search, Mass spectrum visualisation, Formatting, Label-free quantification, Clustering, Peak detection, Validation, Imputation, Standardisation and normalisation, Data filtering, Correlation 2023-05-08 2023-11-09 5 True False False True msconvert, riassigner, abims_xcms_retcor, waveica, matchms_formatter, abims_xcms_xcmsSet, abims_xcms_group, msnbase_readmsdata, ramclustr_define_experiment, matchms_filtering, ramclustr, matchms_similarity, xcms_merge, abims_xcms_fillPeaks UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au 0 2594 3351 1.533333 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_mz_images, cardinal_preprocessing, cardinal_segmentations, join_files_on_column_fuzzy, cardinal_quality_report, maldi_quant_peak_detection, cardinal_classification, Filter1, cardinal_combine, maldi_quant_preprocessing, Grep1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 1957 2810 1.850000 0
Metabolomics Molecular formula assignment and mass recalibration with MFAssignR package https://training.galaxyproject.org//topics/metabolomics/tutorials/mfassignr/tutorial.html Visualisation 2025-05-19 2025-05-19 1 True False False True mfassignr_isofiltr, mfassignr_findRecalSeries, mfassignr_recal, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_snplot, mfassignr_histnoise, mfassignr_kmdnoise, mfassignr_recallist 0 81 99 2.500000 0
Metabolomics Mass spectrometry: LC-MS analysis https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms/tutorial.html Chromatogram visualisation, Chromatographic alignment, Mass spectrum visualisation, Data filtering, Label-free quantification, Peak detection, Validation 2019-07-02 2025-09-21 13 True False False True xcms_export_samplemetadata, Univariate, abims_xcms_retcor, generic_filter, abims_xcms_xcmsSet, abims_xcms_group, msnbase_readmsdata, xcms_plot_chromatogram, Batch_correction, wsdl_hmdb, quality_metrics, abims_CAMERA_annotateDiffreport, xcms_merge, abims_xcms_fillPeaks UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 12586 20605 1.600000 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 tp_cut_tool, qcxms_getres, openbabel_compound_convert, param_value_from_file, qcxms_neutral_run, split_file_to_collection, xtb_molecular_optimization, __FILTER_FAILED_DATASETS__, ctb_im_conformers, tp_cat, qcxms_production_run UseGalaxy.eu UseGalaxy.org.au 0 713662 1641087 3.166667 0
Metabolomics Mass spectrometry: LC-MS preprocessing with XCMS https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html Chromatogram visualisation, Chromatographic alignment, Mass spectrum visualisation, Data filtering, Label-free quantification, Peak detection, Validation 2020-02-04 2024-10-15 14 True True False False xcms_export_samplemetadata, abims_xcms_retcor, intens_check, abims_xcms_xcmsSet, abims_xcms_group, msnbase_readmsdata, xcms_plot_chromatogram, idchoice, abims_xcms_summary, abims_CAMERA_annotateDiffreport, xcms_merge, abims_xcms_fillPeaks UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2851391 7539529 4.750000 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 2845375 7530055 2.450000 0
Metabolomics Mass spectrometry: GC-MS analysis with the metaMS package https://training.galaxyproject.org//topics/metabolomics/tutorials/gcms/tutorial.html Chromatogram visualisation, Chromatographic alignment, Mass spectrum visualisation, Data filtering, Label-free quantification, Peak detection, Validation 2021-09-22 2025-10-01 8 True False False False xcms_export_samplemetadata, abims_xcms_xcmsSet, abims_xcms_group, msnbase_readmsdata, xcms_plot_chromatogram, metams_runGC, xcms_merge, abims_xcms_fillPeaks UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.no 0 1485 2399 1.666667 0
Metabolomics Mass spectrometry: LC-MS data processing https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html 2021-12-14 2024-10-15 8 True False False False Multivariate, generic_filter, normalization, intens_check, Batch_correction, quality_metrics UseGalaxy.fr UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no 0 2752 3727 1.966667 0
Microbiome Introduction to Microbiome Analysis https://training.galaxyproject.org//topics/microbiome/tutorials/introduction/slides.html 2017-06-22 2024-08-08 5 False True True False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 2845375 7530055 2.450000 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 Phylogenetic analysis, DNA barcoding, Sequencing quality control, Sequence read processing, Taxonomic classification, Sequence clustering, Visualisation 2017-06-22 2024-08-09 4 True False False True mothur_screen_seqs, mothur_make_group, mothur_classify_otu, metaphlan2, mothur_unique_seqs, mothur_summary_seqs, mothur_count_seqs, metaphlan2krona, mothur_merge_files, mothur_align_seqs, humann2_renorm_table, humann2, mothur_make_shared, krona-text, mothur_pre_cluster, mothur_make_biom, mothur_classify_seqs, humann2_regroup_table, taxonomy_krona_chart, mothur_cluster_split, mothur_filter_seqs UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 7951 10780 2.716667 0
Microbiome Metatranscriptomics analysis using microbiome RNA-seq data (short) https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis Statistical calculation, Phylogenetic tree editing, Sequence alignment analysis, Phylogenetic analysis, Phylogenetic tree visualisation, Primer removal, Sequence trimming, Sequencing quality control, Taxonomic classification, Conversion, Sequence composition calculation, Read pre-processing, Validation, Visualisation, Species frequency estimation, Sequence similarity search, Sequence comparison, Phylogenetic inference 2020-02-13 2025-06-16 6 True False True True metaphlan, bg_sortmerna, humann_unpack_pathways, tp_find_and_replace, fastq_paired_end_interlacer, humann_rename_table, multiqc, graphlan_annotate, tp_sort_header_tool, humann_renorm_table, humann_regroup_table, humann, combine_metaphlan2_humann2, Grep1, humann_split_stratified_table, graphlan, cutadapt, fastqc, taxonomy_krona_chart, Cut1, export2graphlan UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.no 0 691 881 2.300000 0
Microbiome Building an amplicon sequence variant (ASV) table from 16S data using DADA2 https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Analysis, Visualisation, Deposition, DNA barcoding, Variant calling 2024-06-05 2025-07-03 11 True False True True dada2_makeSequenceTable, Grouping1, tp_replace_in_line, dada2_filterAndTrim, Add_a_column1, tp_replace_in_column, phyloseq_from_dada2, __SORTLIST__, dada2_plotQualityProfile, interactive_tool_phyloseq, dada2_dada, dada2_removeBimeraDenovo, dada2_learnErrors, dada2_assignTaxonomyAddspecies, __UNZIP_COLLECTION__, dada2_mergePairs, collection_element_identifiers, tp_head_tool, dada2_seqCounts, cat1 UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 6280 8875 2.383333 0
Microbiome Taxonomic Profiling and Visualization of Metagenomic Data https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Statistical calculation, Genome annotation, Aggregation, Visualisation, Taxonomic classification 2023-05-03 2025-04-24 6 True False True True interactive_tool_pavian, metaphlan, interactive_tool_phinch, krakentools_kreport2krona, taxonomy_krona_chart, kraken2, est_abundance, __UNZIP_COLLECTION__, kraken_biom UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 11417 15283 2.016667 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, Sequence composition calculation, Validation, Visualisation, Sequencing quality control, Taxonomic classification 2020-11-24 2024-07-31 5 True False False True multiqc, fastqc, tp_replace_in_line, porechop, datamash_reverse, Remove beginning1, taxonomy_krona_chart, kraken2, fastp UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr 0 7623 10518 2.600000 0
Microbiome Clinical Metaproteomics 1: Database-Generation https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-1-database-generation/tutorial.html Tag-based peptide identification, Protein identification, Expression analysis, de Novo sequencing, Target-Decoy 2025-10-19 2025-10-19 0 True False True True metanovo, dbbuilder, uniprotxml_downloader, fasta_merge_files_and_filter_unique_sequences UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.org (Main) 0 0 0 0.000000 0
Microbiome MGnify v5.0 Amplicon Pipeline https://training.galaxyproject.org//topics/microbiome/tutorials/mgnify-amplicon/tutorial.html Metagenomics, Taxonomy, Sequence analysis Comparison, Alignment, Formatting, Validation, Visualisation, Nucleic acid design, Read pre-processing, Sequence feature detection, Statistical calculation, Analysis, k-mer counting, Mapping, Sequence trimming, DNA barcoding, Sequencing quality control, Nucleic acid feature detection, Sequence composition calculation, Sequence contamination filtering 2025-07-30 2025-07-30 2 True False False True bedtools_maskfastabed, cmsearch_deoverlap, Grouping1, param_value_from_file, collapse_dataset, Add_a_column1, tp_find_and_replace, ampvis2_heatmap, trimmomatic, multiqc, bedtools_getfastabed, infernal_cmsearch, biom_convert, query_tabular, gops_concat_1, filter_tabular, ampvis2_load, prinseq, tp_awk_tool, seqprep, __FILTER_FROM_FILE__, fastq_filter, mapseq, wc_gnu, fastq_dl, __UNZIP_COLLECTION__, __MERGE_COLLECTION__, mgnify_seqprep, collection_element_identifiers, cshl_fasta_formatter, fastqc, CONVERTER_gz_to_uncompressed, taxonomy_krona_chart, CONVERTER_uncompressed_to_gz, lotus2, fastp, collection_column_join, __FILTER_EMPTY_DATASETS__, fastq_to_fasta_python 0 102 124 3.116667 0
Microbiome Clinical Metaproteomics 4: Quantitation https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-4-quantitation/tutorial.html Statistical calculation, Visualisation, Heat map generation, Standardisation and normalisation, Clustering, Protein quantification, Principal component plotting, Imputation 2025-10-19 2025-10-19 0 True False True True Grep1, maxquant, Cut1, Grouping1 UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 0 0 0.000000 0
Microbiome Clinical Metaproteomics 3: Verification https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html 2025-10-19 2025-10-19 0 True False True True dbbuilder, Grouping1, uniprotxml_downloader, query_tabular, Remove beginning1, collapse_dataset, Filter1, Cut1, fasta_merge_files_and_filter_unique_sequences, pepquery2, tp_cat UseGalaxy.cz, UseGalaxy.eu UseGalaxy.org (Main), UseGalaxy.org.au 0 0 0 0.000000 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 Genome assembly, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Sequence assembly visualisation, Box-Whisker plot plotting, Data handling, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation, Variant calling, Taxonomic classification, Scatter plot plotting, Aggregation, Phylogenetic tree reconstruction, Validation, Visualisation, De-novo assembly, Mapping assembly, Sequence assembly, Statistical calculation, Mapping, Sequence alignment analysis, Antimicrobial resistance prediction, Sequencing quality control, Multiple sequence alignment, Base-calling, Phylogenetic tree analysis, Multilocus sequence typing, Sequence composition calculation, Cross-assembly, Pairwise sequence alignment, Sequence contamination filtering 2023-01-26 2024-09-27 11 True False True True Grouping1, tp_sorted_uniq, param_value_from_file, porechop, snpSift_filter, tp_multijoin_tool, collapse_dataset, tab2fasta, Add_a_column1, split_file_to_collection, snpSift_extractFields, tp_find_and_replace, fasta_merge_files_and_filter_unique_sequences, flye, __FILTER_FAILED_DATASETS__, Count1, tp_cut_tool, barchart_gnuplot, bcftools_norm, medaka_consensus_pipeline, multiqc, bedtools_getfastabed, tp_replace_in_column, bamtools_split_mapped, table_compute, abricate, Remove beginning1, kraken2, minimap2, nanoplot, samtools_coverage, samtools_fastx, fasttree, compose_text_param, bcftools_consensus, regex1, krakentools_kreport2krona, regexColumn1, clair3, Grep1, Paste1, __BUILD_LIST__, clustalw, newick_display, __FILTER_EMPTY_DATASETS__, krakentools_extract_kraken_reads, mlst, tp_split_on_column, collection_element_identifiers, fastqc, tp_head_tool, CONVERTER_gz_to_uncompressed, samtools_depth, taxonomy_krona_chart, ggplot2_heatmap, fastp, Cut1, collection_column_join, bandage_image, add_line_to_file, fasta2tab UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org.au 0 4630 6981 3.416667 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 Phylogenetic tree editing, Taxonomic classification, Aggregation, Validation, Visualisation, Read pre-processing, Statistical calculation, Phylogenetic tree visualisation, Sequence alignment analysis, Phylogenetic analysis, Primer removal, Sequence trimming, Sequencing quality control, Conversion, Sequence composition calculation, Species frequency estimation, Sequence similarity search, Sequence comparison, Phylogenetic inference 2019-11-21 2025-06-16 6 True True True True metaphlan, Grouping1, bg_sortmerna, humann_unpack_pathways, tp_find_and_replace, fastq_paired_end_interlacer, humann_rename_table, multiqc, graphlan_annotate, tp_sort_header_tool, humann_renorm_table, humann_regroup_table, humann, combine_metaphlan_humann, Grep1, humann_split_stratified_table, graphlan, cutadapt, fastqc, taxonomy_krona_chart, Cut1, export2graphlan UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.eu 0 2851586 7538037 4.316667 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, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi 0 6010 7237 1.250000 0
Microbiome Assembly of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html Metagenomics, Sequence assembly Genome assembly, Sequence assembly visualisation, Data handling, Variant calling, Local alignment, Formatting, Read mapping, Visualisation, Sequence file editing, Read pre-processing, Statistical calculation, Sequence alignment analysis, Sequence trimming, Primer removal, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering, Sequence assembly validation 2022-12-05 2025-06-16 6 True False True True coverm_contig, filter_tabular, random_lines1, cutadapt, fastqc, megahit_contig2fastg, ngsutils_bam_filter, megahit, bg_uniq, bandage_info, collection_column_join, seqtk_subseq, bandage_image, metaspades, bowtie2, quast, bamtools, tp_cat UseGalaxy.cz, UseGalaxy.eu 0 4120 5765 3.033333 0
Microbiome Identification of the micro-organisms in a beer using Nanopore sequencing https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html Metagenomics, Microbial ecology, Taxonomy, Sequence analysis Statistical calculation, Sequence contamination filtering, Aggregation, Sequence composition calculation, Visualisation, Sequencing quality control, Taxonomic classification 2022-09-29 2024-11-29 5 True False True True fastqc, porechop, krakentools_kreport2krona, Filter1, taxonomy_krona_chart, kraken2, fastp GalaxyTrakr, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2502 3630 2.833333 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 Genome assembly, Sequence assembly visualisation, Box-Whisker plot plotting, Antimicrobial resistance prediction, Sequence analysis, De-novo assembly, Scatter plot plotting, Aggregation, Pairwise sequence alignment, Mapping assembly 2019-06-25 2024-06-14 4 True False True True unicycler, miniasm, racon, nanoplot, minimap2, staramr_search, bandage_image, gfa_to_fa, PlasFlow UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 3096 4347 2.950000 0
Microbiome Clinical Metaproteomics 2: Discovery https://training.galaxyproject.org//topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html Statistical calculation, Heat map generation, Standardisation and normalisation, Filtering, Imputation, Formatting, Clustering, Protein quantification, Principal component plotting, Visualisation 2025-10-19 2025-10-19 0 True False True True dbbuilder, msconvert, filter_tabular, Grouping1, fasta_cli, query_tabular, Remove beginning1, maxquant, Filter1, peptide_shaker, search_gui, Cut1, fasta_merge_files_and_filter_unique_sequences, Grep1, ident_params, fasta2tab, tp_cat UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 0 0 0.000000 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 join1, CONVERTER_fasta_to_tabular, ggplot2_histogram, Grouping1, tp_replace_in_column, tp_sorted_uniq, tp_tail_tool, count_gff_features, histogram_rpy, tab2fasta, Filter1, Add_a_column1, minimap2, cat1, Cut1, add_column_headers, sort1, MQoutputfilter UseGalaxy.fr 0 271 311 0.916667 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 2025-10-19 2025-10-19 0 True False True True Grep1, msstatstmt, unipept UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 0 0 0.000000 0
Microbiome Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2 https://training.galaxyproject.org//topics/microbiome/tutorials/lotus2-identifying-fungi/tutorial.html 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 0 622 785 1.600000 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 0 520 812 2.916667 0
Microbiome Binning of metagenomic sequencing data https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html Metagenomics, Sequence assembly Statistical calculation, Genome assembly, Sequence composition calculation, Validation, Sequencing quality control, Sequence assembly validation 2023-12-05 2025-05-15 6 True False True False checkm_lineage_wf, megahit GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.org (Main), UseGalaxy.org.au 0 5215 6400 1.533333 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 26 32 4.183333 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 0 380 611 3.233333 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 analysis, DNA barcoding, Phylogenetic tree generation, Sequencing quality control, Sequence read processing, Taxonomic classification, Sequence clustering, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Visualisation 2019-05-13 2024-06-14 5 True False True True mothur_screen_seqs, mothur_remove_lineage, mothur_classify_otu, collapse_dataset, mothur_unique_seqs, mothur_sub_sample, mothur_heatmap_sim, mothur_summary_seqs, mothur_count_seqs, mothur_venn, mothur_rarefaction_single, mothur_cluster, mothur_chimera_vsearch, mothur_make_shared, mothur_remove_groups, mothur_tree_shared, mothur_dist_shared, mothur_summary_single, mothur_count_groups, newick_display, mothur_remove_seqs, mothur_pre_cluster, mothur_classify_seqs, mothur_dist_seqs, mothur_cluster_split, XY_Plot_1, mothur_filter_seqs UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 4951 8234 4.600000 0
Microbiome 16S Microbial Analysis with mothur (extended) https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html Microbial ecology, Taxonomy, Sequence analysis, Metabarcoding Phylogenetic analysis, DNA barcoding, Phylogenetic tree generation, Sequencing quality control, Sequence read processing, Taxonomic classification, Sequence clustering, Phylogenetic tree analysis, Phylogenetic tree reconstruction, Visualisation 2017-02-12 2024-03-14 4 True False False True mothur_screen_seqs, mothur_remove_lineage, mothur_taxonomy_to_krona, mothur_get_groups, mothur_classify_otu, mothur_unique_seqs, mothur_make_contigs, mothur_sub_sample, mothur_heatmap_sim, mothur_summary_seqs, mothur_count_seqs, mothur_venn, mothur_rarefaction_single, mothur_cluster, mothur_align_seqs, mothur_seq_error, mothur_chimera_vsearch, mothur_make_shared, mothur_remove_groups, mothur_tree_shared, mothur_dist_shared, mothur_summary_single, mothur_count_groups, newick_display, mothur_remove_seqs, mothur_pre_cluster, mothur_make_biom, mothur_classify_seqs, mothur_dist_seqs, taxonomy_krona_chart, mothur_cluster_split, XY_Plot_1, mothur_filter_seqs UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 11419 16756 2.766667 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 Generation, Sequence alignment analysis, Genome indexing, Primer removal, Sequence analysis, Sequencing quality control, Multiple sequence alignment, Local alignment, Sequence alignment, Global alignment, Read mapping, Sequence contamination filtering 2023-05-15 2024-03-20 4 True False False True ivar_consensus, param_value_from_file, Add_a_column1, __ZIP_COLLECTION__, qualimap_bamqc, EMBOSS: maskseq51, samtools_view, mimodd_info, fatovcf, __APPLY_RULES__, bwa_mem, compose_text_param, fasta_regex_finder, samtools_merge, Grep1, ivar_trim, datamash_ops, upload1, rbc_mafft, fastp, Cut1, fasta_compute_length UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org (Main) 0 990 1178 2.400000 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 Statistical calculation, Phylogenetic tree visualisation, Sequence alignment analysis, Antimicrobial resistance prediction, Phylogenetic tree generation, Sequencing quality control, Taxonomic classification, Variant calling, Sequence analysis, Genome visualisation, Local alignment, Sequence alignment, Global alignment, Sequence composition calculation, Validation, Sequence contamination filtering 2020-07-25 2024-07-26 30 True False True True tb_variant_filter, tp_sed_tool, mosdepth, samtools_stats, qualimap_bamqc, multiqc, kraken2, jvarkit_wgscoverageplotter, snippy, bcftools_consensus, EMBOSS:%20seqret84, tp_awk_tool, EMBOSS: seqret84, tbvcfreport, jbrowse, upload1, fastqc, tb_profiler_profile, fastp, __FLATTEN__ 0 7388 11435 3.016667 0
Variant Analysis Avian influenza viral strain analysis from gene segment sequencing data https://training.galaxyproject.org//topics/variant-analysis/tutorials/aiv-analysis/tutorial.html Generation, Data retrieval, Phylogenetic analysis, Genome indexing, Primer removal, Sequence alignment analysis, Data handling, Sequence file editing, Sequence analysis, Sequencing quality control, Multiple sequence alignment, Sequence alignment, Read mapping, De-novo assembly, Sequence contamination filtering 2022-11-21 2024-10-04 10 True False False False qualimap_bamqc, bwa_mem, ivar_consensus, iqtree, upload1, __RELABEL_FROM_FILE__, vapor, samtools_view, bamtools_split_ref, collapse_dataset, rbc_mafft, Show beginning1, tp_find_and_replace, fastp, Grep1, seqtk_subseq UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz 0 1937 2727 2.516667 0
Transcriptomics Whole transcriptome analysis of Arabidopsis thaliana https://training.galaxyproject.org//topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html Sequence trimming, Primer removal, Validation, Sequencing quality control, Differential gene expression analysis, Gene expression analysis, RNA-Seq analysis, Sequence composition calculation, Read mapping, Visualisation, RNA-Seq quantification, Read pre-processing 2021-04-08 2025-08-10 18 True True True True __MERGE_COLLECTION__, multiqc, rbc_mirdeep2_mapper, sample_seqs, targetfinder, deseq2, Filter1, falco, salmon, trim_galore, cat1, Cut1, rbc_mirdeep2_quantifier, filter_by_fasta_ids, sort1 UseGalaxy.cz 0 2705748 7026573 5.016667 0
Sequence analysis Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants https://training.galaxyproject.org//topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html Phylogenetic inference (from molecular sequences), Phylogenetic tree editing, Phylogenetic analysis, Sequence analysis, Multiple sequence alignment 2025-03-26 2025-04-27 2 True False True True iqtree, ete_treeviewer, Remove beginning1, trimal, Filter1, quicktree, rbc_mafft, Cut1, filter_by_fasta_ids, tapscan_classify UseGalaxy.eu 0 200 250 1.283333 0
Sequence analysis NCBI BLAST+ against the MAdLand https://training.galaxyproject.org//topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.html Sequence alignment analysis 2023-01-16 2024-07-31 9 True False False False ncbi_blastx_wrapper, ncbi_blastp_wrapper, bg_diamond Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au GalaxyTrakr, UseGalaxy.no 0 1570 1985 2.933333 0
Single Cell Analysis of plant scRNA-Seq Data with Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-plant/tutorial.html Principal component visualisation, Differential gene expression analysis, Expression profile clustering 2021-04-08 2025-02-13 7 True False True True scanpy_cluster_reduce_dimension, anndata_manipulate, scanpy_remove_confounders, anndata_import, scanpy_inspect, scanpy_plot, scanpy_normalize, scanpy_filter UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2646 3312 1.533333 0
Proteomics Statistical analysis of DIA data https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.html Differential protein expression profiling, Tag-based peptide identification, Spectrum calculation 2020-12-02 2023-11-09 9 True False False True Grep1, Filter1, histogram_rpy, msstats UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.org.au 0 1308 1840 2.650000 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 IDconverter, retrieve_from_hpa, Jvenn, reactome_analysis, cluter_profiler, rna_abbased_data, MQoutputfilter UseGalaxy.be, UseGalaxy.fr 0 3041 4425 2.783333 0
Proteomics Library Generation for DIA Analysis https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html Statistical calculation, Visualisation, Heat map generation, Standardisation and normalisation, Clustering, Protein quantification, Principal component plotting, Imputation 2020-12-02 2025-06-02 12 True False False True OpenSwathDecoyGenerator, diapysef, maxquant, Filter1, OpenSwathAssayGenerator, TargetedFileConverter UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 4501 5876 1.366667 0
Proteomics Detection and quantitation of N-termini (degradomics) via N-TAILS https://training.galaxyproject.org//topics/proteomics/tutorials/ntails/tutorial.html Proteomics 2017-02-14 2025-04-08 16 True False False True FileFilter, HighResPrecursorMassCorrector, PeptideIndexer, FileMerger, ConsensusID, IDMapper, IDMerger, MSGFPlusAdapter, IDFilter, FeatureFinderMultiplex, MzTabExporter, IDConflictResolver, FalseDiscoveryRate 0 835 1156 1.433333 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 Grep1, cardinal_quality_report, cardinal_data_exporter, tp_sort_header_tool UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 2689 4173 1.683333 0
Proteomics Label-free data analysis using MaxQuant https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-label-free/tutorial.html Statistical calculation, Visualisation, Tag-based peptide identification, Heat map generation, Differential protein expression profiling, Standardisation and normalisation, Spectrum calculation, Clustering, Protein quantification, Principal component plotting, Imputation 2020-04-29 2025-05-21 14 True False False True histogram_rpy, maxquant, Filter1, Add_a_column1, Cut1, tp_sort_header_tool, Grep1, msstats UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.org.au 0 19700 28781 1.766667 0
Proteomics metaQuantome 3: Taxonomy https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy Functional clustering, Heat map generation, Filtering, Indexing, Principal component visualisation, Visualisation, Statistical inference, Differential protein expression analysis, Quantification, Query and retrieval 2020-10-29 2024-03-15 14 True False False True metaquantome_sample, metaquantome_expand, metaquantome_stat, metaquantome_db, metaquantome_viz, metaquantome_filter UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 438 576 2.366667 0
Proteomics metaQuantome 1: Data creation https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html Proteomics, Proteogenomics, Biodiversity, Taxonomy Formatting, Label-free quantification, Visualisation, Filtering, Prediction and recognition 2020-10-16 2024-03-14 20 True False False True msconvert, tp_replace_in_column, tp_replace_in_line, regex1, query_tabular, Remove beginning1, Filter1, peptide_shaker, unipept, flashlfq, Cut1, search_gui, Grep1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 879 1492 3.800000 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 tp_cut_tool, IDconverter, retrieve_from_hpa, retr_pepatlas1, prot_features, Jvenn, rna_abbased_data, MQoutputfilter UseGalaxy.be, UseGalaxy.fr 0 1621 2203 2.533333 0
Proteomics Neoantigen 1a: Fusion-Database-Generation https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-fusion-database-generation/tutorial.html Sequence alignment 2025-01-14 2025-07-02 1 True False False True arriba, arriba_get_filters, tp_awk_tool, regex1, rna_star, CONVERTER_gz_to_uncompressed, query_tabular, tab2fasta UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 107 134 1.016667 0
Proteomics Peptide and Protein ID using OpenMS tools https://training.galaxyproject.org//topics/proteomics/tutorials/protein-id-oms/tutorial.html Formatting, Filtering 2017-10-16 2025-04-08 32 True False False True msconvert, XTandemAdapter, PeakPickerHiRes, PeptideIndexer, TextExporter, FidoAdapter, ConsensusID, IDMerger, MSGFPlusAdapter, IDFilter, IDScoreSwitcher, Grep1, FalseDiscoveryRate, IDPosteriorErrorProbability, FileInfo UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 3376 5669 2.933333 0
Proteomics metaQuantome 2: Function https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics Functional clustering, Heat map generation, Filtering, Indexing, Principal component visualisation, Visualisation, Statistical inference, Differential protein expression analysis, Quantification, Query and retrieval 2020-10-29 2024-03-15 14 True False False True metaquantome_sample, metaquantome_expand, metaquantome_stat, metaquantome_db, metaquantome_viz, metaquantome_filter UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 408 579 4.233333 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 PeakPickerHiRes, FileConverter, peptide_shaker, search_gui, Grep1 0 3028 4887 1.900000 0
Proteomics Proteogenomics 1: Database Creation https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html Statistical calculation, Sequence alignment, Transcriptome assembly, RNA-Seq analysis, Sequence annotation, Variant calling 2018-11-20 2025-05-08 29 True False True True custom_pro_db, bed_to_protein_map, cat_multi_datasets, hisat2, tp_replace_in_column, translate_bed, stringtie, query_tabular, tab2fasta, regexColumn1, gffcompare, sqlite_to_tabular, fasta_merge_files_and_filter_unique_sequences, filter_tabular, freebayes, gffcompare_to_bed, fasta2tab UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 5755 9458 2.633333 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_fishers_plot, pdaug_peptide_data_access, pdaug_peptide_sequence_analysis, pdaug_addclasslabel, pdaug_sequence_property_based_descriptors, pdaug_tsvtofasta, pdaug_merge_dataframes, pdaug_basic_plots UseGalaxy.be 0 715 977 2.433333 0
Proteomics Clinical Metaproteomics 1: Database-Generation https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.html Tag-based peptide identification, Protein identification, Expression analysis, de Novo sequencing, Target-Decoy 2024-02-06 2025-07-30 7 True False True True metanovo, dbbuilder, uniprotxml_downloader, fasta_merge_files_and_filter_unique_sequences UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.org (Main) 0 553 848 4.483333 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, XTandemAdapter, PeptideIndexer, histogram_rpy, TextExporter, tp_tail_tool, IDScoreSwitcher, MultiplexResolver, FidoAdapter, IDMapper, ProteinQuantifier, FeatureFinderMultiplex, Grep1, IDConflictResolver, FalseDiscoveryRate, IDPosteriorErrorProbability, FileInfo UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 1333 1872 1.583333 0
Proteomics Neoantigen 5a: Predicting HLA Binding https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-predicting-hla-binding/tutorial.html Genetic variation analysis, Read mapping 2025-01-14 2025-07-02 1 True False False True optitype, tp_awk_tool, query_tabular, seq2hla UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 44 49 0.050000 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 pep_pointer, peptide_genomic_coordinate, ncbi_blastp_wrapper, query_tabular UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 1604 2292 2.700000 0
Proteomics Clinical Metaproteomics 4: Quantitation https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.html Statistical calculation, Visualisation, Heat map generation, Standardisation and normalisation, Clustering, Protein quantification, Principal component plotting, Imputation 2024-02-06 2025-08-10 5 True False True True Grep1, maxquant, Cut1, Grouping1 UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 173 239 3.666667 0
Proteomics Clinical Metaproteomics 3: Verification https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html 2024-02-06 2025-08-10 7 True False True True dbbuilder, Grouping1, uniprotxml_downloader, query_tabular, Remove beginning1, collapse_dataset, Filter1, Cut1, fasta_merge_files_and_filter_unique_sequences, pepquery2, tp_cat UseGalaxy.cz, UseGalaxy.eu UseGalaxy.org (Main), UseGalaxy.org.au 0 186 252 5.416667 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_addclasslabel, pdaug_sequence_property_based_descriptors, pdaug_merge_dataframes, pdaug_basic_plots, pdaug_ml_models UseGalaxy.be 0 1013 1515 2.233333 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 dbbuilder, addValue, tab2fasta, DecoyDatabase, fasta_merge_files_and_filter_unique_sequences, fasta2tab UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 4627 7370 2.133333 0
Proteomics DIA Analysis using OpenSwathWorkflow https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html Formatting, Filtering 2020-12-02 2025-05-20 12 True False False True msconvert, pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, OpenSwathWorkflow, pyprophet_score, Grep1 UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 3014 4242 2.400000 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 query_tabular, sqlite_to_tabular, unipept, search_gui, peptide_shaker UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz 0 2867 4572 2.716667 0
Proteomics Single Cell Proteomics data analysis with bioconductor-scp https://training.galaxyproject.org//topics/proteomics/tutorials/bioconductor-scp/tutorial.html Expression analysis, Visualisation 2025-02-07 2025-02-10 2 True False False False bioconductor_scp, Grouping1 UseGalaxy.eu, UseGalaxy.org.au 0 173 226 1.200000 0
Proteomics Neoantigen 2: Database merge and FragPipe discovery https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.html 2025-01-14 2025-07-02 1 True False False True fragpipe, query_tabular, Remove beginning1, collapse_dataset, fasta_merge_files_and_filter_unique_sequences, Grep1, validate_fasta_database UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.org.au 0 125 150 1.500000 0
Proteomics Secretome Prediction https://training.galaxyproject.org//topics/proteomics/tutorials/secretome-prediction/tutorial.html 2017-04-13 2025-04-08 15 True False False True term_id_vs_term_name, tp_cut_tool, wolf_psort, tp_easyjoin_tool, uniprot, tp_sorted_uniq, Filter1, get_subontology_from, bg_uniq, Grep1, Convert characters1, comp1 0 636 955 1.500000 0
Proteomics Neoantigen 4: Variant Annotation https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-variant-annotation/tutorial.html 2025-01-14 2025-07-02 1 True False False True query_tabular, tab2fasta, regexColumn1, pep_pointer, Convert characters1 UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 58 72 1.683333 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 query_tabular, tab2fasta, mz_to_sqlite, search_gui, ident_params, peptide_shaker UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 1514 2256 4.800000 0
Proteomics Neoantigen 3: PepQuery2 Verification https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-peptide-verification/tutorial.html Formatting, Filtering 2025-01-14 2025-07-02 1 True False False True msconvert, ncbi_blastp_wrapper, query_tabular, tab2fasta, pepquery2 UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 46 54 2.483333 0
Proteomics MaxQuant and MSstats for the analysis of TMT data https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.html Statistical calculation, Visualisation, Heat map generation, Standardisation and normalisation, Clustering, Protein quantification, Principal component plotting, Imputation 2021-08-13 2025-01-08 11 True False False True maxquant, msstatstmt UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.org (Main) 0 4196 5618 1.650000 0
Proteomics Multiomics data analysis using MultiGSEA https://training.galaxyproject.org//topics/proteomics/tutorials/multiGSEA-tutorial/tutorial.html Pathway analysis, Gene-set enrichment analysis, Aggregation 2025-03-10 2025-03-11 2 True False False True Filter1, multigsea, tp_grep_tool UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org.au 0 225 247 1.833333 0
Proteomics Clinical Metaproteomics 2: Discovery https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html Statistical calculation, Heat map generation, Standardisation and normalisation, Filtering, Imputation, Formatting, Clustering, Protein quantification, Principal component plotting, Visualisation 2024-02-06 2025-08-10 5 True False True True dbbuilder, msconvert, filter_tabular, Grouping1, fasta_cli, query_tabular, Remove beginning1, maxquant, Filter1, peptide_shaker, search_gui, Cut1, fasta_merge_files_and_filter_unique_sequences, Grep1, ident_params, fasta2tab, tp_cat UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 329 442 7.366667 0
Proteomics Neoantigen 1b: Non-Reference-Database-Generation https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html Statistical calculation, Sequence alignment, Transcriptome assembly, RNA-Seq analysis, Sequence annotation, Variant calling 2025-01-14 2025-07-02 1 True False False True custom_pro_db, bed_to_protein_map, hisat2, translate_bed, stringtie, CONVERTER_gz_to_uncompressed, query_tabular, tab2fasta, regexColumn1, gffcompare, sqlite_to_tabular, fasta_merge_files_and_filter_unique_sequences, filter_tabular, freebayes, gffcompare_to_bed, fasta2tab, tp_cat UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 59 67 0.533333 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 Grep1, msstatstmt, unipept UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 267 356 2.900000 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 Statistical calculation, Visualisation, Tag-based peptide identification, Heat map generation, Differential protein expression profiling, Standardisation and normalisation, Spectrum calculation, Clustering, Protein quantification, Principal component plotting, Imputation 2021-02-17 2025-09-22 19 True False True True Summary_Statistics1, tp_easyjoin_tool, tp_replace_in_column, uniprot, maxquant, Filter1, datamash_ops, ggplot2_heatmap2, Cut1, Grep1, fasta2tab, msstats UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 8401 13564 2.666667 0
Proteomics Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides https://training.galaxyproject.org//topics/proteomics/tutorials/neoantigen-hla-binding-novel-peptides/tutorial.html 2025-01-14 2025-07-02 1 True False False True table_compute, iedb_api, query_tabular, Remove beginning1, Filter1, Cut1, pepquery2 UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 36 38 1.016667 0
Proteomics EncyclopeDIA https://training.galaxyproject.org//topics/proteomics/tutorials/encyclopedia/tutorial.html Formatting, Filtering 2021-06-21 2025-05-19 12 True False True True msconvert, encyclopedia_searchtolib, encyclopedia_quantify UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 1957 2672 1.766667 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 2845375 7530066 2.450000 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 7613 12321 0.900000 0
Sequence analysis Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes https://training.galaxyproject.org//topics/sequence-analysis/tutorials/viral_primer_design/tutorial.html PCR primer design, Local alignment, Sequence alignment, Sequence alignment analysis, Global alignment, Sequence analysis, Multiple sequence alignment 2025-03-20 2025-03-20 2 True False False True varvamp, rbc_mafft, split_file_to_collection, ncbi_makeblastdb, EMBOSS: degapseq20, fasta_compute_length UseGalaxy.eu 0 473 555 1.083333 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 trimming, Sequence assembly validation 2024-04-16 2024-04-16 2 True False False True ncbi_fcs_gx, ncbi_fcs_adaptor GalaxyTrakr, UseGalaxy.org (Main) 0 1735 2361 2.316667 0
Sequence analysis Mapping https://training.galaxyproject.org//topics/sequence-analysis/tutorials/mapping/tutorial.html Mapping Statistical calculation, Read mapping, Sequence alignment analysis, Data handling, Primer removal, Sequence trimming, Genome visualisation, Sequencing quality control, Sequence composition calculation, Validation, Read pre-processing 2016-10-04 2025-03-31 43 True True True True jbrowse, multiqc, fastqc, bamFilter, trim_galore, bowtie2, samtools_stats UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2909813 7638513 5.166667 0
Sequence analysis Quality and contamination control in bacterial isolate using Illumina MiSeq Data https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html Whole genome sequencing, Genomics, Microbiology, Microbial ecology Statistical calculation, Expression analysis, Sequencing quality control, Taxonomic classification, Cross-assembly, Read mapping, Visualisation, Sequence contamination filtering 2024-07-15 2025-03-20 4 True False True True upload1, falco, kraken2, fastp, est_abundance, recentrifuge UseGalaxy.eu, UseGalaxy.fr UseGalaxy.cz, UseGalaxy.org (Main) 0 1487 1934 2.850000 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 Data handling, Phylogenetic analysis, Demultiplexing, DNA barcoding, Sequencing quality control, Taxonomic classification, Sequence read processing, Sequence clustering, Visualisation, Sequence file editing 2024-01-08 2024-03-05 2 True False False True seqtk_trimfq, tab2fasta, ab1_fastq_converter, fastq_groomer, fastq_to_tabular, ncbi_blastn_wrapper, fastq_masker_by_quality, unzip, mothur_merge_files, seqtk_mergepe, filter_by_fasta_ids, __SORTLIST__, aligned_to_consensus, regex1, cshl_fastq_to_fasta, __FILTER_FROM_FILE__, qiime_align_seqs, cshl_fastx_reverse_complement, collection_element_identifiers, mothur_degap_seqs UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr 0 3137 3947 1.750000 0
Sequence analysis Quality Control https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-control/tutorial.html Statistical calculation, Box-Whisker plot plotting, Sequence trimming, Primer removal, Sequencing quality control, Scatter plot plotting, Sequence composition calculation, Validation, Read pre-processing 2016-10-04 2025-03-29 48 True True True True fastqe, multiqc, cutadapt, fastqc, pycoqc, nanoplot UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.fr 0 2950164 7721541 5.483333 0
Single Cell Bulk RNA Deconvolution with MuSiC https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music/tutorial.html 2022-02-11 2025-02-14 10 True False True True music_deconvolution, music_construct_eset, music_inspect_eset UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 3816 4836 1.616667 0
Single Cell Generating a single cell matrix using Alevin https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin/tutorial.html Sequence composition calculation, RNA-Seq quantification, Gene expression analysis 2021-03-03 2025-05-07 24 True False True True join1, sceasy_convert, anndata_manipulate, alevin, dropletutils_empty_drops, dropletutils_read_10x, anndata_inspect, _ensembl_gtf2gene_list, _salmon_kallisto_mtx_to_10x, Cut1, _dropletBarcodePlot UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 3384 5158 3.516667 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 738970 1703907 3.000000 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, Principal component visualisation, Expression profile clustering 2025-02-12 2025-05-09 8 True False True True column_remove_by_header, decoupler_pseudobulk, anndata_manipulate, tp_awk_tool, tp_replace_in_column, tp_replace_in_line, anndata_inspect, edger, volcanoplot, __EXTRACT_DATASET__, scanpy_filter UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 1366 1586 0.650000 0
Single Cell Pre-processing of 10X Single-Cell RNA Datasets https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html Sequence alignment, Loading, Validation, Community profiling, Sequencing quality control 2019-09-11 2025-04-29 13 True False True True rna_starsolo, dropletutils, multiqc UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 12085 15601 1.866667 0
Single Cell Pre-processing of Single-Cell RNA Data https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing/tutorial.html Sequence alignment, Sequencing quality control, Sequence alignment analysis, Data handling, Read summarisation, Validation, RNA-Seq quantification 2019-02-22 2025-04-08 5 True True False True umi_tools_extract, featurecounts, tp_sed_tool, multiqc, rna_star, umi_tools_count, bamFilter, collection_column_join, __FLATTEN__, samtools_stats UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 2851580 7538145 4.716667 0
Single Cell Single-cell quality control with scater https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scater-qc/tutorial.html Read pre-processing, Sequence visualisation, Sequencing quality control 2019-10-23 2025-02-14 6 True False False True scater_plot_pca, scater_create_qcmetric_ready_sce, scater_plot_dist_scatter, scater_filter UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au UseGalaxy.cz 0 683 773 0.750000 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 Statistical calculation, Generation, Visualisation, Mapping, Genome indexing, Peak calling, Enrichment analysis, Sequencing quality control, Differential gene expression analysis, Expression profile clustering, Sequence alignment, Principal component visualisation, Sequence composition calculation, Read mapping, Imputation, Gene regulatory network analysis 2023-04-24 2025-10-16 10 True False False True bwa_mem, tp_sorted_uniq, fastqc, sinto_barcode, anndata_inspect, episcanpy_preprocess, scanpy_plot, episcanpy_build_matrix, falco, macs2_callpeak, sinto_fragments, bedtools_sortbed UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 5855 6903 1.100000 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 join1, tp_cut_tool, tabular_to_fastq, anndata_ops, sceasy_convert, monocle3_create, dropletutils, tp_tail_tool, dropletutils_read_10x, datamash_transpose, anndata_inspect, regexColumn1, Filter1, seurat_read10x, Cut1, scanpy_filter_cells, fastq_to_tabular UseGalaxy.org (Main) 0 2375 2832 1.316667 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 2812957 7416028 2.450000 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 0 593 829 3.800000 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 sceasy_convert, anndata_ops, retrieve_scxa, hca_matrix_downloader, regexColumn1, scanpy_read_10x, seurat_read10x, tp_find_and_replace, tp_grep_tool 0 536 709 3.950000 0
Single Cell Understanding Barcodes https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-umis/tutorial.html Sequence composition calculation, Statistical calculation, Sequencing quality control 2019-02-20 2025-02-14 11 True False True True umi_tools_extract, fastqc, seq_filter_by_id UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au Galaxy@AuBi, UseGalaxy.no 0 6197 7721 1.233333 0
Single Cell Downstream Single-cell RNA analysis with RaceID https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-raceid/tutorial.html Molecular dynamics, Expression analysis, Expression profile clustering 2019-03-25 2025-02-14 7 True False False True tp_sed_tool, raceid_inspecttrajectory, raceid_trajectory, tp_head_tool, datamash_transpose, raceid_clustering, raceid_filtnormconf, datamash_ops, raceid_inspectclusters UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz, UseGalaxy.org.au 0 1051 1242 1.300000 0
Single Cell Clustering 3K PBMCs with Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html Principal component visualisation, Differential gene expression analysis, Expression profile clustering 2019-12-19 2025-04-29 16 True True True True scanpy_cluster_reduce_dimension, anndata_manipulate, scanpy_remove_confounders, anndata_import, scanpy_inspect, anndata_inspect, scanpy_plot, scanpy_normalize, datamash_ops, scanpy_filter UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no 0 2853222 7541271 4.466667 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 3157 3612 0.966667 0
Single Cell Combining single cell datasets after pre-processing https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html 2022-09-08 2025-04-22 22 True False True True anndata_ops, anndata_manipulate, tp_replace_in_column, anndata_inspect, Cut1, Paste1 UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.be, UseGalaxy.org (Main) 0 2452 3434 2.516667 0
Single Cell Removing the effects of the cell cycle https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html Principal component visualisation, Differential gene expression analysis, Expression profile clustering 2023-01-25 2025-03-11 14 True False False True scanpy_cluster_reduce_dimension, anndata_manipulate, tp_easyjoin_tool, table_compute, addValue, scanpy_regress_variable, anndata_inspect, scanpy_inspect, scanpy_plot, cat1, sort1 0 2050 2419 0.783333 0
Single Cell Single-cell ATAC-seq standard processing with SnapATAC2 https://training.galaxyproject.org//topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html Generation, Essential dynamics, Genome indexing, Differential gene expression analysis, Expression profile clustering, Sequence alignment, Dimensionality reduction, Principal component visualisation, Read mapping, Gene expression profiling 2024-07-11 2025-07-02 5 True False False True anndata_ops, bwa_mem, anndata_manipulate, snapatac2_preprocessing, scanpy_filter, snapatac2_plotting, snapatac2_peaks_and_motif, scanpy_inspect, anndata_inspect, scanpy_plot, Cut1, replace_column_with_key_value_file, snapatac2_clustering, scanpy_normalize, fasta_compute_length 0 1439 1749 1.100000 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 0 269 412 1.033333 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 3181 3775 1.500000 0
Single Cell Converting NCBI Data to the AnnData Format https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html 2023-12-13 2025-03-11 7 True False True True anndata_ops, anndata_manipulate, tp_replace_in_column, unzip, anndata_import, anndata_inspect, Cut1, Paste1, scanpy_filter_cells UseGalaxy.org.au 0 420 497 1.766667 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_compute_graph, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_find_cluster, scanpy_run_tsne, scanpy_run_umap UseGalaxy.org (Main), UseGalaxy.org.au 0 268 302 1.166667 0
Single Cell Multi-sample batch correction with Harmony and SnapATAC2 https://training.galaxyproject.org//topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html Essential dynamics, Dimensionality reduction, Gene expression profiling 2025-02-28 2025-07-02 2 True False False True anndata_manipulate, snapatac2_preprocessing, snapatac2_plotting, collection_element_identifiers, snapatac2_peaks_and_motif, __FILTER_FROM_FILE__, anndata_inspect, Show beginning1, snapatac2_clustering, __EXTRACT_DATASET__, fasta_compute_length UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 421 476 0.933333 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 music_deconvolution, tp_sed_tool, tp_multijoin_tool, collapse_dataset, Add_a_column1, Count1, join1, tp_cut_tool, music_construct_eset, table_compute, Remove beginning1, __DUPLICATE_FILE_TO_COLLECTION__, ggplot2_violin, tp_easyjoin_tool, tp_awk_tool, ggplot2_point, Paste1, annotatemyids, datamash_transpose, Cut1, collection_column_join, bg_column_arrange_by_header UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 97 117 1.050000 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_pca, seurat_filter_cells, retrieve_scxa, seurat_normalise_data, seurat_run_umap, seurat_find_clusters, seurat_scale_data, seurat_find_neighbours, seurat_read10x, seurat_find_markers, seurat_plot, seurat_find_variable_genes UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au 0 1769 2160 1.350000 0
Single Cell Clustering 3K PBMCs with Seurat https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-seurat-pbmc3k/tutorial.html 2025-01-23 2025-05-09 5 True False True True csv_to_tabular, seurat_reduce_dimension, seurat_preprocessing, Filter1, Cut1, seurat_data, seurat_clustering, seurat_plot, seurat_create UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au MISSISSIPPI 0 1100 1301 1.216667 0
Single Cell Filter, plot and explore single-cell RNA-seq data with Scanpy https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html Principal component visualisation, Differential gene expression analysis, Expression profile clustering 2021-03-24 2025-04-23 24 True False True True scanpy_cluster_reduce_dimension, anndata_ops, anndata_manipulate, scanpy_plot_embed, join1, scanpy_find_markers, interactive_tool_cellxgene_vip, scanpy_inspect, anndata_inspect, scanpy_plot, scanpy_normalise_data, scanpy_compute_graph, retrieve_scxa, scanpy_run_pca, scanpy_find_variable_genes, scanpy_scale_data, scanpy_filter_genes, Cut1, scanpy_normalize, scanpy_filter_cells, scanpy_find_cluster, scanpy_run_tsne, scanpy_run_umap, scanpy_filter 0 5175 7894 2.616667 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 2845375 7530072 2.450000 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 4436 5252 1.300000 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_compute_graph, scanpy_run_diffmap, scanpy_run_fdg, anndata_manipulate, scanpy_run_dpt, scanpy_run_paga, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_find_cluster UseGalaxy.org (Main), UseGalaxy.org.au 0 1226 1558 2.250000 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 join1, tp_cut_tool, music_construct_eset, tp_sed_tool, tp_easyjoin_tool, tp_awk_tool, retrieve_scxa, regex1, annotatemyids, datamash_transpose, music_manipulate_eset, anndata_inspect, table_compute, scanpy_read_10x, Cut1, sort1, add_line_to_file UseGalaxy.cz 0 725 1223 2.216667 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 808191 1874843 2.233333 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 6192 7048 0.800000 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 tp_cut_tool, column_remove_by_header, music_construct_eset, tp_sed_tool, tp_easyjoin_tool, tp_awk_tool, annotatemyids, regex1, table_compute, music_manipulate_eset, sort1 UseGalaxy.cz 0 672 1078 1.633333 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 join1, tp_cut_tool, monocle3_reduceDim, monocle3_create, monocle3_partition, monocle3_topmarkers, datamash_transpose, monocle3_learnGraph, monocle3_preprocess, anndata_inspect, regexColumn1, Filter1, monocle3_plotCells, Cut1, monocle3_orderCells, monocle3_diffExp UseGalaxy.eu, UseGalaxy.org (Main) 0 3858 4794 1.500000 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 1890484 4443758 2.316667 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 1288280 2995750 2.316667 0
Statistics and machine learning Machine learning: classification and regression https://training.galaxyproject.org//topics/statistics/tutorials/classification_regression/tutorial.html 2019-03-07 2025-04-08 13 True False False True sklearn_svm_classifier, plotly_ml_performance_plots, sklearn_ensemble, plotly_regression_performance_plots UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 5665 10201 0.766667 0
Statistics and machine learning Clustering in Machine Learning https://training.galaxyproject.org//topics/statistics/tutorials/clustering_machinelearning/tutorial.html Visualisation 2020-05-08 2025-04-08 14 True False False True sklearn_numeric_clustering, csv_to_tabular, ggplot2_point UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 8420 13986 0.933333 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 tp_cut_tool, keras_model_config, keras_model_builder, model_prediction, ml_visualization_ex, sklearn_to_categorical, keras_train_and_eval UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 2364098 5901172 3.116667 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 0 161 204 2.066667 0
Statistics and machine learning Text-mining with the SimText toolset https://training.galaxyproject.org//topics/statistics/tutorials/text-mining_simtext/tutorial.html 2021-04-05 2025-05-07 8 True False False True pubmed_by_queries, pmids_to_pubtator_matrix, interactive_tool_simtext_app UseGalaxy.eu 0 467 643 2.633333 0
Statistics and machine learning Introduction to deep learning https://training.galaxyproject.org//topics/statistics/tutorials/intro_deep_learning/tutorial.html 2020-03-26 2025-04-08 9 True False False True keras_model_config, keras_model_builder, model_prediction, ml_visualization_ex, keras_train_and_eval UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 2413 3092 1.666667 0
Statistics and machine learning Prepare Data from CbioPortal for Flexynesis Integration https://training.galaxyproject.org//topics/statistics/tutorials/flexynesis_cbio_import/tutorial.html 2025-08-10 2025-08-13 2 True False False True tp_cut_tool, flexynesis_cbioportal_import, table_compute, flexynesis_utils, tp_sort_header_tool, __EXTRACT_DATASET__ UseGalaxy.eu 0 25 25 1.300000 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_utils, flexynesis_plot, __EXTRACT_DATASET__ UseGalaxy.eu 0 21 25 6.933333 0
Statistics and machine learning Deep Learning (Part 2) - Recurrent neural networks (RNN) https://training.galaxyproject.org//topics/statistics/tutorials/RNN/tutorial.html 2021-02-23 2025-05-10 15 True True True True keras_model_config, keras_model_builder, model_prediction, ml_visualization_ex, keras_train_and_eval UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no 0 2778439 7279707 3.233333 0
Statistics and machine learning Regression in Machine Learning https://training.galaxyproject.org//topics/statistics/tutorials/regression_machinelearning/tutorial.html 2020-01-25 2025-05-14 19 True True True True sklearn_generalized_linear, Remove beginning1, sklearn_searchcv, sklearn_ensemble, sklearn_build_pipeline, plotly_regression_performance_plots UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no 0 2848584 7534126 3.733333 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, tp_replace_in_column, Add_a_column1, flexynesis_plot, __EXTRACT_DATASET__, datamash_ops UseGalaxy.eu 0 22 25 1.933333 0
Statistics and machine learning Classification in Machine Learning https://training.galaxyproject.org//topics/statistics/tutorials/classification_machinelearning/tutorial.html 2020-04-30 2025-05-14 18 True True True True sklearn_generalized_linear, Remove beginning1, sklearn_searchcv, sklearn_ensemble, sklearn_svm_classifier, sklearn_nn_classifier, plotly_ml_performance_plots, sklearn_build_pipeline UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no 0 2848108 7534082 4.700000 0
Statistics and machine learning Modeling Breast Cancer Subtypes with Flexynesis https://training.galaxyproject.org//topics/statistics/tutorials/flexynesis_classification/tutorial.html 2025-08-13 2025-09-02 3 True False False True join1, tabpfn, flexynesis, tp_cut_tool, tp_easyjoin_tool, table_compute, datamash_transpose, Show beginning1, tp_sort_header_tool, pick_value, flexynesis_plot, __EXTRACT_DATASET__ UseGalaxy.eu 0 49 74 2.350000 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 596722 1334355 4.350000 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 1180 1501 1.500000 0
Statistics and machine learning Interval-Wise Testing for omics data https://training.galaxyproject.org//topics/statistics/tutorials/iwtomics/tutorial.html Comparison, Peak calling, Differential gene expression analysis, Differentially-methylated region identification, Genome annotation 2018-06-14 2023-11-09 17 True False False True iwtomics_testandplot, iwtomics_plotwithscale, iwtomics_loadandplot UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 366 488 2.950000 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_cell_line_predictions, pancancer_external_sample_status_prediction, pancancer_targene_summary_figures, pancancer_alternative_genes_pathwaymapper, pancancer_pathway_count_heatmaps, pancancer_targene_pharmacology, pancancer_compare_within_models, pancancer_classifier, pancancer_within_disease_analysis, pancancer_map_mutation_class, pancancer_apply_weights, pancancer_visualize_decisions 0 773 1212 3.183333 0
Statistics and machine learning Deep Learning (Part 3) - Convolutional neural networks (CNN) https://training.galaxyproject.org//topics/statistics/tutorials/CNN/tutorial.html 2021-04-19 2025-05-09 19 True True True True keras_model_config, keras_model_builder, model_prediction, ml_visualization_ex, sklearn_to_categorical, keras_train_and_eval UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au 0 2703474 6998340 3.333333 0
Statistics and machine learning Basics of machine learning https://training.galaxyproject.org//topics/statistics/tutorials/machinelearning/tutorial.html 2018-11-05 2025-05-13 15 True True True True sklearn_svm_classifier UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.fr, UseGalaxy.no 0 2848088 7533746 5.416667 0
Statistics and machine learning Age prediction using machine learning https://training.galaxyproject.org//topics/statistics/tutorials/age-prediction-with-ml/tutorial.html 2019-01-25 2025-04-08 12 True False False True sklearn_searchcv, plotly_parallel_coordinates_plot, sklearn_ensemble, sklearn_build_pipeline, plotly_regression_performance_plots UseGalaxy.be, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.no 0 13134 21199 0.683333 0
Statistics and machine learning Deep Learning (Part 1) - Feedforward neural networks (FNN) https://training.galaxyproject.org//topics/statistics/tutorials/FNN/tutorial.html 2021-04-28 2024-06-14 12 True True True True keras_model_config, keras_model_builder, model_prediction, keras_train_and_eval, plotly_regression_performance_plots UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.be, UseGalaxy.no 0 2707899 6987342 3.183333 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 866406 2016594 3.316667 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) 0 428 532 0.716667 0
Statistics and machine learning Introduction to Machine Learning using R https://training.galaxyproject.org//topics/statistics/tutorials/intro-to-ml-with-r/tutorial.html 2021-05-21 2024-10-15 15 True False True False interactive_tool_rstudio UseGalaxy.eu, UseGalaxy.org.au 0 4014 6011 1.083333 0
Synthetic Biology Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools https://training.galaxyproject.org//topics/synthetic-biology/tutorials/retrosynthesis_analysis/tutorial.html 2022-06-23 2024-06-14 8 True False True True retropath2, get_sbml_model, rp2paths, rpcompletion, rrparser, rpextractsink 0 562 828 2.633333 0
Synthetic Biology Designing plasmids encoding predicted pathways by using the BASIC assembly method https://training.galaxyproject.org//topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.html 2022-05-12 2024-06-14 8 True False True True dnabot, rpbasicdesign, selenzy-wrapper 0 998 1556 2.750000 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 rpthermo, rpranker, rpfba, rpscore 0 629 936 3.000000 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 2845375 7530082 2.450000 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 1899927 4470799 2.316667 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 0 277 498 2.750000 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 7 7 0.000000 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 21 23 0.016667 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 0 126 147 2.183333 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 0 156 285 1.383333 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 0 217 408 6.466667 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 0 147 160 2.766667 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 0 306 352 4.083333 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 21 21 0.083333 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 84 88 0.283333 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 0 250 272 1.066667 0
Transcriptomics 3: RNA-seq genes to pathways https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html Gene functional annotation, Gene set testing, Gene-set enrichment analysis 2018-12-31 2023-11-09 13 True False False True join1, tp_cut_tool, fgsea, Add_a_column1, goseq, Cut1, tp_sort_header_tool, egsea UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 25961 41683 1.933333 0
Transcriptomics RNA-RNA interactome data analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-interactome/tutorial.html Statistical calculation, Sequence composition calculation, Sequence trimming, Primer removal, Sequencing quality control, Read pre-processing 2020-03-23 2023-11-09 12 True False False True cutadapt, fastqc, chira_merge, query_tabular, chira_map, chira_quantify, chira_collapse, chira_extract UseGalaxy.be, UseGalaxy.no, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org.au 0 1455 2209 2.816667 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, annotatemyids, tp_replace_in_line, limma_voom, mergeCols1 UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.org.au 0 43157 73033 2.266667 0
Transcriptomics Differential abundance testing of small RNAs https://training.galaxyproject.org//topics/transcriptomics/tutorials/srna/tutorial.html Statistical calculation, Sequence trimming, Primer removal, Differential gene expression analysis, Sequencing quality control, Gene expression analysis, Sequence alignment, RNA-Seq analysis, Sequence composition calculation, RNA-Seq quantification, Read pre-processing 2017-06-29 2023-11-09 26 True False False True samtool_filter2, hisat2, fastq_manipulation, fastqc, deseq2, Filter1, salmon, trim_galore, bedtools_bamtofastq UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 6889 12104 2.100000 0
Transcriptomics Small Non-coding RNA Clustering using BlockClust https://training.galaxyproject.org//topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.html 2018-12-14 2023-11-09 8 True False False True blockbuster, samtools_sort, blockclust, tp_sort_header_tool UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 1022 1394 2.983333 0
Transcriptomics Genome-wide alternative splicing analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html Statistical calculation, Data handling, Transcriptome assembly, Sequence annotation, Sequencing quality control, Sequence analysis, Protein sequence analysis, Formatting, Sequence alignment, RNA-Seq analysis, Sequence composition calculation, Validation, Visualisation, De-novo assembly, Sequence contamination filtering, Sequence comparison, Sequence assembly validation 2023-05-17 2025-03-28 11 True True False True stringtie_merge, Add_a_column1, pfamscan, rseqc_geneBody_coverage, cpat, tp_cat, rseqc_infer_experiment, multiqc, gtftobed12, Remove beginning1, gffcompare, gffread, rseqc_read_distribution, rseqc_junction_saturation, tp_awk_tool, rseqc_inner_distance, __FILTER_FROM_FILE__, gene2exon1, pygenomeTracks, rna_quast, tp_uniq_tool, tp_grep_tool, collection_element_identifiers, fastqc, rna_star, addValue, isoformswitchanalyzer, stringtie, Filter1, rseqc_junction_annotation, cat1, Cut1, fastp, __FLATTEN__, sort1 UseGalaxy.cz, UseGalaxy.fr 0 1492096 3435873 4.200000 0
Transcriptomics Visualization of RNA-Seq results with heatmap2 https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html 2018-12-31 2023-11-09 13 True False False True join1, ggplot2_heatmap2, datamash_transpose, Cut1 UseGalaxy.eu, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au 0 77292 127370 1.366667 0
Transcriptomics 1: RNA-Seq reads to counts https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html Statistical calculation, Data handling, Sequence trimming, Primer removal, Sequencing quality control, Sequence composition calculation, Formatting, Sequence alignment, Read summarisation, Validation, RNA-Seq quantification, Read pre-processing 2018-09-23 2024-08-09 33 True False False True picard_MarkDuplicates, rseqc_geneBody_coverage, rseqc_infer_experiment, rseqc_read_distribution, featurecounts, hisat2, multiqc, cutadapt, fastqc, collection_column_join, samtools_idxstats UseGalaxy.eu MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 77499 141130 2.583333 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 152290 250219 1.333333 0
Transcriptomics CLIP-Seq data analysis from pre-processing to motif detection https://training.galaxyproject.org//topics/transcriptomics/tutorials/clipseq/tutorial.html Statistical calculation, Sequence composition calculation, Sequence alignment, Mapping, Sequence trimming, Primer removal, Sequencing quality control, Read pre-processing 2018-08-17 2023-11-09 23 True False False True umi_tools_extract, peakachu, Extract genomic DNA 1, bctools_extract_alignment_ends, umi_tools_dedup, deeptools_plot_correlation, __SORTLIST__, bedtools_genomecoveragebed_bedgraph, rcas, meme_chip, tp_awk_tool, wig_to_bigWig, __MERGE_COLLECTION__, deeptools_plot_fingerprint, bedtools_slopbed, cutadapt, fastqc, rna_star, sort1, deeptools_multi_bam_summary UseGalaxy.no 0 8175 16164 1.883333 0
Transcriptomics De novo transcriptome assembly, annotation, and differential expression analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/full-de-novo/tutorial.html Statistical calculation, Coding region prediction, Transcriptome assembly, Sequencing quality control, Gene functional annotation, Sequence composition calculation, Validation, De-novo assembly, de Novo sequencing 2020-02-13 2023-11-09 8 True False False True trimmomatic, trinity_samples_qccheck, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity, multiqc, trinity_define_clusters_by_cutting_tree, fastqc, trinity_run_de_analysis, transdecoder, trinotate, trinity_contig_exn50_statistic, trinity_filter_low_expr_transcripts, describe_samples, trinity_abundance_estimates_to_matrix UseGalaxy.eu UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no 0 14409 26163 2.433333 0
Transcriptomics GO Enrichment Analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/goenrichment/tutorial.html Gene-set enrichment analysis 2019-01-23 2024-03-05 12 True False False True Filter1, goslimmer, goenrichment Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 23013 37418 1.333333 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_visualization, deseq2, heinz_scoring, Cut1, heinz_bum, heinz UseGalaxy.be, UseGalaxy.eu UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 2847403 7533247 5.700000 0
Transcriptomics RNA-Seq data analysis, clustering and visualisation tutorial https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html RNA-Seq analysis, Gene functional annotation, Differential gene expression analysis 2025-05-28 2025-06-16 5 True False False True Multivariate, Grouping1, tp_easyjoin_tool, table_compute, deseq2, Filter1, tp_sort_header_tool, Add_a_column1, ggplot2_heatmap2, cat1, Show beginning1, Cut1, goseq, deg_annotate, length_and_gc_content, volcanoplot UseGalaxy.eu, UseGalaxy.fr UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main) 0 732 927 1.616667 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 2846374 7531362 6.166667 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 2845375 7530085 2.450000 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 2847918 7533927 4.200000 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 30817 42112 1.683333 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 4222 5412 1.933333 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 10509 12897 1.450000 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 21968 34443 2.183333 0
Transcriptomics Reference-based RNA-Seq data analysis https://training.galaxyproject.org//topics/transcriptomics/tutorials/ref-based/tutorial.html Data handling, Pathway or network visualisation, Differential gene expression analysis, Exonic splicing enhancer prediction, Formatting, Sequence alignment, Read summarisation, Read mapping, Gene functional annotation, Validation, Visualisation, Sequence trimming, Primer removal, Enrichment analysis, Sequencing quality control, Pathway or network analysis, RNA-Seq analysis, Read pre-processing, RNA-Seq quantification 2016-10-05 2025-10-04 104 True False True True Grouping1, tp_replace_in_line, Add_a_column1, pathview, rseqc_geneBody_coverage, deg_annotate, tp_cat, samtools_idxstats, join1, rseqc_infer_experiment, __TAG_FROM_FILE__, multiqc, table_compute, gtftobed12, deseq2, samtools_view, dexseq_count, tp_sort_header_tool, rseqc_read_distribution, ChangeCase, featurecounts, __FILTER_FROM_FILE__, pygenomeTracks, falco, ggplot2_heatmap2, goseq, tp_grep_tool, __MERGE_COLLECTION__, picard_MarkDuplicates, cutadapt, collection_element_identifiers, dexseq, tp_tail_tool, rna_star, Filter1, length_and_gc_content, cat1, Cut1, __FLATTEN__, __EXTRACT_DATASET__ UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 184001 346150 2.800000 0
Transcriptomics Pathway analysis with the MINERVA Platform https://training.galaxyproject.org//topics/transcriptomics/tutorials/minerva-pathways/tutorial.html Statistical calculation, Read summarisation, Data handling, Sequence trimming, Primer removal, Sequencing quality control, Sequence composition calculation, Sequence alignment, RNA-Seq analysis, Gene functional annotation, Validation, RNA-Seq quantification, Read pre-processing, Annotation 2024-03-28 2024-07-26 3 True False False True tp_sorted_uniq, tp_replace_in_line, limma_voom, Add_a_column1, rseqc_geneBody_coverage, join1, multiqc, fasterq_dump, tp_sort_header_tool, rseqc_read_distribution, featurecounts, goseq, Grep1, hisat2, cutadapt, annotatemyids, fastqc, Cut1, collection_column_join, __EXTRACT_DATASET__ UseGalaxy.eu, UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main) 0 592 709 1.666667 0
Transcriptomics De novo transcriptome reconstruction with RNA-Seq https://training.galaxyproject.org//topics/transcriptomics/tutorials/de-novo/tutorial.html Statistical calculation, Read summarisation, Transcriptome assembly, Sequence annotation, Sequencing quality control, Differential gene expression analysis, Sequence alignment, RNA-Seq analysis, Sequence composition calculation, RNA-Seq quantification 2017-02-19 2024-06-14 36 True False True True trimmomatic, featurecounts, hisat2, stringtie_merge, fastqc, stringtie, deseq2, gffcompare, Filter1, deeptools_bam_coverage Galaxy@AuBi, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org.au 0 16548 28564 2.666667 0
Variant Analysis Introduction to Variant analysis https://training.galaxyproject.org//topics/variant-analysis/tutorials/introduction/slides.html 2016-08-19 2023-03-05 2 False True False False UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr 0 2845375 7530086 2.450000 0
Variant Analysis Calling very rare variants https://training.galaxyproject.org//topics/variant-analysis/tutorials/dunovo/tutorial.html Statistical calculation, Generation, Genome indexing, Sequencing quality control, Variant calling, Sequence alignment, Sequence composition calculation, Read mapping 2017-02-22 2024-12-09 21 True False False True bwa_mem, fastqc, bamleftalign, Filter1, make_families, sequence_content_trimmer, allele_counts_1, correct_barcodes, align_families, naive_variant_caller, dunovo UseGalaxy.org (Main) 0 1951 3054 1.766667 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 Statistical calculation, Generation, Sequence alignment analysis, Genome indexing, Data handling, Sequencing quality control, Variant calling, Formatting, Sequence alignment, Sequence composition calculation, Read mapping 2017-02-16 2024-03-15 23 True False False True picard_MarkDuplicates, bwa_mem, fastqc, bamleftalign, vcffilter2, bamFilter, vcf2tsv, picard_MergeSamFiles, Cut1, freebayes UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au 0 8501 15358 2.150000 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 Statistical calculation, Generation, Sequence alignment analysis, Genome indexing, Data handling, Validation, Sequencing quality control, Variant calling, Sequence alignment, Sequence composition calculation, Read mapping, Visualisation 2019-03-13 2025-03-20 16 True False False True bwa_mem, gemini_query, snpEff, trimmomatic, multiqc, tp_easyjoin_tool, fastqc, bamleftalign, samtools_rmdup, bamFilter, falco, samtools_calmd, gemini_annotate, gemini_load, varscan_somatic, bg_column_arrange_by_header UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz, UseGalaxy.fr 0 14265 25688 2.500000 0
Variant Analysis Exome sequencing data analysis for diagnosing a genetic disease https://training.galaxyproject.org//topics/variant-analysis/tutorials/exome-seq/tutorial.html Statistical calculation, Generation, Genome indexing, Genetic variation analysis, Validation, Sequencing quality control, Sequence analysis, Variant calling, Sequence alignment, Sequence composition calculation, Read mapping 2016-08-19 2025-05-11 29 True False True True gemini_inheritance, snpEff_download, bwa_mem, bcftools_norm, snpEff, trimmomatic, multiqc, fastqc, samtools_rmdup, samtools_view, gemini_load, freebayes UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au 0 34742 63322 2.750000 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, snpEff, mimodd_varextract, mimodd_map, tp_find_and_replace, mimodd_varcall, mimodd_vcf_filter, mimodd_varreport UseGalaxy.be, UseGalaxy.eu GalaxyTrakr, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 4297 6325 2.716667 0
Variant Analysis Trio Analysis using Synthetic Datasets from RD-Connect GPAP https://training.galaxyproject.org//topics/variant-analysis/tutorials/trio-analysis/tutorial.html Genetic variation analysis, Sequence analysis 2022-05-19 2024-09-17 13 True False True True gemini_inheritance, bcftools_norm, snpEff, bcftools_merge, pyega3, CONVERTER_gz_to_uncompressed, regexColumn1, Filter1, CONVERTER_uncompressed_to_gz, gene_iobio_display_generation_iframe, gemini_load, tp_grep_tool UseGalaxy.eu UseGalaxy.cz, UseGalaxy.org.au 0 1917 3403 3.666667 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 Generation, Data handling, Genome indexing, Primer removal, Sequence trimming, Sequence alignment, Read pre-processing, Read mapping, Visualisation 2025-02-24 2025-02-24 1 True False False True ncbi_acc_download, bwa_mem, fastq_dump, bcftools_call, tp_awk_tool, tp_replace_in_column, tp_replace_in_line, bcftools_mpileup, ggplot2_point, collapse_dataset, vcf2tsv, Filter1, trim_galore UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main), UseGalaxy.org.au UseGalaxy.cz 0 235 326 1.033333 0
Variant Analysis Calling variants in diploid systems https://training.galaxyproject.org//topics/variant-analysis/tutorials/dip/tutorial.html Statistical calculation, Genetic variation analysis, Sequence analysis, Variant calling 2017-02-20 2025-04-28 17 True False False True gemini_query, snpEff, gemini_db_info, vcfallelicprimitives, gemini_load, freebayes UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au 0 15224 26193 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 Statistical calculation, Generation, Genome indexing, Validation, Copy number estimation, Sequencing quality control, Variant calling, Sequence visualisation, Sequence alignment, Sequence composition calculation, Read mapping, Visualisation, Genome alignment 2022-10-05 2025-03-20 14 True False False True bwa_mem, trimmomatic, multiqc, fastqc, tp_replace_in_line, tp_text_file_with_recurring_lines, __RELABEL_FROM_FILE__, bamleftalign, samtools_rmdup, falco, samtools_calmd, samtools_view, Grep1, __BUILD_LIST__, control_freec, __EXTRACT_DATASET__, circos UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 1819 2336 2.033333 0
Variant Analysis Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs) https://training.galaxyproject.org//topics/variant-analysis/tutorials/beacon_cnv_query/tutorial.html Genetic variation analysis, Database search, Service discovery 2024-08-06 2024-09-27 3 True False False False beacon2_cnv UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org.au 0 161 198 2.616667 0
Variant Analysis Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons https://training.galaxyproject.org//topics/variant-analysis/tutorials/beaconise_1000hg/tutorial.html Database search, Genetic variation analysis, Service discovery 2024-08-06 2024-09-27 3 True False False False beacon2_import, beacon2_cnv, cnv_vcf2json, cnv_phenopacket UseGalaxy.eu 0 296 335 0.516667 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_wiggle_to_scatter, Cut1, circos_gc_skew, deeptools_bam_coverage, circos_interval_to_tile, circos_interval_to_text, circos UseGalaxy.cz, UseGalaxy.fr Galaxy@AuBi, MISSISSIPPI, UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au 0 1379 1753 1.933333 0
Visualisation Visualisation with Circos https://training.galaxyproject.org//topics/visualisation/tutorials/circos/tutorial.html Sequence visualisation 2020-01-10 2024-10-15 22 True True True True random_lines1, upload1, Remove beginning1, Cut1, Grep1, circos Galaxy@AuBi, Galaxy@Pasteur, MISSISSIPPI, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main) UseGalaxy.no 0 2875486 7578211 4.116667 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 1204088 2811787 2.316667 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 2845375 7530089 2.450000 0