Tool	Tutorials
Cut1	Assembly / Decontamination of a genome assembly Assembly / Making sense of a newly assembled genome Contributing to the Galaxy Training Material / Creating a new tutorial Foundations of Data Science / Data Manipulation Olympics Digital Humanities / OpenRefine Tutorial for researching cultural data Digital Humanities / Text-Mining Differences in Chinese Newspaper Articles Ecology / Metabarcoding/eDNA through Obitools Ecology / RAD-Seq Reference-based data analysis Epigenetics / ATAC-Seq data analysis Epigenetics / Infinium Human Methylation BeadChip Using Galaxy and Managing your Data / Workflow Reports Genome Annotation / Dataset construction for bacterial comparative genomics Genome Annotation / Comparative gene analysis in unannotated genomes Genome Annotation / Essential genes detection with Transposon insertion sequencing Introduction to Galaxy Analyses / Data Manipulation Olympics Introduction to Galaxy Analyses / Galaxy Basics for everyone Introduction to Galaxy Analyses / From peaks to genes Introduction to Galaxy Analyses / How to reproduce published Galaxy analyses Microbiome / Clinical Metaproteomics 2: Discovery Microbiome / Clinical Metaproteomics 3: Verification Microbiome / Clinical Metaproteomics 4: Quantitation Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short) Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 3: Verification Proteomics / Clinical Metaproteomics 4: Quantitation Proteomics / Label-free data analysis using MaxQuant Proteomics / MaxQuant and MSstats for the analysis of label-free data Proteomics / metaQuantome 1: Data creation Proteomics / Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides Sequence analysis / Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 Single Cell / Generating a single cell matrix using Alevin Single Cell / Combining single cell datasets after pre-processing Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy Single Cell / Inferring single cell trajectories with Monocle3 Single Cell / Converting between common single cell data formats Single Cell / Converting NCBI Data to the AnnData Format Single Cell / Clustering 3K PBMCs with Seurat Statistics and machine learning / A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana Transcriptomics / Network analysis with Heinz Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial Transcriptomics / 3: RNA-seq genes to pathways Transcriptomics / Visualization of RNA-Seq results with heatmap2 Variant Analysis / Calling variants in non-diploid systems Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data Visualisation / Visualisation with Circos Visualisation / Ploting a Microbial Genome with Circos
Filter1	Assembly / Decontamination of a genome assembly Assembly / Making sense of a newly assembled genome Contributing to the Galaxy Training Material / Creating a new tutorial Foundations of Data Science / Data Manipulation Olympics Digital Humanities / Text-Mining Differences in Chinese Newspaper Articles Ecology / Metabarcoding/eDNA through Obitools Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite Ecology / Life Traits Ecoregionalization workflow Ecology / Cleaning GBIF data for the use in Ecology Ecology / Preparing genomic data for phylogeny reconstruction Ecology / RAD-Seq Reference-based data analysis Ecology / Regional GAM Ecology / Species distribution modeling Epigenetics / ATAC-Seq data analysis Epigenetics / Formation of the Super-Structures on the Inactive X Genome Annotation / Comparative gene analysis in unannotated genomes Genome Annotation / Essential genes detection with Transposon insertion sequencing Introduction to Galaxy Analyses / Data Manipulation Olympics Introduction to Galaxy Analyses / NGS data logistics Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy Metabolomics / Mass spectrometry imaging: Examining the spatial distribution of analytes Metabolomics / Mass spectrometry imaging: Finding differential analytes Microbiome / Identification of the micro-organisms in a beer using Nanopore sequencing Microbiome / Clinical Metaproteomics 2: Discovery Microbiome / Clinical Metaproteomics 3: Verification Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data Proteomics / Statistical analysis of DIA data Proteomics / Library Generation for DIA Analysis Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 3: Verification Proteomics / Label-free data analysis using MaxQuant Proteomics / MaxQuant and MSstats for the analysis of label-free data Proteomics / metaQuantome 1: Data creation Proteomics / Multiomics data analysis using MultiGSEA Proteomics / Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides Proteomics / Secretome Prediction Sequence analysis / Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants Single Cell / Inferring single cell trajectories with Monocle3 Single Cell / Converting between common single cell data formats Single Cell / Clustering 3K PBMCs with Seurat Statistics and machine learning / A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy Transcriptomics / De novo transcriptome reconstruction with RNA-Seq Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / GO Enrichment Analysis Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial Transcriptomics / Differential abundance testing of small RNAs Variant Analysis / Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates Variant Analysis / Calling very rare variants Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis Variant Analysis / Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
devteam/fastqc/fastqc	Assembly / An Introduction to Genome Assembly Assembly / Large genome assembly and polishing Assembly / Assembly of metagenomic sequencing data Assembly / Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) Assembly / Unicycler Assembly Ecology / Metabarcoding/eDNA through Obitools Ecology / RAD-Seq de-novo data analysis Ecology / RAD-Seq Reference-based data analysis Epigenetics / ATAC-Seq data analysis Epigenetics / Identification of the binding sites of the Estrogen receptor Epigenetics / Formation of the Super-Structures on the Inactive X Epigenetics / DNA Methylation data analysis Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) Genome Annotation / CRISPR screen analysis Introduction to Galaxy Analyses / A short introduction to Galaxy Microbiome / Identification of the micro-organisms in a beer using Nanopore sequencing Microbiome / Assembly of metagenomic sequencing data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short) Microbiome / MGnify v5.0 Amplicon Pipeline Microbiome / 16S Microbial analysis with Nanopore data Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Sequence analysis / Mapping Sequence analysis / Quality Control Sequence analysis / SARS-CoV-2 Viral Sample Alignment and Variant Visualization Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets Single Cell / Understanding Barcodes Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection Transcriptomics / De novo transcriptome reconstruction with RNA-Seq Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / RNA-RNA interactome data analysis Transcriptomics / 1: RNA-Seq reads to counts Transcriptomics / Differential abundance testing of small RNAs Variant Analysis / Calling very rare variants Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease Variant Analysis / Calling variants in non-diploid systems Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs Variant Analysis / M. tuberculosis Variant Analysis
Grep1	Assembly / Making sense of a newly assembled genome Climate / Getting your hands-on climate data Ecology / RAD-Seq Reference-based data analysis Epigenetics / ATAC-Seq data analysis Epigenetics / CUT&RUN data analysis Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Genome Annotation / Identification of AMR genes in an assembled bacterial genome Metabolomics / Mass spectrometry imaging: Finding differential analytes Microbiome / Clinical Metaproteomics 2: Discovery Microbiome / Clinical Metaproteomics 4: Quantitation Microbiome / Clinical Metaproteomics 5: Data Interpretation Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short) Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Statistical analysis of DIA data Proteomics / DIA Analysis using OpenSwathWorkflow Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 4: Quantitation Proteomics / Clinical Metaproteomics 5: Data Interpretation Proteomics / Mass spectrometry imaging: Loading and exploring MSI data Proteomics / Label-free data analysis using MaxQuant Proteomics / MaxQuant and MSstats for the analysis of label-free data Proteomics / metaQuantome 1: Data creation Proteomics / Neoantigen 2: Database merge and FragPipe discovery Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL) Proteomics / Secretome Prediction Sequence analysis / Removal of human reads from SARS-CoV-2 sequencing data Transcriptomics / Pathway analysis with the MINERVA Platform Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC Visualisation / Visualisation with Circos
iuc/multiqc/multiqc	Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Assembly / An Introduction to Genome Assembly Assembly / Large genome assembly and polishing Assembly / Unicycler Assembly Contributing to the Galaxy Training Material / Creating content in Markdown Ecology / Data submission using ENA upload Tool Ecology / RAD-Seq Reference-based data analysis Epigenetics / CUT&RUN data analysis Using Galaxy and Managing your Data / Annotate, prepare tests and publish Galaxy workflows in workflow registries Genome Annotation / CRISPR screen analysis Introduction to Galaxy Analyses / NGS data logistics Introduction to Galaxy Analyses / Very Short Introductions: QC Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short) Microbiome / MGnify v5.0 Amplicon Pipeline Microbiome / 16S Microbial analysis with Nanopore data Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Sequence analysis / Mapping Sequence analysis / Quality Control Single Cell / Pre-processing of Single-Cell RNA Data Single Cell / Pre-processing of 10X Single-Cell RNA Datasets Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / 1: RNA-Seq reads to counts Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs Variant Analysis / M. tuberculosis Variant Analysis
Remove beginning1	Foundations of Data Science / Data Manipulation Olympics Digital Humanities / Introduction to Digital Humanities in Galaxy Digital Humanities / OpenRefine Tutorial for researching cultural data Ecology / Biodiversity data exploration Ecology / Regional GAM Epigenetics / Infinium Human Methylation BeadChip Using Galaxy and Managing your Data / Workflow Reports Genome Annotation / Dataset construction for bacterial comparative genomics Genome Annotation / Secondary metabolite discovery Introduction to Galaxy Analyses / Data Manipulation Olympics Introduction to Galaxy Analyses / Galaxy Basics for everyone Introduction to Galaxy Analyses / How to reproduce published Galaxy analyses Microbiome / Clinical Metaproteomics 2: Discovery Microbiome / Clinical Metaproteomics 3: Verification Microbiome / 16S Microbial analysis with Nanopore data Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 3: Verification Proteomics / metaQuantome 1: Data creation Proteomics / Neoantigen 2: Database merge and FragPipe discovery Proteomics / Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides Sequence analysis / Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Statistics and machine learning / Classification in Machine Learning Statistics and machine learning / Regression in Machine Learning Transcriptomics / Genome-wide alternative splicing analysis Visualisation / Visualisation with Circos
upload1	Assembly / Chloroplast genome assembly Assembly / Making sense of a newly assembled genome Assembly / Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) Contributing to the Galaxy Training Material / Creating content in Markdown Foundations of Data Science / Data Manipulation Olympics Ecology / Checking expected species and contamination in bacterial isolate Evolution / Phylogenetic analysis for bacterial comparative genomics Evolution / Tree thinking for tuberculosis evolution and epidemiology Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Using Galaxy and Managing your Data / Workflow Reports Genome Annotation / Identification of AMR genes in an assembled bacterial genome Genome Annotation / Dataset construction for bacterial comparative genomics Genome Annotation / Bacterial Genome Annotation Genome Annotation / Bacterial genome quality control Genome Annotation / Bacterial pangenomics Introduction to Galaxy Analyses / Data Manipulation Olympics Introduction to Galaxy Analyses / Galaxy Basics for genomics Introduction to Galaxy Analyses / Galaxy Basics for everyone Introduction to Galaxy Analyses / From peaks to genes Introduction to Galaxy Analyses / How to reproduce published Galaxy analyses Sequence analysis / Quality and contamination control in bacterial isolate using Illumina MiSeq Data Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data Variant Analysis / Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data Variant Analysis / M. tuberculosis Variant Analysis Visualisation / Visualisation with Circos
nml/collapse_collections/collapse_dataset	Assembly / ERGA post-assembly QC Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Assembly / Making sense of a newly assembled genome Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Computational chemistry / Protein-ligand docking Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring Ecology / Preparing genomic data for phylogeny reconstruction Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Using Galaxy and Managing your Data / Using dataset collections Using Galaxy and Managing your Data / Automating Galaxy workflows using the command line Genome Annotation / Comparative gene analysis in unannotated genomes Genome Annotation / Secondary metabolite discovery Imaging / Analyse HeLa fluorescence siRNA screen Imaging / Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy Introduction to Galaxy Analyses / NGS data logistics Microbiome / Clinical Metaproteomics 3: Verification Microbiome / MGnify v5.0 Amplicon Pipeline Microbiome / 16S Microbial Analysis with mothur (short) Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Clinical Metaproteomics 3: Verification Proteomics / Neoantigen 2: Database merge and FragPipe discovery Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data Variant Analysis / Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates
bgruening/text_processing/tp_cut_tool	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Contributing to the Galaxy Training Material / Creating a new tutorial Ecology / Ecoregionalization workflow tutorial Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite Ecology / Biodiversity data exploration Ecology / Life Traits Ecoregionalization workflow Ecology / Obis marine indicators Ecology / Species distribution modeling Metabolomics / Predicting EI+ mass spectra with QCxMS Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Biomarker candidate identification Proteomics / Secretome Prediction Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution Single Cell / Inferring single cell trajectories with Monocle3 Single Cell / Converting between common single cell data formats Statistics and machine learning / Prepare Data from CbioPortal for Flexynesis Integration Statistics and machine learning / Modeling Breast Cancer Subtypes with Flexynesis Statistics and machine learning / Image classification in Galaxy with fruit 360 dataset Transcriptomics / 2: RNA-seq counts to genes Transcriptomics / 3: RNA-seq genes to pathways Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
bgruening/text_processing/tp_cat	Assembly / Decontamination of a genome assembly Assembly / Making sense of a newly assembled genome Assembly / Assembly of metagenomic sequencing data Computational chemistry / Protein-ligand docking Computational chemistry / Protein target prediction of a bioactive ligand with Align-it and ePharmaLib Contributing to the Galaxy Training Material / Creating a new tutorial Foundations of Data Science / Data Manipulation Olympics Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Using Galaxy and Managing your Data / SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc Introduction to Galaxy Analyses / Data Manipulation Olympics Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy Metabolomics / Predicting EI+ mass spectra with QCxMS Microbiome / Clinical Metaproteomics 2: Discovery Microbiome / Clinical Metaproteomics 3: Verification Microbiome / Assembly of metagenomic sequencing data Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 3: Verification Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Reference-based RNA-Seq data analysis
bgruening/text_processing/tp_sort_header_tool	Assembly / Making sense of a newly assembled genome Foundations of Data Science / Data Manipulation Olympics Digital Humanities / OpenRefine Tutorial for researching cultural data Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite Ecology / RAD-Seq Reference-based data analysis Epigenetics / ATAC-Seq data analysis Genome Annotation / Essential genes detection with Transposon insertion sequencing Introduction to Galaxy Analyses / Data Manipulation Olympics Introduction to Galaxy Analyses / Galaxy Basics for genomics Introduction to Galaxy Analyses / From peaks to genes Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short) Proteomics / Mass spectrometry imaging: Loading and exploring MSI data Proteomics / Label-free data analysis using MaxQuant Statistics and machine learning / Prepare Data from CbioPortal for Flexynesis Integration Statistics and machine learning / Modeling Breast Cancer Subtypes with Flexynesis Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial Transcriptomics / 3: RNA-seq genes to pathways Transcriptomics / Small Non-coding RNA Clustering using BlockClust
Grouping1	Foundations of Data Science / Data Manipulation Olympics Using Galaxy and Managing your Data / Workflow Reports Genome Annotation / Bacterial Genome Annotation Introduction to Galaxy Analyses / Data Manipulation Olympics Introduction to Galaxy Analyses / Galaxy Basics for everyone Introduction to Galaxy Analyses / From peaks to genes Introduction to Galaxy Analyses / How to reproduce published Galaxy analyses Microbiome / Clinical Metaproteomics 2: Discovery Microbiome / Clinical Metaproteomics 3: Verification Microbiome / Clinical Metaproteomics 4: Quantitation Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / MGnify v5.0 Amplicon Pipeline Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Single Cell Proteomics data analysis with bioconductor-scp Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 3: Verification Proteomics / Clinical Metaproteomics 4: Quantitation Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial
devteam/column_maker/Add_a_column1	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Foundations of Data Science / Data Manipulation Olympics Digital Humanities / Text-Mining Differences in Chinese Newspaper Articles Genome Annotation / Comparative gene analysis in unannotated genomes Genome Annotation / Essential genes detection with Transposon insertion sequencing Introduction to Galaxy Analyses / Data Manipulation Olympics Introduction to Galaxy Analyses / From peaks to genes Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data Microbiome / MGnify v5.0 Amplicon Pipeline Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Label-free data analysis using MaxQuant Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Statistics and machine learning / Identifing Survival Markers of Brain tumor with Flexynesis Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial Transcriptomics / 3: RNA-seq genes to pathways Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
iuc/query_tabular/query_tabular	Using Galaxy and Managing your Data / SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis Microbiome / Clinical Metaproteomics 2: Discovery Microbiome / Clinical Metaproteomics 3: Verification Microbiome / MGnify v5.0 Amplicon Pipeline Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 3: Verification Proteomics / Metaproteomics tutorial Proteomics / metaQuantome 1: Data creation Proteomics / Neoantigen 2: Database merge and FragPipe discovery Proteomics / Neoantigen 1a: Fusion-Database-Generation Proteomics / Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Proteomics / Neoantigen 3: PepQuery2 Verification Proteomics / Neoantigen 5a: Predicting HLA Binding Proteomics / Neoantigen 4: Variant Annotation Proteomics / Proteogenomics 1: Database Creation Proteomics / Proteogenomics 2: Database Search Proteomics / Proteogenomics 3: Novel peptide analysis Transcriptomics / RNA-RNA interactome data analysis
galaxyp/regex_find_replace/regexColumn1	Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools Foundations of Data Science / Data Manipulation Olympics Digital Humanities / OpenRefine Tutorial for researching cultural data Ecology / Ecoregionalization workflow tutorial Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite Ecology / Biodiversity data exploration Ecology / Life Traits Ecoregionalization workflow Ecology / Regional GAM Genome Annotation / Comparative gene analysis in unannotated genomes Introduction to Galaxy Analyses / Data Manipulation Olympics Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Proteomics / Neoantigen 4: Variant Annotation Proteomics / Proteogenomics 1: Database Creation Single Cell / Importing files from public atlases Single Cell / Inferring single cell trajectories with Monocle3 Single Cell / Converting between common single cell data formats Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
iuc/jbrowse/jbrowse	Assembly / Chloroplast genome assembly Assembly / Making sense of a newly assembled genome Genome Annotation / Identification of AMR genes in an assembled bacterial genome Genome Annotation / Genome annotation with Maker Genome Annotation / Genome annotation with Maker (short) Genome Annotation / Genome annotation with Prokka Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes) Genome Annotation / Refining Genome Annotations with Apollo (eukaryotes) Genome Annotation / Bacterial Genome Annotation Genome Annotation / Genome annotation with Braker3 Genome Annotation / Comparison of two annotation tools - Helixer and Braker3 Genome Annotation / Genome annotation with Funannotate Genome Annotation / Genome annotation with Helixer Sequence analysis / Mapping Sequence analysis / SARS-CoV-2 Viral Sample Alignment and Variant Visualization Variant Analysis / Microbial Variant Calling Variant Analysis / M. tuberculosis Variant Analysis Visualisation / Genomic Data Visualisation with JBrowse
bgruening/text_processing/tp_awk_tool	Climate / Getting your hands-on climate data Ecology / Regional GAM Epigenetics / DNA Methylation data analysis Genome Annotation / CRISPR screen analysis Genome Annotation / From small to large-scale genome comparison Genome Annotation / Secondary metabolite discovery Microbiome / MGnify v5.0 Amplicon Pipeline Proteomics / Neoantigen 1a: Fusion-Database-Generation Proteomics / Neoantigen 5a: Predicting HLA Binding Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution Single Cell / Pseudobulk Analysis with Decoupler and EdgeR Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection Transcriptomics / Genome-wide alternative splicing analysis Variant Analysis / Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates Variant Analysis / M. tuberculosis Variant Analysis
iuc/fastp/fastp	Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Assembly / Large genome assembly and polishing Assembly / Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) Ecology / Taxonomic Analysis of eDNA Introduction to Galaxy Analyses / NGS data logistics Introduction to Galaxy Analyses / Very Short Introductions: QC Microbiome / Identification of the micro-organisms in a beer using Nanopore sequencing Microbiome / MGnify v5.0 Amplicon Pipeline Microbiome / 16S Microbial analysis with Nanopore data Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Sequence analysis / Quality and contamination control in bacterial isolate using Illumina MiSeq Data Transcriptomics / Genome-wide alternative splicing analysis Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis Variant Analysis / M. tuberculosis Variant Analysis
join1	Assembly / Making sense of a newly assembled genome Foundations of Data Science / Data Manipulation Olympics Ecology / Metabarcoding/eDNA through Obitools Genome Annotation / Comparative gene analysis in unannotated genomes Introduction to Galaxy Analyses / Data Manipulation Olympics Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Generating a single cell matrix using Alevin Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy Single Cell / Inferring single cell trajectories with Monocle3 Single Cell / Converting between common single cell data formats Statistics and machine learning / Modeling Breast Cancer Subtypes with Flexynesis Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / 3: RNA-seq genes to pathways Transcriptomics / Visualization of RNA-Seq results with heatmap2
iuc/datamash_ops/datamash_ops	Assembly / Making sense of a newly assembled genome Climate / Getting your hands-on climate data Foundations of Data Science / Data Manipulation Olympics Digital Humanities / OpenRefine Tutorial for researching cultural data Digital Humanities / Text-Mining Differences in Chinese Newspaper Articles Using Galaxy and Managing your Data / Workflow Reports Introduction to Galaxy Analyses / Data Manipulation Olympics Introduction to Galaxy Analyses / Galaxy Basics for genomics Introduction to Galaxy Analyses / Galaxy Basics for everyone Introduction to Galaxy Analyses / How to reproduce published Galaxy analyses Proteomics / MaxQuant and MSstats for the analysis of label-free data Single Cell / Downstream Single-cell RNA analysis with RaceID Single Cell / Clustering 3K PBMCs with Scanpy Statistics and machine learning / Identifing Survival Markers of Brain tumor with Flexynesis Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data Variant Analysis / Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
devteam/bwa/bwa_mem	Assembly / Chloroplast genome assembly Using Galaxy and Managing your Data / Using dataset collections Introduction to Galaxy Analyses / NGS data logistics Sequence analysis / Removal of human reads from SARS-CoV-2 sequencing data Sequence analysis / SARS-CoV-2 Viral Sample Alignment and Variant Visualization Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data Variant Analysis / Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates Variant Analysis / Calling very rare variants Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease Variant Analysis / Calling variants in non-diploid systems Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
lparsons/cutadapt/cutadapt	Assembly / Assembly of metagenomic sequencing data Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Contributing to the Galaxy Training Material / Creating a new tutorial Ecology / Data submission using ENA upload Tool Epigenetics / ATAC-Seq data analysis Genome Annotation / CRISPR screen analysis Genome Annotation / Essential genes detection with Transposon insertion sequencing Microbiome / Assembly of metagenomic sequencing data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short) Sequence analysis / Quality Control Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / RNA-RNA interactome data analysis Transcriptomics / 1: RNA-Seq reads to counts
bgruening/text_processing/tp_replace_in_line	Assembly / Making sense of a newly assembled genome Digital Humanities / Introduction to Digital Humanities in Galaxy Digital Humanities / Text-Mining Differences in Chinese Newspaper Articles Ecology / Preparing genomic data for phylogeny reconstruction Ecology / RAD-Seq Reference-based data analysis Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 Microbiome / 16S Microbial analysis with Nanopore data Proteomics / metaQuantome 1: Data creation Sequence analysis / Removal of human reads from SARS-CoV-2 sequencing data Single Cell / Pseudobulk Analysis with Decoupler and EdgeR Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / 2: RNA-seq counts to genes Variant Analysis / Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC
cat1	Assembly / Making sense of a newly assembled genome Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Foundations of Data Science / Data Manipulation Olympics Ecology / RAD-Seq Reference-based data analysis Epigenetics / Formation of the Super-Structures on the Inactive X Genome Annotation / Dataset construction for bacterial comparative genomics Genome Annotation / Comparative gene analysis in unannotated genomes Introduction to Galaxy Analyses / Data Manipulation Olympics Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data Single Cell / Removing the effects of the cell cycle Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial
__EXTRACT_DATASET__	Assembly / ERGA post-assembly QC Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools Epigenetics / CUT&RUN data analysis Genome Annotation / Essential genes detection with Transposon insertion sequencing Imaging / Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools Imaging / Using BioImage.IO models for image analysis in Galaxy Single Cell / Pseudobulk Analysis with Decoupler and EdgeR Single Cell / Multi-sample batch correction with Harmony and SnapATAC2 Statistics and machine learning / Prepare Data from CbioPortal for Flexynesis Integration Statistics and machine learning / Modeling Breast Cancer Subtypes with Flexynesis Statistics and machine learning / Identifing Survival Markers of Brain tumor with Flexynesis Statistics and machine learning / Unsupervised Analysis of Bone Marrow Cells with Flexynesis Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Reference-based RNA-Seq data analysis Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC
bgruening/text_processing/tp_replace_in_column	Assembly / Making sense of a newly assembled genome Genome Annotation / Bacterial Genome Annotation Introduction to Galaxy Analyses / From peaks to genes Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / MaxQuant and MSstats for the analysis of label-free data Proteomics / metaQuantome 1: Data creation Proteomics / Proteogenomics 1: Database Creation Single Cell / Pseudobulk Analysis with Decoupler and EdgeR Single Cell / Combining single cell datasets after pre-processing Single Cell / Converting NCBI Data to the AnnData Format Statistics and machine learning / Identifing Survival Markers of Brain tumor with Flexynesis Variant Analysis / Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates
iuc/anndata_inspect/anndata_inspect	Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Pseudobulk Analysis with Decoupler and EdgeR Single Cell / Multi-sample batch correction with Harmony and SnapATAC2 Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 Single Cell / Generating a single cell matrix using Alevin Single Cell / Combining single cell datasets after pre-processing Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy Single Cell / Removing the effects of the cell cycle Single Cell / Inferring single cell trajectories with Monocle3 Single Cell / Converting between common single cell data formats Single Cell / Converting NCBI Data to the AnnData Format Single Cell / Clustering 3K PBMCs with Scanpy
bgruening/text_processing/tp_find_and_replace	Assembly / ERGA post-assembly QC Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) Computational chemistry / Protein-ligand docking Digital Humanities / Introduction to Digital Humanities in Galaxy Ecology / Species distribution modeling Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short) Microbiome / MGnify v5.0 Amplicon Pipeline Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Single Cell / Importing files from public atlases Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data Variant Analysis / Mapping and molecular identification of phenotype-causing mutations
bgruening/text_processing/tp_grep_tool	Assembly / Making sense of a newly assembled genome Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Computational chemistry / Protein-ligand docking Computational chemistry / High Throughput Molecular Dynamics and Analysis Computational chemistry / Running molecular dynamics simulations using GROMACS Digital Humanities / Introduction to Digital Humanities in Galaxy Digital Humanities / OpenRefine Tutorial for researching cultural data Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Proteomics / Multiomics data analysis using MultiGSEA Single Cell / Importing files from public atlases Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Reference-based RNA-Seq data analysis Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
iuc/busco/busco	Assembly / ERGA post-assembly QC Assembly / Genome Assembly Quality Control Assembly / Genome assembly using PacBio data Assembly / Large genome assembly and polishing Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Ecology / Preparing genomic data for phylogeny reconstruction Genome Annotation / Genome annotation with Maker Genome Annotation / Genome annotation with Maker (short) Genome Annotation / Genome annotation with Braker3 Genome Annotation / Comparison of two annotation tools - Helixer and Braker3 Genome Annotation / Genome annotation with Funannotate Genome Annotation / Genome annotation with Helixer
bgruening/text_processing/tp_easyjoin_tool	Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Genome Annotation / Essential genes detection with Transposon insertion sequencing Proteomics / MaxQuant and MSstats for the analysis of label-free data Proteomics / Secretome Prediction Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution Single Cell / Removing the effects of the cell cycle Statistics and machine learning / Modeling Breast Cancer Subtypes with Flexynesis Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
iuc/anndata_manipulate/anndata_manipulate	Single Cell / Pseudobulk Analysis with Decoupler and EdgeR Single Cell / Multi-sample batch correction with Harmony and SnapATAC2 Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 Single Cell / Generating a single cell matrix using Alevin Single Cell / Combining single cell datasets after pre-processing Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy Single Cell / Removing the effects of the cell cycle Single Cell / Inferring single cell trajectories with Scanpy Single Cell / Converting NCBI Data to the AnnData Format Single Cell / Analysis of plant scRNA-Seq Data with Scanpy Single Cell / Clustering 3K PBMCs with Scanpy
galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences	Microbiome / Clinical Metaproteomics 1: Database-Generation Microbiome / Clinical Metaproteomics 2: Discovery Microbiome / Clinical Metaproteomics 3: Verification Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Clinical Metaproteomics 1: Database-Generation Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 3: Verification Proteomics / Protein FASTA Database Handling Proteomics / Neoantigen 2: Database merge and FragPipe discovery Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Proteomics / Proteogenomics 1: Database Creation
imgteam/unzip/unzip	Ecology / Ecoregionalization workflow tutorial Ecology / Metabarcoding/eDNA through Obitools Ecology / Life Traits Ecoregionalization workflow Imaging / Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines Imaging / Analyse HeLa fluorescence siRNA screen Imaging / Introduction to Image Analysis using Galaxy Imaging / Object tracking using CellProfiler Imaging / Voronoi segmentation Imaging / Training Custom YOLO Models for Segmentation of Bioimages Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus Single Cell / Converting NCBI Data to the AnnData Format
galaxyp/regex_find_replace/regex1	Ecology / Data submission using ENA upload Tool Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite Ecology / Marine Omics identifying biosynthetic gene clusters Ecology / Cleaning GBIF data using OpenRefine Ecology / Preparing genomic data for phylogeny reconstruction Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / metaQuantome 1: Data creation Proteomics / Neoantigen 1a: Fusion-Database-Generation Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution
bgruening/text_processing/tp_sorted_uniq	Contributing to the Galaxy Training Material / Creating a new tutorial Foundations of Data Science / Data Manipulation Olympics Using Galaxy and Managing your Data / Workflow Reports Introduction to Galaxy Analyses / Data Manipulation Olympics Introduction to Galaxy Analyses / Galaxy Basics for everyone Introduction to Galaxy Analyses / How to reproduce published Galaxy analyses Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Secretome Prediction Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets Transcriptomics / Pathway analysis with the MINERVA Platform
devteam/tabular_to_fasta/tab2fasta	Genome Annotation / Comparative gene analysis in unannotated genomes Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Protein FASTA Database Handling Proteomics / Neoantigen 1a: Fusion-Database-Generation Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Proteomics / Neoantigen 3: PepQuery2 Verification Proteomics / Neoantigen 4: Variant Annotation Proteomics / Proteogenomics 1: Database Creation Proteomics / Proteogenomics 2: Database Search Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
sort1	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Computational chemistry / Protein target prediction of a bioactive ligand with Align-it and ePharmaLib Digital Humanities / Text-Mining Differences in Chinese Newspaper Articles Genome Annotation / Dataset construction for bacterial comparative genomics Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution Single Cell / Removing the effects of the cell cycle Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana
devteam/bowtie2/bowtie2	Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Assembly / Assembly of metagenomic sequencing data Contributing to the Galaxy Training Material / Creating a new tutorial Epigenetics / ATAC-Seq data analysis Epigenetics / CUT&RUN data analysis Epigenetics / Identification of the binding sites of the Estrogen receptor Epigenetics / Formation of the Super-Structures on the Inactive X Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer Genome Annotation / Identification of AMR genes in an assembled bacterial genome Microbiome / Assembly of metagenomic sequencing data Sequence analysis / Mapping
iuc/falco/falco	Assembly / Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data Ecology / Data submission using ENA upload Tool Epigenetics / CUT&RUN data analysis Epigenetics / DNA Methylation data analysis Using Galaxy and Managing your Data / Annotate, prepare tests and publish Galaxy workflows in workflow registries Sequence analysis / Quality and contamination control in bacterial isolate using Illumina MiSeq Data Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana Transcriptomics / Reference-based RNA-Seq data analysis Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
iuc/quast/quast	Assembly / Genome Assembly Quality Control Assembly / An Introduction to Genome Assembly Assembly / Genome assembly using PacBio data Assembly / Large genome assembly and polishing Assembly / Assembly of metagenomic sequencing data Assembly / Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) Assembly / Unicycler Assembly Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Assembly / Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data Microbiome / Assembly of metagenomic sequencing data
bgruening/text_processing/tp_sed_tool	Assembly / Decontamination of a genome assembly Assembly / Making sense of a newly assembled genome Contributing to the Galaxy Training Material / Creating a new tutorial Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution Single Cell / Pre-processing of Single-Cell RNA Data Single Cell / Downstream Single-cell RNA analysis with RaceID Variant Analysis / M. tuberculosis Variant Analysis
iuc/bandage/bandage_image	Assembly / ERGA post-assembly QC Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Assembly / Chloroplast genome assembly Assembly / Large genome assembly and polishing Assembly / Assembly of metagenomic sequencing data Assembly / Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) Microbiome / Assembly of metagenomic sequencing data Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Microbiome / Antibiotic resistance detection
iuc/table_compute/table_compute	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution Single Cell / Removing the effects of the cell cycle Statistics and machine learning / Prepare Data from CbioPortal for Flexynesis Integration Statistics and machine learning / Modeling Breast Cancer Subtypes with Flexynesis Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial
iuc/ggplot2_point/ggplot2_point	Climate / Getting your hands-on climate data Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools Ecology / Regional GAM Using Galaxy and Managing your Data / Workflow Reports Introduction to Galaxy Analyses / Galaxy Basics for everyone Introduction to Galaxy Analyses / How to reproduce published Galaxy analyses Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Statistics and machine learning / Clustering in Machine Learning Variant Analysis / Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates
pjbriggs/trimmomatic/trimmomatic	Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Microbiome / MGnify v5.0 Amplicon Pipeline Sequence analysis / Removal of human reads from SARS-CoV-2 sequencing data Transcriptomics / De novo transcriptome reconstruction with RNA-Seq Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
Count1	Foundations of Data Science / Data Manipulation Olympics Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite Ecology / Taxonomic Analysis of eDNA Ecology / Cleaning GBIF data for the use in Ecology Ecology / RAD-Seq Reference-based data analysis Ecology / Regional GAM Introduction to Galaxy Analyses / Data Manipulation Olympics Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution
iuc/filter_tabular/filter_tabular	Assembly / Assembly of metagenomic sequencing data Digital Humanities / OpenRefine Tutorial for researching cultural data Ecology / Ecoregionalization workflow tutorial Microbiome / Clinical Metaproteomics 2: Discovery Microbiome / Assembly of metagenomic sequencing data Microbiome / MGnify v5.0 Amplicon Pipeline Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Proteomics / Proteogenomics 1: Database Creation
iuc/collection_column_join/collection_column_join	Assembly / Assembly of metagenomic sequencing data Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Microbiome / Assembly of metagenomic sequencing data Microbiome / MGnify v5.0 Amplicon Pipeline Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Single Cell / Pre-processing of Single-Cell RNA Data Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / 1: RNA-Seq reads to counts
iuc/datamash_transpose/datamash_transpose	Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite Epigenetics / CUT&RUN data analysis Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Inferring single cell trajectories with Monocle3 Single Cell / Converting between common single cell data formats Single Cell / Downstream Single-cell RNA analysis with RaceID Statistics and machine learning / Modeling Breast Cancer Subtypes with Flexynesis Transcriptomics / Visualization of RNA-Seq results with heatmap2
crs4/taxonomy_krona_chart/taxonomy_krona_chart	Microbiome / Identification of the micro-organisms in a beer using Nanopore sequencing Microbiome / Analyses of metagenomics data - The global picture Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short) Microbiome / MGnify v5.0 Amplicon Pipeline Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial analysis with Nanopore data Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Microbiome / Taxonomic Profiling and Visualization of Metagenomic Data
galaxyp/maxquant/maxquant	Microbiome / Clinical Metaproteomics 2: Discovery Microbiome / Clinical Metaproteomics 4: Quantitation Proteomics / Library Generation for DIA Analysis Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 4: Quantitation Proteomics / Label-free data analysis using MaxQuant Proteomics / MaxQuant and MSstats for the analysis of label-free data Proteomics / MaxQuant and MSstats for the analysis of TMT data
galaxyp/msconvert/msconvert	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) Microbiome / Clinical Metaproteomics 2: Discovery Proteomics / DIA Analysis using OpenSwathWorkflow Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / EncyclopeDIA Proteomics / metaQuantome 1: Data creation Proteomics / Neoantigen 3: PepQuery2 Verification Proteomics / Peptide and Protein ID using OpenMS tools
interactive_tool_rstudio	Foundations of Data Science / Version Control with Git Foundations of Data Science / Advanced R in Galaxy Foundations of Data Science / R basics in Galaxy Evolution / Tree thinking for tuberculosis evolution and epidemiology Using Galaxy and Managing your Data / RStudio in Galaxy Statistics and machine learning / Introduction to Machine Learning using R Transcriptomics / RNA Seq Counts to Viz in R Transcriptomics / Visualization of RNA-Seq results with Volcano Plot in R
iuc/kraken2/kraken2	Assembly / Decontamination of a genome assembly Ecology / Checking expected species and contamination in bacterial isolate Microbiome / Identification of the micro-organisms in a beer using Nanopore sequencing Microbiome / 16S Microbial analysis with Nanopore data Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Microbiome / Taxonomic Profiling and Visualization of Metagenomic Data Sequence analysis / Quality and contamination control in bacterial isolate using Illumina MiSeq Data Variant Analysis / M. tuberculosis Variant Analysis
iuc/samtools_view/samtools_view	Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Introduction to Galaxy Analyses / NGS data logistics Transcriptomics / Reference-based RNA-Seq data analysis Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC
iuc/rgrnastar/rna_star	Genome Annotation / Genome annotation with Braker3 Genome Annotation / Comparison of two annotation tools - Helixer and Braker3 Genome Annotation / Genome annotation with Funannotate Proteomics / Neoantigen 1a: Fusion-Database-Generation Single Cell / Pre-processing of Single-Cell RNA Data Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Reference-based RNA-Seq data analysis
iuc/collection_element_identifiers/collection_element_identifiers	Ecology / Data submission using ENA upload Tool Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 Microbiome / MGnify v5.0 Amplicon Pipeline Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus Single Cell / Multi-sample batch correction with Harmony and SnapATAC2 Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Reference-based RNA-Seq data analysis
galaxyp/dbbuilder/dbbuilder	Microbiome / Clinical Metaproteomics 1: Database-Generation Microbiome / Clinical Metaproteomics 2: Discovery Microbiome / Clinical Metaproteomics 3: Verification Proteomics / Clinical Metaproteomics 1: Database-Generation Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 3: Verification Proteomics / Protein FASTA Database Handling
devteam/fasta_to_tabular/fasta2tab	Microbiome / Clinical Metaproteomics 2: Discovery Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Protein FASTA Database Handling Proteomics / MaxQuant and MSstats for the analysis of label-free data Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Proteomics / Proteogenomics 1: Database Creation
Paste1	Ecology / Data submission using ENA upload Tool Ecology / Regional GAM Using Galaxy and Managing your Data / Creating, Editing and Importing Galaxy Workflows Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Single Cell / Combining single cell datasets after pre-processing Single Cell / Converting NCBI Data to the AnnData Format
devteam/gffread/gffread	Genome Annotation / Genome annotation with Maker Genome Annotation / Genome annotation with Maker (short) Genome Annotation / Genome annotation with Braker3 Genome Annotation / Comparison of two annotation tools - Helixer and Braker3 Genome Annotation / Genome annotation with Helixer Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc Transcriptomics / Genome-wide alternative splicing analysis
devteam/samtools_stats/samtools_stats	Assembly / ERGA post-assembly QC Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Introduction to Galaxy Analyses / NGS data logistics Sequence analysis / Mapping Single Cell / Pre-processing of Single-Cell RNA Data Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis Variant Analysis / M. tuberculosis Variant Analysis
iuc/minimap2/minimap2	Assembly / ERGA post-assembly QC Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Assembly / Large genome assembly and polishing Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Microbiome / Antibiotic resistance detection
iuc/nanoplot/nanoplot	Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Assembly / Chloroplast genome assembly Assembly / Large genome assembly and polishing Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Microbiome / Antibiotic resistance detection Sequence analysis / Quality Control
Show beginning1	Foundations of Data Science / Data Manipulation Olympics Using Galaxy and Managing your Data / Creating, Editing and Importing Galaxy Workflows Introduction to Galaxy Analyses / Data Manipulation Olympics Single Cell / Multi-sample batch correction with Harmony and SnapATAC2 Statistics and machine learning / Modeling Breast Cancer Subtypes with Flexynesis Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data
bgruening/trim_galore/trim_galore	Epigenetics / CUT&RUN data analysis Epigenetics / Identification of the binding sites of the Estrogen receptor Epigenetics / Formation of the Super-Structures on the Inactive X Sequence analysis / Mapping Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana Transcriptomics / Differential abundance testing of small RNAs Variant Analysis / Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates
devteam/picard/picard_MarkDuplicates	Epigenetics / ATAC-Seq data analysis Epigenetics / CUT&RUN data analysis Introduction to Galaxy Analyses / NGS data logistics Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / 1: RNA-Seq reads to counts Variant Analysis / Calling variants in non-diploid systems Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
bgruening/text_processing/tp_tail_tool	Epigenetics / DNA Methylation data analysis Genome Annotation / Bacterial Genome Annotation Introduction to Galaxy Analyses / From peaks to genes Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL) Single Cell / Converting between common single cell data formats Transcriptomics / Reference-based RNA-Seq data analysis
iuc/scanpy_plot/scanpy_plot	Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy Single Cell / Removing the effects of the cell cycle Single Cell / Analysis of plant scRNA-Seq Data with Scanpy Single Cell / Clustering 3K PBMCs with Scanpy
ebi-gxa/anndata_ops/anndata_ops	Single Cell / Importing files from public atlases Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 Single Cell / Combining single cell datasets after pre-processing Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy Single Cell / Converting between common single cell data formats Single Cell / Converting NCBI Data to the AnnData Format
iuc/hisat2/hisat2	Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Proteomics / Proteogenomics 1: Database Creation Transcriptomics / De novo transcriptome reconstruction with RNA-Seq Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / 1: RNA-Seq reads to counts Transcriptomics / Differential abundance testing of small RNAs
devteam/bamtools_filter/bamFilter	Epigenetics / ATAC-Seq data analysis Epigenetics / CUT&RUN data analysis Sequence analysis / Mapping Single Cell / Pre-processing of Single-Cell RNA Data Variant Analysis / Calling variants in non-diploid systems Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
iuc/snpeff/snpEff	Introduction to Galaxy Analyses / NGS data logistics Variant Analysis / Calling variants in diploid systems Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease Variant Analysis / Mapping and molecular identification of phenotype-causing mutations Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
galaxyp/peptideshaker/search_gui	Microbiome / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Metaproteomics tutorial Proteomics / metaQuantome 1: Data creation Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker Proteomics / Proteogenomics 2: Database Search
galaxyp/peptideshaker/peptide_shaker	Microbiome / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Metaproteomics tutorial Proteomics / metaQuantome 1: Data creation Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker Proteomics / Proteogenomics 2: Database Search
param_value_from_file	Digital Humanities / OpenRefine Tutorial for researching cultural data Imaging / Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy Metabolomics / Predicting EI+ mass spectra with QCxMS Microbiome / MGnify v5.0 Amplicon Pipeline Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
bgruening/text_processing/tp_head_tool	Digital Humanities / OpenRefine Tutorial for researching cultural data Using Galaxy and Managing your Data / Using Workflow Parameters Introduction to Galaxy Analyses / Galaxy Basics for genomics Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Single Cell / Downstream Single-cell RNA analysis with RaceID
rnateam/mafft/rbc_mafft	Evolution / Phylogenetics - Back to basics Genome Annotation / Comparative gene analysis in unannotated genomes Sequence analysis / Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants Sequence analysis / Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
bgruening/split_file_on_column/tp_split_on_column	Foundations of Data Science / Data Manipulation Olympics Genome Annotation / Comparative gene analysis in unannotated genomes Imaging / Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy Introduction to Galaxy Analyses / Data Manipulation Olympics Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data
CONVERTER_gz_to_uncompressed	Assembly / ERGA post-assembly QC Microbiome / MGnify v5.0 Amplicon Pipeline Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Neoantigen 1a: Fusion-Database-Generation Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
iuc/fasta_stats/fasta-stats	Assembly / Chloroplast genome assembly Assembly / De Bruijn Graph Assembly Assembly / Genome assembly using PacBio data Assembly / Large genome assembly and polishing Genome Annotation / Genome annotation with Maker Genome Annotation / Genome annotation with Braker3
bgruening/openbabel_compound_convert/openbabel_compound_convert	Computational chemistry / Protein-ligand docking Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring Computational chemistry / High Throughput Molecular Dynamics and Analysis Computational chemistry / Data management in Medicinal Chemistry FAIR Data, Workflows, and Research / Data management in Medicinal Chemistry Metabolomics / Predicting EI+ mass spectra with QCxMS
iuc/macs2/macs2_callpeak	Epigenetics / ATAC-Seq data analysis Epigenetics / CUT&RUN data analysis Epigenetics / Identification of the binding sites of the Estrogen receptor Epigenetics / Formation of the Super-Structures on the Inactive X Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets
bgruening/deeptools_compute_matrix/deeptools_compute_matrix	Epigenetics / ATAC-Seq data analysis Epigenetics / CUT&RUN data analysis Epigenetics / Identification of the binding sites of the Estrogen receptor Epigenetics / Formation of the Super-Structures on the Inactive X Epigenetics / DNA Methylation data analysis Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
iuc/deseq2/deseq2	Transcriptomics / De novo transcriptome reconstruction with RNA-Seq Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana Transcriptomics / Network analysis with Heinz Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial Transcriptomics / Differential abundance testing of small RNAs
devteam/samtools_idxstats/samtools_idxstats	Epigenetics / ATAC-Seq data analysis Epigenetics / Identification of the binding sites of the Estrogen receptor Epigenetics / Formation of the Super-Structures on the Inactive X Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / 1: RNA-Seq reads to counts
__MERGE_COLLECTION__	Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Microbiome / MGnify v5.0 Amplicon Pipeline Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana Transcriptomics / Reference-based RNA-Seq data analysis
iuc/scanpy_inspect/scanpy_inspect	Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy Single Cell / Removing the effects of the cell cycle Single Cell / Analysis of plant scRNA-Seq Data with Scanpy Single Cell / Clustering 3K PBMCs with Scanpy
iuc/scanpy_filter/scanpy_filter	Single Cell / Pseudobulk Analysis with Decoupler and EdgeR Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy Single Cell / Analysis of plant scRNA-Seq Data with Scanpy Single Cell / Clustering 3K PBMCs with Scanpy
interactive_tool_panoply	Climate / Getting your hands-on climate data Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) Climate / Visualize Climate data with Panoply netCDF viewer Climate / Sentinel 5P data visualisation Ecology / Visualize EBV cube data with Panoply netCDF viewer
imgteam/binary2labelimage/ip_binary_to_labelimage	Imaging / Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines Imaging / Analyse HeLa fluorescence siRNA screen Imaging / Introduction to Image Analysis using Galaxy Imaging / Using BioImage.IO models for image analysis in Galaxy Imaging / Voronoi segmentation
imgteam/2d_auto_threshold/ip_threshold	Imaging / Analyse HeLa fluorescence siRNA screen Imaging / Introduction to Image Analysis using Galaxy Imaging / Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy Imaging / Using BioImage.IO models for image analysis in Galaxy Imaging / Voronoi segmentation
iuc/annotatemyids/annotatemyids	Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / 2: RNA-seq counts to genes
devteam/freebayes/freebayes	Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Proteomics / Proteogenomics 1: Database Creation Variant Analysis / Calling variants in diploid systems Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease Variant Analysis / Calling variants in non-diploid systems
Summary_Statistics1	Ecology / Cleaning GBIF data for the use in Ecology Ecology / RAD-Seq Reference-based data analysis Metabolomics / Mass spectrometry imaging: Finding differential analytes Proteomics / MaxQuant and MSstats for the analysis of label-free data Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
wc_gnu	Foundations of Data Science / Data Manipulation Olympics Digital Humanities / Introduction to Digital Humanities in Galaxy Ecology / Metabarcoding/eDNA through Obitools Introduction to Galaxy Analyses / Data Manipulation Olympics Microbiome / MGnify v5.0 Amplicon Pipeline
interactive_tool_jupyter_notebook	Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab Ecology / Ecoregionalization workflow tutorial Using Galaxy and Managing your Data / Use Jupyter notebooks in Galaxy Using Galaxy and Managing your Data / JupyterLab in Galaxy Genome Annotation / Secondary metabolite discovery
iuc/volcanoplot/volcanoplot	Genome Annotation / CRISPR screen analysis Single Cell / Pseudobulk Analysis with Decoupler and EdgeR Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial Transcriptomics / Visualization of RNA-Seq results with Volcano Plot Transcriptomics / Visualization of RNA-Seq results with Volcano Plot in R
devteam/ncbi_blast_plus/ncbi_blastp_wrapper	Foundations of Data Science / Learning about one gene across biological resources and formats Genome Annotation / Functional annotation of protein sequences Proteomics / Neoantigen 3: PepQuery2 Verification Proteomics / Proteogenomics 3: Novel peptide analysis Sequence analysis / NCBI BLAST+ against the MAdLand
iuc/stringtie/stringtie	Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Proteomics / Proteogenomics 1: Database Creation Transcriptomics / De novo transcriptome reconstruction with RNA-Seq Transcriptomics / Genome-wide alternative splicing analysis
iuc/bedtools/bedtools_intersectbed	Assembly / Making sense of a newly assembled genome Epigenetics / ATAC-Seq data analysis Epigenetics / CUT&RUN data analysis Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) Introduction to Galaxy Analyses / Galaxy Basics for genomics
devteam/fasta_compute_length/fasta_compute_length	Assembly / Making sense of a newly assembled genome Sequence analysis / Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes Single Cell / Multi-sample batch correction with Harmony and SnapATAC2 Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
iuc/sra_tools/fasterq_dump	Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Using Galaxy and Managing your Data / SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis Introduction to Galaxy Analyses / NGS data logistics Transcriptomics / Pathway analysis with the MINERVA Platform Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
iuc/seqtk/seqtk_subseq	Assembly / Assembly of metagenomic sequencing data Contributing to the Galaxy Training Material / Creating a new tutorial Microbiome / Assembly of metagenomic sequencing data Sequence analysis / Removal of human reads from SARS-CoV-2 sequencing data Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data
bgruening/unique/bg_uniq	Assembly / Assembly of metagenomic sequencing data Ecology / Data submission using ENA upload Tool Genome Annotation / Dataset construction for bacterial comparative genomics Microbiome / Assembly of metagenomic sequencing data Proteomics / Secretome Prediction
random_lines1	Assembly / Making sense of a newly assembled genome Assembly / Assembly of metagenomic sequencing data Contributing to the Galaxy Training Material / Creating a new tutorial Microbiome / Assembly of metagenomic sequencing data Visualisation / Visualisation with Circos
devteam/ncbi_blast_plus/ncbi_blastn_wrapper	Assembly / Decontamination of a genome assembly Ecology / Data submission using ENA upload Tool Ecology / Metabarcoding/eDNA through Obitools Ecology / Taxonomic Analysis of eDNA Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
iuc/bandage/bandage_info	Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Assembly / Chloroplast genome assembly Assembly / Assembly of metagenomic sequencing data Assembly / Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data Microbiome / Assembly of metagenomic sequencing data
bgruening/flye/flye	Assembly / Chloroplast genome assembly Assembly / Genome assembly using PacBio data Assembly / Large genome assembly and polishing Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
bgruening/model_prediction/model_prediction	Statistics and machine learning / Deep Learning (Part 3) - Convolutional neural networks (CNN) Statistics and machine learning / Deep Learning (Part 1) - Feedforward neural networks (FNN) Statistics and machine learning / Deep Learning (Part 2) - Recurrent neural networks (RNN) Statistics and machine learning / Image classification in Galaxy with fruit 360 dataset Statistics and machine learning / Introduction to deep learning
bgruening/keras_train_and_eval/keras_train_and_eval	Statistics and machine learning / Deep Learning (Part 3) - Convolutional neural networks (CNN) Statistics and machine learning / Deep Learning (Part 1) - Feedforward neural networks (FNN) Statistics and machine learning / Deep Learning (Part 2) - Recurrent neural networks (RNN) Statistics and machine learning / Image classification in Galaxy with fruit 360 dataset Statistics and machine learning / Introduction to deep learning
bgruening/keras_model_config/keras_model_config	Statistics and machine learning / Deep Learning (Part 3) - Convolutional neural networks (CNN) Statistics and machine learning / Deep Learning (Part 1) - Feedforward neural networks (FNN) Statistics and machine learning / Deep Learning (Part 2) - Recurrent neural networks (RNN) Statistics and machine learning / Image classification in Galaxy with fruit 360 dataset Statistics and machine learning / Introduction to deep learning
bgruening/keras_model_builder/keras_model_builder	Statistics and machine learning / Deep Learning (Part 3) - Convolutional neural networks (CNN) Statistics and machine learning / Deep Learning (Part 1) - Feedforward neural networks (FNN) Statistics and machine learning / Deep Learning (Part 2) - Recurrent neural networks (RNN) Statistics and machine learning / Image classification in Galaxy with fruit 360 dataset Statistics and machine learning / Introduction to deep learning
bgruening/get_pdb/get_pdb	Computational chemistry / Protein-ligand docking Computational chemistry / High Throughput Molecular Dynamics and Analysis Computational chemistry / Running molecular dynamics simulations using GROMACS Computational chemistry / Data management in Medicinal Chemistry FAIR Data, Workflows, and Research / Data management in Medicinal Chemistry
bgruening/split_file_to_collection/split_file_to_collection	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring Computational chemistry / Protein target prediction of a bioactive ligand with Align-it and ePharmaLib Metabolomics / Predicting EI+ mass spectra with QCxMS Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Sequence analysis / Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes
bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap	Epigenetics / ATAC-Seq data analysis Epigenetics / CUT&RUN data analysis Epigenetics / Identification of the binding sites of the Estrogen receptor Epigenetics / Formation of the Super-Structures on the Inactive X Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint	Epigenetics / CUT&RUN data analysis Epigenetics / Identification of the binding sites of the Estrogen receptor Epigenetics / Formation of the Super-Structures on the Inactive X Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
bgruening/deeptools_bam_coverage/deeptools_bam_coverage	Epigenetics / Identification of the binding sites of the Estrogen receptor Epigenetics / Formation of the Super-Structures on the Inactive X Genome Annotation / Essential genes detection with Transposon insertion sequencing Transcriptomics / De novo transcriptome reconstruction with RNA-Seq Visualisation / Ploting a Microbial Genome with Circos
iuc/featurecounts/featurecounts	Single Cell / Pre-processing of Single-Cell RNA Data Transcriptomics / De novo transcriptome reconstruction with RNA-Seq Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / 1: RNA-Seq reads to counts
__FLATTEN__	Epigenetics / CUT&RUN data analysis Single Cell / Pre-processing of Single-Cell RNA Data Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Reference-based RNA-Seq data analysis Variant Analysis / M. tuberculosis Variant Analysis
__FILTER_FROM_FILE__	Microbiome / MGnify v5.0 Amplicon Pipeline Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus Single Cell / Multi-sample batch correction with Harmony and SnapATAC2 Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Reference-based RNA-Seq data analysis
csv_to_tabular	Using Galaxy and Managing your Data / Workflow Reports Introduction to Galaxy Analyses / Galaxy Basics for everyone Introduction to Galaxy Analyses / How to reproduce published Galaxy analyses Single Cell / Clustering 3K PBMCs with Seurat Statistics and machine learning / Clustering in Machine Learning
bgruening/music_construct_eset/music_construct_eset	Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Single Cell / Bulk RNA Deconvolution with MuSiC Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution
iuc/scanpy_normalize/scanpy_normalize	Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy Single Cell / Analysis of plant scRNA-Seq Data with Scanpy Single Cell / Clustering 3K PBMCs with Scanpy
iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy Single Cell / Removing the effects of the cell cycle Single Cell / Analysis of plant scRNA-Seq Data with Scanpy Single Cell / Clustering 3K PBMCs with Scanpy
ebi-gxa/retrieve_scxa/retrieve_scxa	Single Cell / Importing files from public atlases Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
interactive_tool_odv	Climate / Analyse Argo data Climate / Ocean Data View (ODV) Climate / Ocean's variables study Climate / Nitrate DMQC for autonomous platforms such as Argo floats
ebi-gxa/scanpy_compute_graph/scanpy_compute_graph	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME Single Cell / Scanpy Parameter Iterator Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy Single Cell / Inferring single cell trajectories with Scanpy
imgteam/2d_simple_filter/ip_filter_standard	Imaging / Analyse HeLa fluorescence siRNA screen Imaging / Introduction to Image Analysis using Galaxy Imaging / Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy Imaging / Voronoi segmentation
imgteam/2d_histogram_equalization/ip_histogram_equalization	Imaging / Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines Imaging / Introduction to Image Analysis using Galaxy Imaging / Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy Imaging / Training Custom YOLO Models for Segmentation of Bioimages
imgteam/overlay_images/ip_overlay_images	Imaging / Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines Imaging / Introduction to Image Analysis using Galaxy Imaging / Using BioImage.IO models for image analysis in Galaxy Imaging / Voronoi segmentation
iuc/gffcompare/gffcompare	Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Proteomics / Proteogenomics 1: Database Creation Transcriptomics / De novo transcriptome reconstruction with RNA-Seq Transcriptomics / Genome-wide alternative splicing analysis
wig_to_bigWig	Epigenetics / ATAC-Seq data analysis Epigenetics / CUT&RUN data analysis Epigenetics / DNA Methylation data analysis Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/gemini_load/gemini_load	Variant Analysis / Calling variants in diploid systems Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
galaxyp/uniprotxml_downloader/uniprotxml_downloader	Microbiome / Clinical Metaproteomics 1: Database-Generation Microbiome / Clinical Metaproteomics 3: Verification Proteomics / Clinical Metaproteomics 1: Database-Generation Proteomics / Clinical Metaproteomics 3: Verification
galaxyp/pepquery2/pepquery2	Microbiome / Clinical Metaproteomics 3: Verification Proteomics / Clinical Metaproteomics 3: Verification Proteomics / Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides Proteomics / Neoantigen 3: PepQuery2 Verification
galaxyp/unipept/unipept	Microbiome / Clinical Metaproteomics 5: Data Interpretation Proteomics / Clinical Metaproteomics 5: Data Interpretation Proteomics / Metaproteomics tutorial Proteomics / metaQuantome 1: Data creation
iuc/snpsift/snpSift_extractFields	Using Galaxy and Managing your Data / Using dataset collections Introduction to Galaxy Analyses / NGS data logistics Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
__UNZIP_COLLECTION__	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 Microbiome / MGnify v5.0 Amplicon Pipeline Microbiome / Taxonomic Profiling and Visualization of Metagenomic Data Sequence analysis / Removal of human reads from SARS-CoV-2 sequencing data
lecorguille/xcms_xcmsset/abims_xcms_xcmsSet	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) Metabolomics / Mass spectrometry: GC-MS analysis with the metaMS package Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
lecorguille/xcms_merge/xcms_merge	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) Metabolomics / Mass spectrometry: GC-MS analysis with the metaMS package Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
lecorguille/xcms_group/abims_xcms_group	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) Metabolomics / Mass spectrometry: GC-MS analysis with the metaMS package Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) Metabolomics / Mass spectrometry: GC-MS analysis with the metaMS package Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
lecorguille/msnbase_readmsdata/msnbase_readmsdata	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) Metabolomics / Mass spectrometry: GC-MS analysis with the metaMS package Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
iuc/newick_utils/newick_display	Evolution / Phylogenetics - Back to basics Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short) Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
devteam/bwa/bwa	Galaxy Server administration / Reference Data with Data Managers Ecology / RAD-Seq Reference-based data analysis Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) Introduction to Galaxy Analyses / NGS data logistics
ecology/xarray_metadata_info/xarray_metadata_info	Climate / Analyse Argo data Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools Ecology / Visualization of Climate Data using NetCDF xarray Map Plotting
iuc/compose_text_param/compose_text_param	Digital Humanities / OpenRefine Tutorial for researching cultural data Using Galaxy and Managing your Data / Automating Galaxy workflows using the command line Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
iuc/bcftools_consensus/bcftools_consensus	Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Using Galaxy and Managing your Data / Automating Galaxy workflows using the command line Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Variant Analysis / M. tuberculosis Variant Analysis
iuc/circos/circos	Assembly / Making sense of a newly assembled genome Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC Visualisation / Visualisation with Circos Visualisation / Ploting a Microbial Genome with Circos
devteam/merge_cols/mergeCols1	Assembly / Making sense of a newly assembled genome Ecology / Ecoregionalization workflow tutorial Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite Transcriptomics / 2: RNA-seq counts to genes
Convert characters1	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Ecology / RAD-Seq Reference-based data analysis Proteomics / Neoantigen 4: Variant Annotation Proteomics / Secretome Prediction
bgruening/diamond/bg_diamond	Assembly / ERGA post-assembly QC Genome Annotation / Functional annotation of protein sequences Genome Annotation / Comparative gene analysis in unannotated genomes Sequence analysis / NCBI BLAST+ against the MAdLand
iuc/porechop/porechop	Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) Microbiome / Identification of the micro-organisms in a beer using Nanopore sequencing Microbiome / 16S Microbial analysis with Nanopore data Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/bwa_mem2/bwa_mem2	Assembly / ERGA post-assembly QC Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Introduction to Galaxy Analyses / NGS data logistics
iuc/meryl/meryl	Assembly / ERGA post-assembly QC Assembly / Genome Assembly Quality Control Assembly / Large genome assembly and polishing Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
bgruening/ml_visualization_ex/ml_visualization_ex	Statistics and machine learning / Deep Learning (Part 3) - Convolutional neural networks (CNN) Statistics and machine learning / Deep Learning (Part 2) - Recurrent neural networks (RNN) Statistics and machine learning / Image classification in Galaxy with fruit 360 dataset Statistics and machine learning / Introduction to deep learning
bgruening/deeptools_plot_correlation/deeptools_plot_correlation	Epigenetics / Identification of the binding sites of the Estrogen receptor Epigenetics / Formation of the Super-Structures on the Inactive X Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary	Epigenetics / Identification of the binding sites of the Estrogen receptor Epigenetics / Formation of the Super-Structures on the Inactive X Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
devteam/freebayes/bamleftalign	Variant Analysis / Calling very rare variants Variant Analysis / Calling variants in non-diploid systems Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
nilesh/rseqc/rseqc_read_distribution	Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / 1: RNA-Seq reads to counts
nilesh/rseqc/rseqc_geneBody_coverage	Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / 1: RNA-Seq reads to counts
iuc/pygenometracks/pygenomeTracks	Epigenetics / ATAC-Seq data analysis Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Reference-based RNA-Seq data analysis
iuc/goseq/goseq	Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial Transcriptomics / 3: RNA-seq genes to pathways
iuc/ggplot2_heatmap2/ggplot2_heatmap2	Proteomics / MaxQuant and MSstats for the analysis of label-free data Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial Transcriptomics / Visualization of RNA-Seq results with heatmap2
bgruening/sklearn_ensemble/sklearn_ensemble	Statistics and machine learning / Age prediction using machine learning Statistics and machine learning / Classification in Machine Learning Statistics and machine learning / Machine learning: classification and regression Statistics and machine learning / Regression in Machine Learning
bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots	Statistics and machine learning / Deep Learning (Part 1) - Feedforward neural networks (FNN) Statistics and machine learning / Age prediction using machine learning Statistics and machine learning / Machine learning: classification and regression Statistics and machine learning / Regression in Machine Learning
devteam/histogram/histogram_rpy	Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data Proteomics / Statistical analysis of DIA data Proteomics / Label-free data analysis using MaxQuant Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
bgruening/wordcloud/wordcloud	Digital Humanities / Introduction to Digital Humanities in Galaxy Digital Humanities / OpenRefine Tutorial for researching cultural data Digital Humanities / Text-Mining Differences in Chinese Newspaper Articles
iuc/sqlite_to_tabular/sqlite_to_tabular	Proteomics / Metaproteomics tutorial Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Proteomics / Proteogenomics 1: Database Creation
iuc/anndata_import/anndata_import	Single Cell / Converting NCBI Data to the AnnData Format Single Cell / Analysis of plant scRNA-Seq Data with Scanpy Single Cell / Clustering 3K PBMCs with Scanpy
ebi-gxa/seurat_read10x/seurat_read10x	Single Cell / Importing files from public atlases Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat Single Cell / Converting between common single cell data formats
iuc/sceasy_convert/sceasy_convert	Single Cell / Importing files from public atlases Single Cell / Generating a single cell matrix using Alevin Single Cell / Converting between common single cell data formats
ebi-gxa/scanpy_plot_embed/scanpy_plot_embed	Single Cell / Scanpy Parameter Iterator Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy Single Cell / Inferring single cell trajectories with Scanpy
ebi-gxa/scanpy_find_cluster/scanpy_find_cluster	Single Cell / Scanpy Parameter Iterator Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy Single Cell / Inferring single cell trajectories with Scanpy
ebi-gxa/scanpy_filter_cells/scanpy_filter_cells	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy Single Cell / Converting between common single cell data formats Single Cell / Converting NCBI Data to the AnnData Format
imgteam/image_info/ip_imageinfo	Imaging / Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools Imaging / Introduction to Image Analysis using Galaxy Imaging / Voronoi segmentation
imgteam/2d_feature_extraction/ip_2d_feature_extraction	Imaging / Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools Imaging / Analyse HeLa fluorescence siRNA screen Imaging / Voronoi segmentation
bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert	Using Galaxy and Managing your Data / Creating high resolution images of Galaxy Workflows Imaging / Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools Imaging / Training Custom YOLO Models for Segmentation of Bioimages
devteam/fastq_to_tabular/fastq_to_tabular	Contributing to the Galaxy Training Material / Creating a new tutorial Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus Single Cell / Converting between common single cell data formats
galaxyp/filter_by_fasta_ids/filter_by_fasta_ids	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus Sequence analysis / Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana
iuc/umi_tools_extract/umi_tools_extract	Single Cell / Pre-processing of Single-Cell RNA Data Single Cell / Understanding Barcodes Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/snpeff_sars_cov_2/snpeff_sars_cov_2	Using Galaxy and Managing your Data / SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis Introduction to Galaxy Analyses / NGS data logistics Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
iuc/lofreq_call/lofreq_call	Using Galaxy and Managing your Data / Using dataset collections Introduction to Galaxy Analyses / NGS data logistics Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
devteam/samtools_rmdup/samtools_rmdup	Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
iuc/qualimap_bamqc/qualimap_bamqc	Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data Variant Analysis / M. tuberculosis Variant Analysis
proteore/proteore_filter_keywords_values/MQoutputfilter	Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data Proteomics / Biomarker candidate identification Proteomics / Annotating a protein list identified by LC-MS/MS experiments
galaxyp/msstatstmt/msstatstmt	Microbiome / Clinical Metaproteomics 5: Data Interpretation Proteomics / Clinical Metaproteomics 5: Data Interpretation Proteomics / MaxQuant and MSstats for the analysis of TMT data
__SORTLIST__	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/metaphlan/metaphlan	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short) Microbiome / Taxonomic Profiling and Visualization of Metagenomic Data
galaxyp/peptideshaker/ident_params	Microbiome / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Proteogenomics 2: Database Search
iuc/krakentools_kreport2krona/krakentools_kreport2krona	Microbiome / Identification of the micro-organisms in a beer using Nanopore sequencing Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Microbiome / Taxonomic Profiling and Visualization of Metagenomic Data
iuc/bcftools_norm/bcftools_norm	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
galaxyp/cardinal_quality_report/cardinal_quality_report	Metabolomics / Mass spectrometry imaging: Examining the spatial distribution of analytes Metabolomics / Mass spectrometry imaging: Finding differential analytes Proteomics / Mass spectrometry imaging: Loading and exploring MSI data
lecorguille/xcms_retcor/abims_xcms_retcor	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram	Metabolomics / Mass spectrometry: GC-MS analysis with the metaMS package Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
lecorguille/xcms_export_samplemetadata/xcms_export_samplemetadata	Metabolomics / Mass spectrometry: GC-MS analysis with the metaMS package Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
iuc/iqtree/iqtree	Evolution / Phylogenetics - Back to basics Sequence analysis / Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data
iuc/fasttree/fasttree	Evolution / Phylogenetics - Back to basics Evolution / Phylogenetic analysis for bacterial comparative genomics Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/snippy/snippy	Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Variant Analysis / Microbial Variant Calling Variant Analysis / M. tuberculosis Variant Analysis
devteam/fastqtofasta/fastq_to_fasta_python	Ecology / Data submission using ENA upload Tool Using Galaxy and Managing your Data / SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis Microbiome / MGnify v5.0 Amplicon Pipeline
__RELABEL_FROM_FILE__	Ecology / Data submission using ENA upload Tool Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC
__FILTER_EMPTY_DATASETS__	Ecology / Data submission using ENA upload Tool Microbiome / MGnify v5.0 Amplicon Pipeline Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
addValue	Ecology / RAD-Seq Reference-based data analysis Proteomics / Protein FASTA Database Handling Transcriptomics / Genome-wide alternative splicing analysis
iuc/bracken/est_abundance	Ecology / Checking expected species and contamination in bacterial isolate Microbiome / Taxonomic Profiling and Visualization of Metagenomic Data Sequence analysis / Quality and contamination control in bacterial isolate using Illumina MiSeq Data
iuc/column_remove_by_header/column_remove_by_header	Ecology / Life Traits Ecoregionalization workflow Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution Single Cell / Pseudobulk Analysis with Decoupler and EdgeR
devteam/fastq_groomer/fastq_groomer	Ecology / Data submission using ENA upload Tool Ecology / Metabarcoding/eDNA through Obitools Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
ecology/xarray_coords_info/xarray_coords_info	Climate / Analyse Argo data Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools Ecology / Visualization of Climate Data using NetCDF xarray Map Plotting
ecology/spocc_occ/spocc_occ	Climate / Getting your hands-on earth data Ecology / Cleaning GBIF data for the use in Ecology Ecology / Species distribution modeling
tabular_to_csv	Foundations of Data Science / Data Manipulation Olympics Ecology / Species distribution modeling Introduction to Galaxy Analyses / Data Manipulation Olympics
bgruening/interproscan/interproscan	Ecology / Marine Omics identifying biosynthetic gene clusters Genome Annotation / Genome annotation with Funannotate Genome Annotation / Functional annotation of protein sequences
iuc/omark/omark	Genome Annotation / Genome annotation with Braker3 Genome Annotation / Comparison of two annotation tools - Helixer and Braker3 Genome Annotation / Genome annotation with Helixer
devteam/clustalw/clustalw	Ecology / Preparing genomic data for phylogeny reconstruction Genome Annotation / From small to large-scale genome comparison Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/jcvi_gff_stats/jcvi_gff_stats	Genome Annotation / Genome annotation with Maker Genome Annotation / Genome annotation with Maker (short) Genome Annotation / Genome annotation with Helixer
devteam/add_value/addValue	Assembly / Making sense of a newly assembled genome Single Cell / Removing the effects of the cell cycle Transcriptomics / Genome-wide alternative splicing analysis
iuc/gfa_to_fa/gfa_to_fa	Assembly / Genome assembly using PacBio data Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Microbiome / Antibiotic resistance detection
iuc/bedtools/bedtools_bamtobed	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Epigenetics / ATAC-Seq data analysis Epigenetics / CUT&RUN data analysis
iuc/samtools_fastx/samtools_fastx	Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Sequence analysis / Removal of human reads from SARS-CoV-2 sequencing data
__ZIP_COLLECTION__	Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Sequence analysis / Removal of human reads from SARS-CoV-2 sequencing data Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
iuc/unicycler/unicycler	Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Assembly / Unicycler Assembly Microbiome / Antibiotic resistance detection
iuc/megahit/megahit	Assembly / Assembly of metagenomic sequencing data Microbiome / Assembly of metagenomic sequencing data Microbiome / Binning of metagenomic sequencing data
bgruening/gfastats/gfastats	Assembly / ERGA post-assembly QC Assembly / Decontamination of a genome assembly Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
iuc/genomescope/genomescope	Assembly / ERGA post-assembly QC Assembly / Large genome assembly and polishing Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
barchart_gnuplot	Assembly / Large genome assembly and polishing Digital Humanities / OpenRefine Tutorial for researching cultural data Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/merqury/merqury	Assembly / ERGA post-assembly QC Assembly / Genome Assembly Quality Control Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
bgruening/flexynesis_plot/flexynesis_plot	Statistics and machine learning / Modeling Breast Cancer Subtypes with Flexynesis Statistics and machine learning / Identifing Survival Markers of Brain tumor with Flexynesis Statistics and machine learning / Unsupervised Analysis of Bone Marrow Cells with Flexynesis
bgruening/flexynesis/flexynesis	Statistics and machine learning / Modeling Breast Cancer Subtypes with Flexynesis Statistics and machine learning / Identifing Survival Markers of Brain tumor with Flexynesis Statistics and machine learning / Unsupervised Analysis of Bone Marrow Cells with Flexynesis
bgruening/sklearn_searchcv/sklearn_searchcv	Statistics and machine learning / Age prediction using machine learning Statistics and machine learning / Classification in Machine Learning Statistics and machine learning / Regression in Machine Learning
bgruening/sklearn_build_pipeline/sklearn_build_pipeline	Statistics and machine learning / Age prediction using machine learning Statistics and machine learning / Classification in Machine Learning Statistics and machine learning / Regression in Machine Learning
chemteam/md_converter/md_converter	Computational chemistry / High Throughput Molecular Dynamics and Analysis Computational chemistry / Data management in Medicinal Chemistry FAIR Data, Workflows, and Research / Data management in Medicinal Chemistry
bgruening/qed/ctb_silicos_qed	Computational chemistry / Data management in Medicinal Chemistry FAIR Data, Workflows, and Research / Data management in Medicinal Chemistry Genome Annotation / Secondary metabolite discovery
bgruening/openbabel_svg_depiction/openbabel_svg_depiction	Computational chemistry / Protein-ligand docking Computational chemistry / Data management in Medicinal Chemistry FAIR Data, Workflows, and Research / Data management in Medicinal Chemistry
bgruening/chembl/chembl	Computational chemistry / Protein-ligand docking Computational chemistry / Data management in Medicinal Chemistry FAIR Data, Workflows, and Research / Data management in Medicinal Chemistry
iuc/bedtools/bedtools_sortbed	Assembly / Making sense of a newly assembled genome Epigenetics / Formation of the Super-Structures on the Inactive X Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets
bgruening/deeptools_bam_compare/deeptools_bam_compare	Epigenetics / Identification of the binding sites of the Estrogen receptor Epigenetics / Formation of the Super-Structures on the Inactive X Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
nilesh/rseqc/rseqc_infer_experiment	Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / 1: RNA-Seq reads to counts
bgruening/sklearn_svm_classifier/sklearn_svm_classifier	Statistics and machine learning / Classification in Machine Learning Statistics and machine learning / Machine learning: classification and regression Statistics and machine learning / Basics of machine learning
devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer	Assembly / An Introduction to Genome Assembly Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/mothur_unique_seqs/mothur_unique_seqs	Microbiome / Analyses of metagenomics data - The global picture Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_summary_seqs/mothur_summary_seqs	Microbiome / Analyses of metagenomics data - The global picture Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_screen_seqs/mothur_screen_seqs	Microbiome / Analyses of metagenomics data - The global picture Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_pre_cluster/mothur_pre_cluster	Microbiome / Analyses of metagenomics data - The global picture Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_make_shared/mothur_make_shared	Microbiome / Analyses of metagenomics data - The global picture Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_filter_seqs/mothur_filter_seqs	Microbiome / Analyses of metagenomics data - The global picture Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_count_seqs/mothur_count_seqs	Microbiome / Analyses of metagenomics data - The global picture Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_cluster_split/mothur_cluster_split	Microbiome / Analyses of metagenomics data - The global picture Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_classify_seqs/mothur_classify_seqs	Microbiome / Analyses of metagenomics data - The global picture Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_classify_otu/mothur_classify_otu	Microbiome / Analyses of metagenomics data - The global picture Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
crs4/prokka/prokka	Assembly / Chloroplast genome assembly Assembly / Unicycler Assembly Genome Annotation / Genome annotation with Prokka
galaxyp/msstats/msstats	Proteomics / Statistical analysis of DIA data Proteomics / Label-free data analysis using MaxQuant Proteomics / MaxQuant and MSstats for the analysis of label-free data
devteam/intersect/gops_intersect_1	Genome Annotation / Comparative gene analysis in unannotated genomes Introduction to Galaxy Analyses / From peaks to genes Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy
iuc/beacon2_cnv/beacon2_cnv	Variant Analysis / Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs) Variant Analysis / Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons
melpetera/intensity_checks/intens_check	Metabolomics / Mass spectrometry: LC-MS data processing Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
interactive_tool_openrefine	Digital Humanities / OpenRefine Tutorial for researching cultural data Ecology / Cleaning GBIF data using OpenRefine
bgruening/diff/diff	Digital Humanities / Introduction to Digital Humanities in Galaxy Digital Humanities / Text-Mining Differences in Chinese Newspaper Articles
galaxyp/openms_xtandemadapter/XTandemAdapter	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/openms_textexporter/TextExporter	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/openms_peptideindexer/PeptideIndexer	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/openms_idscoreswitcher/IDScoreSwitcher	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/openms_fileinfo/FileInfo	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/openms_fidoadapter/FidoAdapter	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
bgruening/uniprot_rest_interface/uniprot	Proteomics / MaxQuant and MSstats for the analysis of label-free data Proteomics / Secretome Prediction
proteore/proteore_venn_diagram/Jvenn	Proteomics / Biomarker candidate identification Proteomics / Annotating a protein list identified by LC-MS/MS experiments
proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa	Proteomics / Biomarker candidate identification Proteomics / Annotating a protein list identified by LC-MS/MS experiments
proteore/proteore_id_converter/IDconverter	Proteomics / Biomarker candidate identification Proteomics / Annotating a protein list identified by LC-MS/MS experiments
proteore/proteore_expression_rnaseq_abbased/rna_abbased_data	Proteomics / Biomarker candidate identification Proteomics / Annotating a protein list identified by LC-MS/MS experiments
jay/pdaug_sequence_property_based_descriptors/pdaug_sequence_property_based_descriptors	Proteomics / Machine Learning Modeling of Anticancer Peptides Proteomics / Peptide Library Data Analysis
jay/pdaug_merge_dataframes/pdaug_merge_dataframes	Proteomics / Machine Learning Modeling of Anticancer Peptides Proteomics / Peptide Library Data Analysis
jay/pdaug_basic_plots/pdaug_basic_plots	Proteomics / Machine Learning Modeling of Anticancer Peptides Proteomics / Peptide Library Data Analysis
jay/pdaug_addclasslabel/pdaug_addclasslabel	Proteomics / Machine Learning Modeling of Anticancer Peptides Proteomics / Peptide Library Data Analysis
galaxyp/translate_bed/translate_bed	Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Proteomics / Proteogenomics 1: Database Creation
galaxyp/gffcompare_to_bed/gffcompare_to_bed	Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Proteomics / Proteogenomics 1: Database Creation
galaxyp/custom_pro_db/custom_pro_db	Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Proteomics / Proteogenomics 1: Database Creation
galaxyp/bed_to_protein_map/bed_to_protein_map	Proteomics / Neoantigen 1b: Non-Reference-Database-Generation Proteomics / Proteogenomics 1: Database Creation
galaxyp/metaquantome_viz/metaquantome_viz	Proteomics / metaQuantome 2: Function Proteomics / metaQuantome 3: Taxonomy
galaxyp/metaquantome_stat/metaquantome_stat	Proteomics / metaQuantome 2: Function Proteomics / metaQuantome 3: Taxonomy
galaxyp/metaquantome_sample/metaquantome_sample	Proteomics / metaQuantome 2: Function Proteomics / metaQuantome 3: Taxonomy
galaxyp/metaquantome_filter/metaquantome_filter	Proteomics / metaQuantome 2: Function Proteomics / metaQuantome 3: Taxonomy
galaxyp/metaquantome_expand/metaquantome_expand	Proteomics / metaQuantome 2: Function Proteomics / metaQuantome 3: Taxonomy
galaxyp/metaquantome_db/metaquantome_db	Proteomics / metaQuantome 2: Function Proteomics / metaQuantome 3: Taxonomy
galaxyp/pep_pointer/pep_pointer	Proteomics / Neoantigen 4: Variant Annotation Proteomics / Proteogenomics 3: Novel peptide analysis
comp1	Introduction to Galaxy Analyses / Galaxy Basics for genomics Proteomics / Secretome Prediction
bgruening/music_manipulate_eset/music_manipulate_eset	Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution
iuc/dropletutils/dropletutils	Single Cell / Converting between common single cell data formats Single Cell / Pre-processing of 10X Single-Cell RNA Datasets
ebi-gxa/monocle3_create/monocle3_create	Single Cell / Inferring single cell trajectories with Monocle3 Single Cell / Converting between common single cell data formats
iuc/scanpy_remove_confounders/scanpy_remove_confounders	Single Cell / Analysis of plant scRNA-Seq Data with Scanpy Single Cell / Clustering 3K PBMCs with Scanpy
iuc/snapatac2_preprocessing/snapatac2_preprocessing	Single Cell / Multi-sample batch correction with Harmony and SnapATAC2 Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2
iuc/snapatac2_plotting/snapatac2_plotting	Single Cell / Multi-sample batch correction with Harmony and SnapATAC2 Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2
iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif	Single Cell / Multi-sample batch correction with Harmony and SnapATAC2 Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2
iuc/snapatac2_clustering/snapatac2_clustering	Single Cell / Multi-sample batch correction with Harmony and SnapATAC2 Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2
ebi-gxa/scanpy_read_10x/scanpy_read_10x	Single Cell / Importing files from public atlases Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution
ebi-gxa/dropletutils_read_10x/dropletutils_read_10x	Single Cell / Generating a single cell matrix using Alevin Single Cell / Converting between common single cell data formats
bgruening/music_deconvolution/music_deconvolution	Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Single Cell / Bulk RNA Deconvolution with MuSiC
ebi-gxa/scanpy_run_umap/scanpy_run_umap	Single Cell / Scanpy Parameter Iterator Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
ebi-gxa/scanpy_run_tsne/scanpy_run_tsne	Single Cell / Scanpy Parameter Iterator Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
ecology/xarray_select/xarray_select	Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools
climate/climate_stripes/climate_stripes	Climate / Getting your hands-on climate data Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools
ecology/argo_getdata/argo_getdata	Climate / Analyse Argo data Climate / Getting your hands-on earth data
imgteam/count_objects/ip_count_objects	Imaging / Introduction to Image Analysis using Galaxy Imaging / Voronoi segmentation
imgteam/bfconvert/ip_convertimage	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME Imaging / Voronoi segmentation
bgruening/cp_save_images/cp_save_images	Imaging / Object tracking using CellProfiler Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape	Imaging / Object tracking using CellProfiler Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_measure_object_intensity/cp_measure_object_intensity	Imaging / Object tracking using CellProfiler Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_identify_primary_objects/cp_identify_primary_objects	Imaging / Object tracking using CellProfiler Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet	Imaging / Object tracking using CellProfiler Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_common/cp_common	Imaging / Object tracking using CellProfiler Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_cellprofiler/cp_cellprofiler	Imaging / Object tracking using CellProfiler Imaging / Nucleoli segmentation and feature extraction using CellProfiler
iuc/idr_download_by_ids/idr_download_by_ids	Imaging / Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines Imaging / Nucleoli segmentation and feature extraction using CellProfiler
imgteam/spot_detection_2d/ip_spot_detection_2d	Imaging / Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines Imaging / Tracking of mitochondria and capturing mitoflashes
imgteam/points2labelimage/ip_points_to_label	Imaging / Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines Imaging / Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools
imgteam/split_image/ip_split_image	Imaging / Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools Imaging / Using BioImage.IO models for image analysis in Galaxy
imgteam/image_math/image_math	Imaging / Using BioImage.IO models for image analysis in Galaxy Imaging / Voronoi segmentation
bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file	Epigenetics / DNA Methylation data analysis Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2
bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias	Epigenetics / Identification of the binding sites of the Estrogen receptor Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
iuc/pe_histogram/pe_histogram	Epigenetics / ATAC-Seq data analysis Epigenetics / CUT&RUN data analysis
devteam/bam_to_sam/bam_to_sam	Contributing to the Galaxy Training Material / Creating a new tutorial Epigenetics / Identification of the binding sites of the Estrogen receptor
climate/c3s/c3s	Climate / Getting your hands-on earth data Contributing to the Galaxy Training Material / Creating a new tutorial
iuc/goenrichment/goenrichment	Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data Transcriptomics / GO Enrichment Analysis
iuc/limma_voom/limma_voom	Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / 2: RNA-seq counts to genes
bgruening/salmon/salmon	Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana Transcriptomics / Differential abundance testing of small RNAs
ethevenot/multivariate/Multivariate	Metabolomics / Mass spectrometry: LC-MS data processing Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial
iuc/stringtie/stringtie_merge	Transcriptomics / De novo transcriptome reconstruction with RNA-Seq Transcriptomics / Genome-wide alternative splicing analysis
gene2exon1	Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy Transcriptomics / Genome-wide alternative splicing analysis
iuc/meme_chip/meme_chip	Epigenetics / CUT&RUN data analysis Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/extract_genomic_dna/Extract genomic DNA 1	Epigenetics / CUT&RUN data analysis Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/sra_tools/fastq_dump	Using Galaxy and Managing your Data / SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis Variant Analysis / Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates
iuc/lofreq_viterbi/lofreq_viterbi	Introduction to Galaxy Analyses / NGS data logistics Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
iuc/lofreq_indelqual/lofreq_indelqual	Introduction to Galaxy Analyses / NGS data logistics Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
devteam/vcf2tsv/vcf2tsv	Variant Analysis / Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates Variant Analysis / Calling variants in non-diploid systems
iuc/gemini_query/gemini_query	Variant Analysis / Calling variants in diploid systems Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
devteam/samtools_calmd/samtools_calmd	Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
bgruening/column_arrange_by_header/bg_column_arrange_by_header	Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
iuc/gemini_inheritance/gemini_inheritance	Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
mbernt/fasta_regex_finder/fasta_regex_finder	Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data Variant Analysis / Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
iuc/ivar_consensus/ivar_consensus	Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
iuc/snpeff/snpEff_download	Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease Variant Analysis / Mapping and molecular identification of phenotype-causing mutations
galaxyp/metanovo/metanovo	Microbiome / Clinical Metaproteomics 1: Database-Generation Proteomics / Clinical Metaproteomics 1: Database-Generation
rnateam/sortmerna/bg_sortmerna	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/humann_unpack_pathways/humann_unpack_pathways	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/humann_split_stratified_table/humann_split_stratified_table	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/humann_renorm_table/humann_renorm_table	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/humann_rename_table/humann_rename_table	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/humann_regroup_table/humann_regroup_table	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/humann/humann	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/graphlan_annotate/graphlan_annotate	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/graphlan/graphlan	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/export2graphlan/export2graphlan	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/mothur_venn/mothur_venn	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_tree_shared/mothur_tree_shared	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_summary_single/mothur_summary_single	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_sub_sample/mothur_sub_sample	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_remove_seqs/mothur_remove_seqs	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_remove_lineage/mothur_remove_lineage	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_remove_groups/mothur_remove_groups	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_rarefaction_single/mothur_rarefaction_single	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_heatmap_sim/mothur_heatmap_sim	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_dist_shared/mothur_dist_shared	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_dist_seqs/mothur_dist_seqs	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_count_groups/mothur_count_groups	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_cluster/mothur_cluster	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_chimera_vsearch/mothur_chimera_vsearch	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
devteam/xy_plot/XY_Plot_1	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
galaxyp/peptideshaker/fasta_cli	Microbiome / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 2: Discovery
bgruening/text_processing/tp_multijoin_tool	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution
bgruening/add_line_to_file/add_line_to_file	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution
__BUILD_LIST__	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC
iuc/bedtools/bedtools_getfastabed	Microbiome / MGnify v5.0 Amplicon Pipeline Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
earlhaminst/lotus2/lotus2	Microbiome / Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2 Microbiome / MGnify v5.0 Amplicon Pipeline
CONVERTER_uncompressed_to_gz	Microbiome / MGnify v5.0 Amplicon Pipeline Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
__FILTER_FAILED_DATASETS__	Metabolomics / Predicting EI+ mass spectra with QCxMS Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
galaxyp/cardinal_mz_images/cardinal_mz_images	Metabolomics / Mass spectrometry imaging: Examining the spatial distribution of analytes Metabolomics / Mass spectrometry imaging: Finding differential analytes
galaxyp/cardinal_data_exporter/cardinal_data_exporter	Metabolomics / Mass spectrometry imaging: Examining the spatial distribution of analytes Proteomics / Mass spectrometry imaging: Loading and exploring MSI data
melpetera/generic_filter/generic_filter	Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS data processing
melpetera/batchcorrection/Batch_correction	Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS data processing
lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport	Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
ethevenot/qualitymetrics/quality_metrics	Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS data processing
iuc/tbprofiler/tb_profiler_profile	Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Variant Analysis / M. tuberculosis Variant Analysis
iuc/tb_variant_filter/tb_variant_filter	Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Variant Analysis / M. tuberculosis Variant Analysis
ecology/ab1_fastq_converter/ab1_fastq_converter	Ecology / Data submission using ENA upload Tool Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
devteam/fastq_filter/fastq_filter	Ecology / Data submission using ENA upload Tool Microbiome / MGnify v5.0 Amplicon Pipeline
interactive_tool_copernicus_notebook	Climate / Sentinel 5P data visualisation Ecology / From NDVI data with OpenEO to time series visualisation with Holoviews
devteam/fastq_to_fasta/cshl_fastq_to_fasta	Ecology / Taxonomic Analysis of eDNA Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
iuc/recentrifuge/recentrifuge	Ecology / Checking expected species and contamination in bacterial isolate Sequence analysis / Quality and contamination control in bacterial isolate using Illumina MiSeq Data
ecology/ecoregion_taxa_seeker/ecoregion_taxa_seeker	Ecology / Ecoregionalization workflow tutorial Ecology / Life Traits Ecoregionalization workflow
ecology/ecoregion_geonearestneighbor/ecoregion_GeoNearestNeighbor	Ecology / Ecoregionalization workflow tutorial Ecology / Life Traits Ecoregionalization workflow
ecology/ecoregion_eco_map/ecoregion_eco_map	Ecology / Ecoregionalization workflow tutorial Ecology / Life Traits Ecoregionalization workflow
ecology/ecoregion_brt_analysis/ecoregion_brt_analysis	Ecology / Ecoregionalization workflow tutorial Ecology / Life Traits Ecoregionalization workflow
ecology/obis_data/obis_data	Climate / Getting your hands-on earth data Ecology / Obis marine indicators
peterjc/seq_filter_by_id/seq_filter_by_id	Ecology / Metabarcoding/eDNA through Obitools Single Cell / Understanding Barcodes
iuc/stacks_procrad/stacks_procrad	Ecology / RAD-Seq de-novo data analysis Ecology / RAD-Seq Reference-based data analysis
iuc/stacks_populations/stacks_populations	Ecology / RAD-Seq de-novo data analysis Ecology / RAD-Seq Reference-based data analysis
ecology/xarray_mapplot/xarray_mapplot	Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools Ecology / Visualization of Climate Data using NetCDF xarray Map Plotting
bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage	Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools Ecology / Visualization of Climate Data using NetCDF xarray Map Plotting
iuc/stacks_denovomap/stacks_denovomap	Ecology / RAD-Seq de-novo data analysis Ecology / RAD-Seq to construct genetic maps
iuc/snpsift/snpSift_filter	Using Galaxy and Managing your Data / Automating Galaxy workflows using the command line Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/pangolin/pangolin	Using Galaxy and Managing your Data / Automating Galaxy workflows using the command line Variant Analysis / Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
gga/apollo_iframe/iframe	Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes) Genome Annotation / Refining Genome Annotations with Apollo (eukaryotes)
gga/apollo_create_or_update/create_or_update	Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes) Genome Annotation / Refining Genome Annotations with Apollo (eukaryotes)
iuc/ncbi_acc_download/ncbi_acc_download	Genome Annotation / Secondary metabolite discovery Variant Analysis / Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates
iuc/bedtools/bedtools_maskfastabed	Genome Annotation / Masking repeats with RepeatMasker Microbiome / MGnify v5.0 Amplicon Pipeline
bgruening/repeat_masker/repeatmasker_wrapper	Ecology / Preparing genomic data for phylogeny reconstruction Genome Annotation / Masking repeats with RepeatMasker
iuc/funannotate_predict/funannotate_predict	Ecology / Preparing genomic data for phylogeny reconstruction Genome Annotation / Genome annotation with Funannotate
devteam/picard/picard_MergeSamFiles	Genome Annotation / Genome annotation with Funannotate Variant Analysis / Calling variants in non-diploid systems
galaxyp/eggnog_mapper/eggnog_mapper	Genome Annotation / Genome annotation with Funannotate Genome Annotation / Functional annotation of protein sequences
iuc/braker3/braker3	Genome Annotation / Genome annotation with Braker3 Genome Annotation / Comparison of two annotation tools - Helixer and Braker3
genouest/helixer/helixer	Genome Annotation / Comparison of two annotation tools - Helixer and Braker3 Genome Annotation / Genome annotation with Helixer
genouest/braker3/braker3	Genome Annotation / Genome annotation with Braker3 Genome Annotation / Comparison of two annotation tools - Helixer and Braker3
nml/staramr/staramr_search	Genome Annotation / Identification of AMR genes in an assembled bacterial genome Microbiome / Antibiotic resistance detection
iuc/tbl2gff3/tbl2gff3	Genome Annotation / Identification of AMR genes in an assembled bacterial genome Genome Annotation / Bacterial Genome Annotation
iuc/bakta/bakta	Genome Annotation / Identification of AMR genes in an assembled bacterial genome Genome Annotation / Bacterial Genome Annotation
iuc/maker_map_ids/maker_map_ids	Genome Annotation / Genome annotation with Maker Genome Annotation / Genome annotation with Maker (short)
iuc/maker/maker	Genome Annotation / Genome annotation with Maker Genome Annotation / Genome annotation with Maker (short)
bgruening/hifiasm/hifiasm	Assembly / Genome assembly using PacBio data Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
devteam/fasta_filter_by_length/fasta_filter_by_length	Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Assembly / Making sense of a newly assembled genome
nml/metaspades/metaspades	Assembly / Assembly of metagenomic sequencing data Microbiome / Assembly of metagenomic sequencing data
iuc/ngsutils_bam_filter/ngsutils_bam_filter	Assembly / Assembly of metagenomic sequencing data Microbiome / Assembly of metagenomic sequencing data
iuc/megahit_contig2fastg/megahit_contig2fastg	Assembly / Assembly of metagenomic sequencing data Microbiome / Assembly of metagenomic sequencing data
iuc/coverm_contig/coverm_contig	Assembly / Assembly of metagenomic sequencing data Microbiome / Assembly of metagenomic sequencing data
devteam/bamtools/bamtools	Assembly / Assembly of metagenomic sequencing data Microbiome / Assembly of metagenomic sequencing data
iuc/pretext_snapshot/pretext_snapshot	Assembly / ERGA post-assembly QC Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
iuc/pretext_map/pretext_map	Assembly / ERGA post-assembly QC Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
iuc/bellerophon/bellerophon	Assembly / ERGA post-assembly QC Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
iuc/medaka_consensus_pipeline/medaka_consensus_pipeline	Assembly / Large genome assembly and polishing Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
bgruening/racon/racon	Assembly / Large genome assembly and polishing Microbiome / Antibiotic resistance detection
iuc/chromeister/chromeister	Assembly / Genome Assembly Quality Control Genome Annotation / From small to large-scale genome comparison
interactive_tool_ml_jupyter_notebook	Statistics and machine learning / Fine tune large protein model (ProtTrans) using HuggingFace Statistics and machine learning / A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy
bgruening/sklearn_generalized_linear/sklearn_generalized_linear	Statistics and machine learning / Classification in Machine Learning Statistics and machine learning / Regression in Machine Learning
bgruening/flexynesis_utils/flexynesis_utils	Statistics and machine learning / Prepare Data from CbioPortal for Flexynesis Integration Statistics and machine learning / Unsupervised Analysis of Bone Marrow Cells with Flexynesis
bgruening/sklearn_to_categorical/sklearn_to_categorical	Statistics and machine learning / Deep Learning (Part 3) - Convolutional neural networks (CNN) Statistics and machine learning / Image classification in Galaxy with fruit 360 dataset
chemteam/gmx_solvate/gmx_solvate	Computational chemistry / High Throughput Molecular Dynamics and Analysis Computational chemistry / Running molecular dynamics simulations using GROMACS
chemteam/gmx_sim/gmx_sim	Computational chemistry / High Throughput Molecular Dynamics and Analysis Computational chemistry / Running molecular dynamics simulations using GROMACS
chemteam/gmx_setup/gmx_setup	Computational chemistry / High Throughput Molecular Dynamics and Analysis Computational chemistry / Running molecular dynamics simulations using GROMACS
chemteam/gmx_em/gmx_em	Computational chemistry / High Throughput Molecular Dynamics and Analysis Computational chemistry / Running molecular dynamics simulations using GROMACS
chemteam/gmx_editconf/gmx_editconf	Computational chemistry / High Throughput Molecular Dynamics and Analysis Computational chemistry / Running molecular dynamics simulations using GROMACS
chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis	Computational chemistry / Analysis of molecular dynamics simulations Computational chemistry / High Throughput Molecular Dynamics and Analysis
chemteam/bio3d_rmsf/bio3d_rmsf	Computational chemistry / Analysis of molecular dynamics simulations Computational chemistry / High Throughput Molecular Dynamics and Analysis
chemteam/bio3d_rmsd/bio3d_rmsd	Computational chemistry / Analysis of molecular dynamics simulations Computational chemistry / High Throughput Molecular Dynamics and Analysis
chemteam/bio3d_pca/bio3d_pca	Computational chemistry / Analysis of molecular dynamics simulations Computational chemistry / High Throughput Molecular Dynamics and Analysis
bgruening/natural_product_likeness/ctb_np-likeness-calculator	Computational chemistry / Protein-ligand docking Genome Annotation / Secondary metabolite discovery
bgruening/chemfp/ctb_chemfp_mol2fps	Computational chemistry / Protein-ligand docking Genome Annotation / Secondary metabolite discovery
bgruening/ctb_im_rxn_maker/ctb_im_rxn_maker	Computational chemistry / Data management in Medicinal Chemistry FAIR Data, Workflows, and Research / Data management in Medicinal Chemistry
iuc/length_and_gc_content/length_and_gc_content	Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial
iuc/gtftobed12/gtftobed12	Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Reference-based RNA-Seq data analysis
iuc/deg_annotate/deg_annotate	Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / RNA-Seq data analysis, clustering and visualisation tutorial
bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots	Statistics and machine learning / Classification in Machine Learning Statistics and machine learning / Machine learning: classification and regression
iuc/mothur_merge_files/mothur_merge_files	Microbiome / Analyses of metagenomics data - The global picture Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
iuc/mothur_make_biom/mothur_make_biom	Microbiome / Analyses of metagenomics data - The global picture Microbiome / 16S Microbial Analysis with mothur (extended)
iuc/mothur_align_seqs/mothur_align_seqs	Microbiome / Analyses of metagenomics data - The global picture Microbiome / 16S Microbial Analysis with mothur (extended)
devteam/ncbi_blast_plus/ncbi_blastx_wrapper	Sequence analysis / NCBI BLAST+ against the MAdLand
iuc/cnv_vcf2json/cnv_vcf2json	Variant Analysis / Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons
iuc/cnv_phenopacket/cnv_phenopacket	Variant Analysis / Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons
iuc/beacon2_import/beacon2_import	Variant Analysis / Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons
iuc/vapor/vapor	Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data
iuc/bamtools_split_ref/bamtools_split_ref	Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data
iuc/checkm_lineage_wf/checkm_lineage_wf	Microbiome / Binning of metagenomic sequencing data
marie-tremblay-metatoul/normalization/normalization	Metabolomics / Mass spectrometry: LC-MS data processing
yguitton/metams_rungc/metams_runGC	Metabolomics / Mass spectrometry: GC-MS analysis with the metaMS package
interactive_tool_qgis	Ecology / QGIS Web Feature Services
iuc/ppanggolin_msa/ppanggolin_msa	Genome Annotation / Bacterial pangenomics
iuc/ppanggolin_all/ppanggolin_all	Genome Annotation / Bacterial pangenomics
iuc/drep_dereplicate/drep_dereplicate	Genome Annotation / Bacterial genome quality control
iuc/checkm2/checkm2	Genome Annotation / Bacterial genome quality control
iuc/ncbi_datasets/datasets_download_genome	Genome Annotation / Dataset construction for bacterial comparative genomics
iuc/chopin2/chopin2	Statistics and machine learning / Supervised Learning with Hyperdimensional Computing
melpetera/idchoice/idchoice	Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
lecorguille/xcms_summary/abims_xcms_summary	Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
iuc/jq/jq	Using Galaxy and Managing your Data / SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis
devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey	Galaxy Server administration / Reference Data with Data Managers
devteam/data_manager_bwa_mem_index_builder/bwa_mem_index_builder_data_manager	Galaxy Server administration / Reference Data with Data Managers
richard-burhans/ncbi_fcs_adaptor/ncbi_fcs_adaptor	Sequence analysis / Screening assembled genomes for contamination using NCBI FCS
iuc/ncbi_fcs_gx/ncbi_fcs_gx	Sequence analysis / Screening assembled genomes for contamination using NCBI FCS
iuc/pycoqc/pycoqc	Sequence analysis / Quality Control
iuc/fastqe/fastqe	Sequence analysis / Quality Control
iuc/varvamp/varvamp	Sequence analysis / Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes
devteam/ncbi_blast_plus/ncbi_makeblastdb	Sequence analysis / Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes
devteam/emboss_5/EMBOSS: degapseq20	Sequence analysis / Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes
iuc/trimal/trimal	Sequence analysis / Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants
iuc/quicktree/quicktree	Sequence analysis / Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants
iuc/ete_treeviewer/ete_treeviewer	Sequence analysis / Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants
bgruening/tapscan/tapscan_classify	Sequence analysis / Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants
iuc/seqtk/seqtk_trimfq	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
iuc/seqtk/seqtk_mergepe	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
iuc/qiime_align_seqs/qiime_align_seqs	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
iuc/mothur_degap_seqs/mothur_degap_seqs	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
ecology/aligned_to_consensus/aligned_to_consensus	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
devteam/fastx_reverse_complement/cshl_fastx_reverse_complement	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
devteam/fastq_masker_by_quality/fastq_masker_by_quality	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
iuc/circos/circos_wiggle_to_scatter	Visualisation / Ploting a Microbial Genome with Circos
iuc/circos/circos_interval_to_tile	Visualisation / Ploting a Microbial Genome with Circos
iuc/circos/circos_interval_to_text	Visualisation / Ploting a Microbial Genome with Circos
iuc/circos/circos_gc_skew	Visualisation / Ploting a Microbial Genome with Circos
gff2bed1	Visualisation / Ploting a Microbial Genome with Circos
recetox/bioconductor_scp/bioconductor_scp	Proteomics / Single Cell Proteomics data analysis with bioconductor-scp
galaxyp/flashlfq/flashlfq	Proteomics / metaQuantome 1: Data creation
peterjc/tmhmm_and_signalp/wolf_psort	Proteomics / Secretome Prediction
term_id_vs_term_name	Proteomics / Secretome Prediction
get_subontology_from	Proteomics / Secretome Prediction
jay/pdaug_tsvtofasta/pdaug_tsvtofasta	Proteomics / Peptide Library Data Analysis
jay/pdaug_peptide_sequence_analysis/pdaug_peptide_sequence_analysis	Proteomics / Peptide Library Data Analysis
jay/pdaug_peptide_data_access/pdaug_peptide_data_access	Proteomics / Peptide Library Data Analysis
jay/pdaug_fishers_plot/pdaug_fishers_plot	Proteomics / Peptide Library Data Analysis
galaxyp/openms_proteinquantifier/ProteinQuantifier	Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/openms_multiplexresolver/MultiplexResolver	Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/openms_idmapper/IDMapper	Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/openms_idconflictresolver/IDConflictResolver	Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex	Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
iuc/multigsea/multigsea	Proteomics / Multiomics data analysis using MultiGSEA
galaxyp/openms_peakpickerhires/PeakPickerHiRes	Proteomics / Peptide and Protein ID using OpenMS tools
galaxyp/openms_msgfplusadapter/MSGFPlusAdapter	Proteomics / Peptide and Protein ID using OpenMS tools
galaxyp/openms_idmerger/IDMerger	Proteomics / Peptide and Protein ID using OpenMS tools
galaxyp/openms_idfilter/IDFilter	Proteomics / Peptide and Protein ID using OpenMS tools
galaxyp/openms_consensusid/ConsensusID	Proteomics / Peptide and Protein ID using OpenMS tools
PeakPickerHiRes	Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker
FileConverter	Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker
galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib	Proteomics / EncyclopeDIA
galaxyp/encyclopedia_quantify/encyclopedia_quantify	Proteomics / EncyclopeDIA
galaxyp/pyprophet_score/pyprophet_score	Proteomics / DIA Analysis using OpenSwathWorkflow
galaxyp/pyprophet_protein/pyprophet_protein	Proteomics / DIA Analysis using OpenSwathWorkflow
galaxyp/pyprophet_peptide/pyprophet_peptide	Proteomics / DIA Analysis using OpenSwathWorkflow
galaxyp/pyprophet_merge/pyprophet_merge	Proteomics / DIA Analysis using OpenSwathWorkflow
galaxyp/pyprophet_export/pyprophet_export	Proteomics / DIA Analysis using OpenSwathWorkflow
galaxyp/openms_openswathworkflow/OpenSwathWorkflow	Proteomics / DIA Analysis using OpenSwathWorkflow
proteore/proteore_reactome/reactome_analysis	Proteomics / Annotating a protein list identified by LC-MS/MS experiments
proteore/proteore_clusterprofiler/cluter_profiler	Proteomics / Annotating a protein list identified by LC-MS/MS experiments
proteore/proteore_prot_features/prot_features	Proteomics / Biomarker candidate identification
proteore/proteore_ms_observation_pepatlas/retr_pepatlas1	Proteomics / Biomarker candidate identification
jay/pdaug_ml_models/pdaug_ml_models	Proteomics / Machine Learning Modeling of Anticancer Peptides
galaxyp/openms_decoydatabase/DecoyDatabase	Proteomics / Protein FASTA Database Handling
iuc/seq2hla/seq2hla	Proteomics / Neoantigen 5a: Predicting HLA Binding
iuc/optitype/optitype	Proteomics / Neoantigen 5a: Predicting HLA Binding
artbio/concatenate_multiple_datasets/cat_multi_datasets	Proteomics / Proteogenomics 1: Database Creation
PeptideIndexer	Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS
MzTabExporter	Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS
MSGFPlusAdapter	Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS
IDMerger	Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS
IDMapper	Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS
IDFilter	Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS
IDConflictResolver	Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS
HighResPrecursorMassCorrector	Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS
FileMerger	Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS
FileFilter	Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS
FeatureFinderMultiplex	Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS
FalseDiscoveryRate	Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS
ConsensusID	Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS
galaxyp/validate_fasta_database/validate_fasta_database	Proteomics / Neoantigen 2: Database merge and FragPipe discovery
galaxyp/fragpipe/fragpipe	Proteomics / Neoantigen 2: Database merge and FragPipe discovery
iuc/arriba_get_filters/arriba_get_filters	Proteomics / Neoantigen 1a: Fusion-Database-Generation
iuc/arriba/arriba	Proteomics / Neoantigen 1a: Fusion-Database-Generation
galaxyp/peptide_genomic_coordinate/peptide_genomic_coordinate	Proteomics / Proteogenomics 3: Novel peptide analysis
galaxyp/openms_targetedfileconverter/TargetedFileConverter	Proteomics / Library Generation for DIA Analysis
galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator	Proteomics / Library Generation for DIA Analysis
galaxyp/openms_openswathassaygenerator/OpenSwathAssayGenerator	Proteomics / Library Generation for DIA Analysis
galaxyp/diapysef/diapysef	Proteomics / Library Generation for DIA Analysis
galaxyp/mz_to_sqlite/mz_to_sqlite	Proteomics / Proteogenomics 2: Database Search
iuc/iedb_api/iedb_api	Proteomics / Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides
muon-spectroscopy-computational-project/pm_uep_opt/pm_uep_opt	Materials Science / Finding the muon stopping site with pymuon-suite in Galaxy
muon-spectroscopy-computational-project/pm_muairss_read/pm_muairss_read	Materials Science / Finding the muon stopping site with pymuon-suite in Galaxy
iuc/snpeff/snpEff_build_gb	Introduction to Galaxy Analyses / NGS data logistics
bgruening/music_compare/music_compare	Single Cell / Comparing inferred cell compositions using MuSiC deconvolution
iuc/raceid_trajectory/raceid_trajectory	Single Cell / Downstream Single-cell RNA analysis with RaceID
iuc/raceid_inspecttrajectory/raceid_inspecttrajectory	Single Cell / Downstream Single-cell RNA analysis with RaceID
iuc/raceid_inspectclusters/raceid_inspectclusters	Single Cell / Downstream Single-cell RNA analysis with RaceID
iuc/raceid_filtnormconf/raceid_filtnormconf	Single Cell / Downstream Single-cell RNA analysis with RaceID
iuc/raceid_clustering/raceid_clustering	Single Cell / Downstream Single-cell RNA analysis with RaceID
iuc/sinto_fragments/sinto_fragments	Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets
iuc/sinto_barcode/sinto_barcode	Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets
iuc/episcanpy_preprocess/episcanpy_preprocess	Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets
iuc/episcanpy_build_matrix/episcanpy_build_matrix	Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets
iuc/gprofiler_gost/gprofiler_gost	Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data
iuc/scater_plot_pca/scater_plot_pca	Single Cell / Single-cell quality control with scater
iuc/scater_plot_dist_scatter/scater_plot_dist_scatter	Single Cell / Single-cell quality control with scater
iuc/scater_filter/scater_filter	Single Cell / Single-cell quality control with scater
iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce	Single Cell / Single-cell quality control with scater
ebi-gxa/monocle3_topmarkers/monocle3_topmarkers	Single Cell / Inferring single cell trajectories with Monocle3
ebi-gxa/monocle3_reducedim/monocle3_reduceDim	Single Cell / Inferring single cell trajectories with Monocle3
ebi-gxa/monocle3_preprocess/monocle3_preprocess	Single Cell / Inferring single cell trajectories with Monocle3
ebi-gxa/monocle3_plotcells/monocle3_plotCells	Single Cell / Inferring single cell trajectories with Monocle3
ebi-gxa/monocle3_partition/monocle3_partition	Single Cell / Inferring single cell trajectories with Monocle3
ebi-gxa/monocle3_ordercells/monocle3_orderCells	Single Cell / Inferring single cell trajectories with Monocle3
ebi-gxa/monocle3_learngraph/monocle3_learnGraph	Single Cell / Inferring single cell trajectories with Monocle3
ebi-gxa/monocle3_diffexp/monocle3_diffExp	Single Cell / Inferring single cell trajectories with Monocle3
iuc/edger/edger	Single Cell / Pseudobulk Analysis with Decoupler and EdgeR
ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk	Single Cell / Pseudobulk Analysis with Decoupler and EdgeR
iuc/ggplot2_violin/ggplot2_violin	Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution
__DUPLICATE_FILE_TO_COLLECTION__	Single Cell / Evaluating Reference Data for Bulk RNA Deconvolution
iuc/umi_tools_count/umi_tools_count	Single Cell / Pre-processing of Single-Cell RNA Data
iuc/rna_starsolo/rna_starsolo	Single Cell / Pre-processing of 10X Single-Cell RNA Datasets
ebi-gxa/scanpy_run_paga/scanpy_run_paga	Single Cell / Inferring single cell trajectories with Scanpy
ebi-gxa/scanpy_run_fdg/scanpy_run_fdg	Single Cell / Inferring single cell trajectories with Scanpy
ebi-gxa/scanpy_run_dpt/scanpy_run_dpt	Single Cell / Inferring single cell trajectories with Scanpy
ebi-gxa/scanpy_run_diffmap/scanpy_run_diffmap	Single Cell / Inferring single cell trajectories with Scanpy
ebi-gxa/scanpy_plot_trajectory/scanpy_plot_trajectory	Single Cell / Inferring single cell trajectories with Scanpy
ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator	Single Cell / Scanpy Parameter Iterator
ebi-gxa/seurat_scale_data/seurat_scale_data	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_run_umap/seurat_run_umap	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_run_pca/seurat_run_pca	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_plot/seurat_plot	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_normalise_data/seurat_normalise_data	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_find_neighbours/seurat_find_neighbours	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_find_markers/seurat_find_markers	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_find_clusters/seurat_find_clusters	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_filter_cells/seurat_filter_cells	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/sceasy_convert/sceasy_convert	Single Cell / Converting between common single cell data formats
devteam/tabular_to_fastq/tabular_to_fastq	Single Cell / Converting between common single cell data formats
iuc/seurat_reduce_dimension/seurat_reduce_dimension	Single Cell / Clustering 3K PBMCs with Seurat
iuc/seurat_preprocessing/seurat_preprocessing	Single Cell / Clustering 3K PBMCs with Seurat
iuc/seurat_plot/seurat_plot	Single Cell / Clustering 3K PBMCs with Seurat
iuc/seurat_data/seurat_data	Single Cell / Clustering 3K PBMCs with Seurat
iuc/seurat_create/seurat_create	Single Cell / Clustering 3K PBMCs with Seurat
iuc/seurat_clustering/seurat_clustering	Single Cell / Clustering 3K PBMCs with Seurat
devteam/cut_columns/Cut1	Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2
ebi-gxa/hca_matrix_downloader/hca_matrix_downloader	Single Cell / Importing files from public atlases
ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x	Single Cell / Generating a single cell matrix using Alevin
ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list	Single Cell / Generating a single cell matrix using Alevin
ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops	Single Cell / Generating a single cell matrix using Alevin
ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot	Single Cell / Generating a single cell matrix using Alevin
bgruening/alevin/alevin	Single Cell / Generating a single cell matrix using Alevin
bgruening/music_inspect_eset/music_inspect_eset	Single Cell / Bulk RNA Deconvolution with MuSiC
ebi-gxa/scanpy_regress_variable/scanpy_regress_variable	Single Cell / Removing the effects of the cell cycle
ebi-gxa/scanpy_scale_data/scanpy_scale_data	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
ebi-gxa/scanpy_run_pca/scanpy_run_pca	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
ebi-gxa/scanpy_normalise_data/scanpy_normalise_data	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
ebi-gxa/scanpy_find_markers/scanpy_find_markers	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
ebi-gxa/scanpy_filter_genes/scanpy_filter_genes	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
interactive_tool_cellxgene_vip	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
tduigou/rrparser/rrparser	Synthetic Biology / Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
tduigou/rpextractsink/rpextractsink	Synthetic Biology / Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
tduigou/rpcompletion/rpcompletion	Synthetic Biology / Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
tduigou/rp2paths/rp2paths	Synthetic Biology / Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
tduigou/retropath2/retropath2	Synthetic Biology / Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
tduigou/get_sbml_model/get_sbml_model	Synthetic Biology / Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
tduigou/selenzy/selenzy-wrapper	Synthetic Biology / Designing plasmids encoding predicted pathways by using the BASIC assembly method
tduigou/rpbasicdesign/rpbasicdesign	Synthetic Biology / Designing plasmids encoding predicted pathways by using the BASIC assembly method
tduigou/dnabot/dnabot	Synthetic Biology / Designing plasmids encoding predicted pathways by using the BASIC assembly method
tduigou/rpthermo/rpthermo	Synthetic Biology / Evaluating and ranking a set of pathways based on multiple metrics
tduigou/rpscore/rpscore	Synthetic Biology / Evaluating and ranking a set of pathways based on multiple metrics
tduigou/rpranker/rpranker	Synthetic Biology / Evaluating and ranking a set of pathways based on multiple metrics
iuc/rpfba/rpfba	Synthetic Biology / Evaluating and ranking a set of pathways based on multiple metrics
climate/psy_maps/psy_maps	Climate / Getting your hands-on climate data
climate/cds_essential_variability/cds_essential_variability	Climate / Getting your hands-on climate data
climate/ctsm_fates/ctsm_fates	Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES)
ecology/tool_odv_history/tool_odv_history	Climate / Nitrate DMQC for autonomous platforms such as Argo floats
ecology/tool_odv/tool_odv	Climate / Nitrate DMQC for autonomous platforms such as Argo floats
ecology/tool_biogeochemical_calibration/tool_biogeochemical_calibration	Climate / Nitrate DMQC for autonomous platforms such as Argo floats
ecology/harmonize_insitu_to_netcdf/harmonize_insitu_to_netcdf	Climate / Nitrate DMQC for autonomous platforms such as Argo floats
ecology/divand_full_analysis/divand_full_analysis	Climate / Ocean's variables study
interactive_tool_divand	Climate / Ocean's variables study
ecology/xarray_netcdf2netcdf/xarray_netcdf2netcdf	Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools
ecology/timeseries_extraction/timeseries_extraction	Climate / Analyse Argo data
interactive_tool_pangeo_notebook	Climate / Pangeo Notebook in Galaxy - Introduction to Xarray
interactive_tool_copernicus	Climate / Sentinel 5P data visualisation
imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features	Imaging / Analyse HeLa fluorescence siRNA screen
watsocam/palom/palom	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
perssond/quantification/quantification	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
perssond/coreograph/unet_coreograph	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
perssond/basic_illumination/basic_illumination	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
perssond/ashlar/ashlar	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
goeckslab/vitessce_spatial/vitessce_spatial	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
goeckslab/squidpy_spatial/squidpy_spatial	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
goeckslab/scimap_phenotyping/scimap_phenotyping	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
goeckslab/rename_tiff_channels/rename_tiff_channels	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
goeckslab/mesmer/mesmer	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
goeckslab/gate_finder/gate_finder	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
goeckslab/celesta/celesta	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
bgruening/yolo_training/yolo_training	Imaging / Training Custom YOLO Models for Segmentation of Bioimages
bgruening/json2yolosegment/json2yolosegment	Imaging / Training Custom YOLO Models for Segmentation of Bioimages
interactive_tool_anylabeling	Imaging / Training Custom YOLO Models for Segmentation of Bioimages
imgteam/points_association_nn/ip_points_association_nn	Imaging / Tracking of mitochondria and capturing mitoflashes
imgteam/curve_fitting/ip_curve_fitting	Imaging / Tracking of mitochondria and capturing mitoflashes
imgteam/voronoi_tesselation/voronoi_tessellation	Imaging / Voronoi segmentation
imgteam/repeat_channels/repeat_channels	Imaging / Voronoi segmentation
imgteam/colorize_labels/colorize_labels	Imaging / Voronoi segmentation
bgruening/cp_relate_objects/cp_relate_objects	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_measure_texture/cp_measure_texture	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_measure_image_quality/cp_measure_image_quality	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_measure_image_intensity/cp_measure_image_intensity	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_measure_granularity/cp_measure_granularity	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_mask_image/cp_mask_image	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_image_math/cp_image_math	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_gray_to_color/cp_gray_to_color	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_display_data_on_image/cp_display_data_on_image	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
interactive_tool_qupath	Imaging / Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools
bgruening/cp_track_objects/cp_track_objects	Imaging / Object tracking using CellProfiler
bgruening/cp_tile/cp_tile	Imaging / Object tracking using CellProfiler
bgruening/cp_overlay_outlines/cp_overlay_outlines	Imaging / Object tracking using CellProfiler
bgruening/cp_color_to_gray/cp_color_to_gray	Imaging / Object tracking using CellProfiler
imgteam/segmetrics/ip_segmetrics	Imaging / Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy
ufz/omero_roi_import/omero_roi_import	Imaging / Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy
ufz/omero_metadata_import/omero_metadata_import	Imaging / Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy
ufz/omero_import/omero_import	Imaging / Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy
ufz/omero_get_value/omero_get_value	Imaging / Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy
ufz/omero_get_id/omero_get_id	Imaging / Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy
ufz/omero_filter/omero_filter	Imaging / Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy
bgruening/bioimage_inference/bioimage_inference	Imaging / Using BioImage.IO models for image analysis in Galaxy
rnateam/metilene/metilene	Epigenetics / DNA Methylation data analysis
iuc/bwameth/bwameth	Epigenetics / DNA Methylation data analysis
bgruening/pileometh/pileometh	Epigenetics / DNA Methylation data analysis
bgruening/deeptools_plot_profile/deeptools_plot_profile	Epigenetics / DNA Methylation data analysis
kpbioteam/ewastools/minfi_analysis	Epigenetics / Infinium Human Methylation BeadChip
kpbioteam/clusterprofiler_go/clusterprofiler_go	Epigenetics / Infinium Human Methylation BeadChip
kpbioteam/clusterprofiler_bitr/clusterprofiler_bitr	Epigenetics / Infinium Human Methylation BeadChip
kpbioteam/chipeakanno_annopeaks/chipeakanno_annopeaks	Epigenetics / Infinium Human Methylation BeadChip
bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias	Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
bgruening/hicexplorer_hicpca/hicexplorer_hicpca	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
bgruening/hicexplorer_hicinfo/hicexplorer_hicinfo	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
bgruening/hicexplorer_hicfindrestrictionsites/hicexplorer_hicfindrestrictionsites	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
bgruening/hicexplorer_hicdetectloops/hicexplorer_hicdetectloops	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
iuc/idr/idr	Epigenetics / CUT&RUN data analysis
iuc/goslimmer/goslimmer	Transcriptomics / GO Enrichment Analysis
iuc/heinz/heinz_visualization	Transcriptomics / Network analysis with Heinz
iuc/heinz/heinz_scoring	Transcriptomics / Network analysis with Heinz
iuc/heinz/heinz_bum	Transcriptomics / Network analysis with Heinz
iuc/heinz/heinz	Transcriptomics / Network analysis with Heinz
iuc/bedtools/bedtools_bamtofastq	Transcriptomics / Differential abundance testing of small RNAs
devteam/samtool_filter2/samtool_filter2	Transcriptomics / Differential abundance testing of small RNAs
devteam/fastq_manipulation/fastq_manipulation	Transcriptomics / Differential abundance testing of small RNAs
rnateam/targetfinder/targetfinder	Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana
rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier	Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana
rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper	Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana
peterjc/sample_seqs/sample_seqs	Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana
rnateam/blockclust/blockclust	Transcriptomics / Small Non-coding RNA Clustering using BlockClust
rnateam/blockbuster/blockbuster	Transcriptomics / Small Non-coding RNA Clustering using BlockClust
devteam/samtools_sort/samtools_sort	Transcriptomics / Small Non-coding RNA Clustering using BlockClust
iuc/trinotate/trinotate	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_samples_qccheck/trinity_samples_qccheck	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_run_de_analysis/trinity_run_de_analysis	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_filter_low_expr_transcripts/trinity_filter_low_expr_transcripts	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_define_clusters_by_cutting_tree/trinity_define_clusters_by_cutting_tree	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_contig_exn50_statistic/trinity_contig_exn50_statistic	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity/trinity	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/transdecoder/transdecoder	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/describe_samples/describe_samples	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/fgsea/fgsea	Transcriptomics / 3: RNA-seq genes to pathways
iuc/egsea/egsea	Transcriptomics / 3: RNA-seq genes to pathways
nilesh/rseqc/rseqc_junction_saturation	Transcriptomics / Genome-wide alternative splicing analysis
nilesh/rseqc/rseqc_junction_annotation	Transcriptomics / Genome-wide alternative splicing analysis
nilesh/rseqc/rseqc_inner_distance	Transcriptomics / Genome-wide alternative splicing analysis
iuc/rnaquast/rna_quast	Transcriptomics / Genome-wide alternative splicing analysis
iuc/isoformswitchanalyzer/isoformswitchanalyzer	Transcriptomics / Genome-wide alternative splicing analysis
bgruening/text_processing/tp_uniq_tool	Transcriptomics / Genome-wide alternative splicing analysis
bgruening/pfamscan/pfamscan	Transcriptomics / Genome-wide alternative splicing analysis
bgruening/cpat/cpat	Transcriptomics / Genome-wide alternative splicing analysis
rnateam/rcas/rcas	Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
rnateam/peakachu/peakachu	Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/umi_tools_dedup/umi_tools_dedup	Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/bedtools/bedtools_slopbed	Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/bedtools/bedtools_genomecoveragebed_bedgraph	Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/bctools_extract_alignment_ends/bctools_extract_alignment_ends	Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/chira_quantify/chira_quantify	Transcriptomics / RNA-RNA interactome data analysis
iuc/chira_merge/chira_merge	Transcriptomics / RNA-RNA interactome data analysis
iuc/chira_map/chira_map	Transcriptomics / RNA-RNA interactome data analysis
iuc/chira_extract/chira_extract	Transcriptomics / RNA-RNA interactome data analysis
iuc/chira_collapse/chira_collapse	Transcriptomics / RNA-RNA interactome data analysis
iuc/bcftools_mpileup/bcftools_mpileup	Variant Analysis / Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates
iuc/bcftools_call/bcftools_call	Variant Analysis / Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates
devteam/vcffilter/vcffilter2	Variant Analysis / Calling variants in non-diploid systems
iuc/control_freec/control_freec	Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC
bgruening/text_processing/tp_text_file_with_recurring_lines	Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC
iuc/nextclade/nextclade	Variant Analysis / Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
iuc/gemini_db_info/gemini_db_info	Variant Analysis / Calling variants in diploid systems
devteam/vcfallelicprimitives/vcfallelicprimitives	Variant Analysis / Calling variants in diploid systems
iuc/tbvcfreport/tbvcfreport	Variant Analysis / M. tuberculosis Variant Analysis
iuc/mosdepth/mosdepth	Variant Analysis / M. tuberculosis Variant Analysis
iuc/jvarkit_wgscoverageplotter/jvarkit_wgscoverageplotter	Variant Analysis / M. tuberculosis Variant Analysis
devteam/emboss_5/EMBOSS:%20seqret84	Variant Analysis / M. tuberculosis Variant Analysis
devteam/emboss_5/EMBOSS: seqret84	Variant Analysis / M. tuberculosis Variant Analysis
iuc/varscan_somatic/varscan_somatic	Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
iuc/gemini_annotate/gemini_annotate	Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
iuc/geneiobio/gene_iobio_display_generation_iframe	Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
iuc/ega_download_client/pyega3	Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
iuc/bcftools_merge/bcftools_merge	Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
wolma/mimodd_main/mimodd_info	Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
iuc/ucsc_fatovcf/fatovcf	Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
iuc/samtools_merge/samtools_merge	Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
iuc/ivar_trim/ivar_trim	Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
devteam/emboss_5/EMBOSS: maskseq51	Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
__APPLY_RULES__	Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
wolma/mimodd_main/mimodd_vcf_filter	Variant Analysis / Mapping and molecular identification of phenotype-causing mutations
wolma/mimodd_main/mimodd_varreport	Variant Analysis / Mapping and molecular identification of phenotype-causing mutations
wolma/mimodd_main/mimodd_varextract	Variant Analysis / Mapping and molecular identification of phenotype-causing mutations
wolma/mimodd_main/mimodd_varcall	Variant Analysis / Mapping and molecular identification of phenotype-causing mutations
wolma/mimodd_main/mimodd_map	Variant Analysis / Mapping and molecular identification of phenotype-causing mutations
bebatut/combine_metaphlan2_humann2/combine_metaphlan_humann	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data
bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona	Microbiome / 16S Microbial Analysis with mothur (extended)
iuc/mothur_seq_error/mothur_seq_error	Microbiome / 16S Microbial Analysis with mothur (extended)
iuc/mothur_make_contigs/mothur_make_contigs	Microbiome / 16S Microbial Analysis with mothur (extended)
iuc/mothur_get_groups/mothur_get_groups	Microbiome / 16S Microbial Analysis with mothur (extended)
iuc/ggplot2_histogram/ggplot2_histogram	Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data
estrain/add_column_headers/add_column_headers	Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data
devteam/count_gff_features/count_gff_features	Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data
CONVERTER_fasta_to_tabular	Microbiome / Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data
iuc/datamash_reverse/datamash_reverse	Microbiome / 16S Microbial analysis with Nanopore data
iuc/phyloseq_from_dada2/phyloseq_from_dada2	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_seqcounts/dada2_seqCounts	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_removebimeradenovo/dada2_removeBimeraDenovo	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_plotqualityprofile/dada2_plotQualityProfile	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_mergepairs/dada2_mergePairs	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_makesequencetable/dada2_makeSequenceTable	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_learnerrors/dada2_learnErrors	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_filterandtrim/dada2_filterAndTrim	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_dada/dada2_dada	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
interactive_tool_phyloseq	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/kraken_biom/kraken_biom	Microbiome / Taxonomic Profiling and Visualization of Metagenomic Data
interactive_tool_phinch	Microbiome / Taxonomic Profiling and Visualization of Metagenomic Data
interactive_tool_pavian	Microbiome / Taxonomic Profiling and Visualization of Metagenomic Data
iuc/krakentools_beta_diversity/krakentools_beta_diversity	Microbiome / Calculating α and β diversity from microbiome taxonomic data
iuc/krakentools_alpha_diversity/krakentools_alpha_diversity	Microbiome / Calculating α and β diversity from microbiome taxonomic data
iuc/samtools_depth/samtools_depth	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/samtools_coverage/samtools_coverage	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/mlst/mlst	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/krakentools_extract_kraken_reads/krakentools_extract_kraken_reads	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/ggplot2_heatmap/ggplot2_heatmap	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/clair3/clair3	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/bamtools_split_mapped/bamtools_split_mapped	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/abricate/abricate	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
rnateam/cmsearch_deoverlap/cmsearch_deoverlap	Microbiome / MGnify v5.0 Amplicon Pipeline
iuc/seqprep/seqprep	Microbiome / MGnify v5.0 Amplicon Pipeline
iuc/prinseq/prinseq	Microbiome / MGnify v5.0 Amplicon Pipeline
iuc/mapseq/mapseq	Microbiome / MGnify v5.0 Amplicon Pipeline
iuc/fastq_dl/fastq_dl	Microbiome / MGnify v5.0 Amplicon Pipeline
iuc/biom_convert/biom_convert	Microbiome / MGnify v5.0 Amplicon Pipeline
iuc/ampvis2_load/ampvis2_load	Microbiome / MGnify v5.0 Amplicon Pipeline
iuc/ampvis2_heatmap/ampvis2_heatmap	Microbiome / MGnify v5.0 Amplicon Pipeline
devteam/fasta_formatter/cshl_fasta_formatter	Microbiome / MGnify v5.0 Amplicon Pipeline
devteam/concat/gops_concat_1	Microbiome / MGnify v5.0 Amplicon Pipeline
bgruening/mgnify_seqprep/mgnify_seqprep	Microbiome / MGnify v5.0 Amplicon Pipeline
bgruening/infernal/infernal_cmsearch	Microbiome / MGnify v5.0 Amplicon Pipeline
iuc/plasflow/PlasFlow	Microbiome / Antibiotic resistance detection
iuc/miniasm/miniasm	Microbiome / Antibiotic resistance detection
galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing	Metabolomics / Mass spectrometry imaging: Finding differential analytes
galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection	Metabolomics / Mass spectrometry imaging: Finding differential analytes
galaxyp/cardinal_segmentations/cardinal_segmentations	Metabolomics / Mass spectrometry imaging: Finding differential analytes
galaxyp/cardinal_preprocessing/cardinal_preprocessing	Metabolomics / Mass spectrometry imaging: Finding differential analytes
galaxyp/cardinal_combine/cardinal_combine	Metabolomics / Mass spectrometry imaging: Finding differential analytes
galaxyp/cardinal_classification/cardinal_classification	Metabolomics / Mass spectrometry imaging: Finding differential analytes
bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy	Metabolomics / Mass spectrometry imaging: Finding differential analytes
recetox/mfassignr_snplot/mfassignr_snplot	Metabolomics / Molecular formula assignment and mass recalibration with MFAssignR package
recetox/mfassignr_recallist/mfassignr_recallist	Metabolomics / Molecular formula assignment and mass recalibration with MFAssignR package
recetox/mfassignr_recal/mfassignr_recal	Metabolomics / Molecular formula assignment and mass recalibration with MFAssignR package
recetox/mfassignr_mfassigncho/mfassignr_mfassignCHO	Metabolomics / Molecular formula assignment and mass recalibration with MFAssignR package
recetox/mfassignr_mfassign/mfassignr_mfassign	Metabolomics / Molecular formula assignment and mass recalibration with MFAssignR package
recetox/mfassignr_kmdnoise/mfassignr_kmdnoise	Metabolomics / Molecular formula assignment and mass recalibration with MFAssignR package
recetox/mfassignr_isofiltr/mfassignr_isofiltr	Metabolomics / Molecular formula assignment and mass recalibration with MFAssignR package
recetox/mfassignr_histnoise/mfassignr_kmdnoise	Metabolomics / Molecular formula assignment and mass recalibration with MFAssignR package
recetox/mfassignr_histnoise/mfassignr_histnoise	Metabolomics / Molecular formula assignment and mass recalibration with MFAssignR package
recetox/mfassignr_findrecalseries/mfassignr_findRecalSeries	Metabolomics / Molecular formula assignment and mass recalibration with MFAssignR package
recetox/xtb_molecular_optimization/xtb_molecular_optimization	Metabolomics / Predicting EI+ mass spectra with QCxMS
recetox/qcxms_production_run/qcxms_production_run	Metabolomics / Predicting EI+ mass spectra with QCxMS
recetox/qcxms_neutral_run/qcxms_neutral_run	Metabolomics / Predicting EI+ mass spectra with QCxMS
recetox/qcxms_getres/qcxms_getres	Metabolomics / Predicting EI+ mass spectra with QCxMS
bgruening/ctb_im_conformers/ctb_im_conformers	Metabolomics / Predicting EI+ mass spectra with QCxMS
galaxyp/cardinal_spectra_plots/cardinal_spectra_plots	Metabolomics / Mass spectrometry imaging: Examining the spatial distribution of analytes
galaxyp/cardinal_filtering/cardinal_filtering	Metabolomics / Mass spectrometry imaging: Examining the spatial distribution of analytes
recetox/waveica/waveica	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
recetox/riassigner/riassigner	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
recetox/ramclustr_define_experiment/ramclustr_define_experiment	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
recetox/ramclustr/ramclustr	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
recetox/matchms_similarity/matchms_similarity	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
recetox/matchms_formatter/matchms_formatter	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
recetox/matchms_filtering/matchms_filtering	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
fgiacomoni/hmdb_ms_search/wsdl_hmdb	Metabolomics / Mass spectrometry: LC-MS analysis
ethevenot/univariate/Univariate	Metabolomics / Mass spectrometry: LC-MS analysis
iuc/raxml/raxml	Evolution / Tree thinking for tuberculosis evolution and epidemiology
mvdbeek/add_input_name_as_column/addName	Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters
iuc/snp_sites/snp_sites	Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters
iuc/snp_dists/snp_dists	Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters
iuc/clustering_from_distmat/clustering_from_distmat	Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters
ecology/tool_anonymization/tool_anonymization	Ecology / Biodiversity data exploration
ecology/ecology_stat_presence_abs/ecology_stat_presence_abs	Ecology / Biodiversity data exploration
ecology/ecology_presence_abs_abund/ecology_presence_abs_abund	Ecology / Biodiversity data exploration
ecology/ecology_link_between_var/ecology_link_between_var	Ecology / Biodiversity data exploration
ecology/ecology_homogeneity_normality/ecology_homogeneity_normality	Ecology / Biodiversity data exploration
ecology/ecology_beta_diversity/ecology_beta_diversity	Ecology / Biodiversity data exploration
iuc/prodigal/prodigal	Ecology / Marine Omics identifying biosynthetic gene clusters
ecology/sanntis_marine/sanntis_marine	Ecology / Marine Omics identifying biosynthetic gene clusters
ecology/SanntiS_marine/SanntiS_marine	Ecology / Marine Omics identifying biosynthetic gene clusters
interactive_tool_holoviz	Ecology / From NDVI data with OpenEO to time series visualisation with Holoviews
ecology/gdal_ogr2ogr/gdal_ogr2ogr	Ecology / Cleaning GBIF data for the use in Ecology
interactive_tool_metashrimps	Ecology / Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS
kellrott/regex_replace/regex_replace	Ecology / RAD-Seq Reference-based data analysis
iuc/stacks_refmap/stacks_refmap	Ecology / RAD-Seq Reference-based data analysis
devteam/bwa_wrappers/bwa_wrapper	Ecology / RAD-Seq Reference-based data analysis
ecology/wormsmeasurements/WormsMeasurements	Ecology / Life Traits Ecoregionalization workflow
ecology/claraguess/ClaraGuess	Ecology / Life Traits Ecoregionalization workflow
ecology/ecoregion_cluster_estimate/ecoregion_cluster_estimate	Ecology / Ecoregionalization workflow tutorial
ecology/ecoregion_clara_cluster/ecoregion_clara_cluster	Ecology / Ecoregionalization workflow tutorial
padge/phykit/phykit_alignment_based	Ecology / Preparing genomic data for phylogeny reconstruction
padge/clipkit/clipkit	Ecology / Preparing genomic data for phylogeny reconstruction
iuc/proteinortho_grab_proteins/proteinortho_grab_proteins	Ecology / Preparing genomic data for phylogeny reconstruction
iuc/proteinortho/proteinortho	Ecology / Preparing genomic data for phylogeny reconstruction
bgruening/glimmer_gbk_to_orf/glimmer_gbk_to_orf	Ecology / Preparing genomic data for phylogeny reconstruction
ecology/obisindicators/obisindicators	Ecology / Obis marine indicators
iuc/obi_uniq/obi_uniq	Ecology / Metabarcoding/eDNA through Obitools
iuc/obi_tab/obi_tab	Ecology / Metabarcoding/eDNA through Obitools
iuc/obi_stat/obi_stat	Ecology / Metabarcoding/eDNA through Obitools
iuc/obi_ngsfilter/obi_ngsfilter	Ecology / Metabarcoding/eDNA through Obitools
iuc/obi_illumina_pairend/obi_illumina_pairend	Ecology / Metabarcoding/eDNA through Obitools
iuc/obi_grep/obi_grep	Ecology / Metabarcoding/eDNA through Obitools
iuc/obi_clean/obi_clean	Ecology / Metabarcoding/eDNA through Obitools
iuc/obi_annotate/obi_annotate	Ecology / Metabarcoding/eDNA through Obitools
mnhn65mo/tabular_to_csv/tab2csv_R	Ecology / Regional GAM
mnhn65mo/regionalgam/flight-curve	Ecology / Regional GAM
mnhn65mo/csv_to_tabular/csv2tab_R	Ecology / Regional GAM
ecology/regionalgam_plot_trend/regionalgam_plot_trend	Ecology / Regional GAM
ecology/regionalgam_gls/regionalgam_gls	Ecology / Regional GAM
ecology/regionalgam_glmmpql/regionalgam_glmmpql	Ecology / Regional GAM
ecology/regionalgam_flight_curve/regionalgam_flight_curve	Ecology / Regional GAM
ecology/regionalgam_autocor_acf/regionalgam_autocor_acf	Ecology / Regional GAM
ecology/regionalgam_ab_index/regionalgam_ab_index	Ecology / Regional GAM
mergeCols1	Ecology / Regional GAM
climate/cdo_operations/cdo_operations	Ecology / Visualization of Climate Data using NetCDF xarray Map Plotting
interactive_tool_wallace	Ecology / Species distribution modeling
ecology/cb_ivr/cb_ivr	Ecology / Champs blocs indicators
ecology/cb_div/cb_div	Ecology / Champs blocs indicators
ecology/cb_dissim/cb_dissim	Ecology / Champs blocs indicators
cb_qecb	Ecology / Champs blocs indicators
cb_ivr	Ecology / Champs blocs indicators
cb_eco	Ecology / Champs blocs indicators
iuc/stacks_genotypes/stacks_genotypes	Ecology / RAD-Seq to construct genetic maps
ecology/pampa_presabs/pampa_presabs	Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite
ecology/pampa_plotglm/pampa_plotglm	Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite
ecology/pampa_glmsp/pampa_glmsp	Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite
ecology/pampa_glmcomm/pampa_glmcomm	Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite
ecology/pampa_communitymetrics/pampa_communitymetrics	Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite
ecology/srs_spectral_indices/srs_spectral_indices	Ecology / Sentinel 2 biodiversity
ecology/srs_process_data/srs_process_data	Ecology / Sentinel 2 biodiversity
ecology/srs_preprocess_s2/srs_preprocess_s2	Ecology / Sentinel 2 biodiversity
ecology/srs_pca/srs_pca	Ecology / Sentinel 2 biodiversity
ecology/srs_global_indices/srs_global_indices	Ecology / Sentinel 2 biodiversity
ecology/srs_diversity_maps/srs_diversity_maps	Ecology / Sentinel 2 biodiversity
ecology/phylogenetic_occupancy_matcher/phylogenetic_occupancy_matcher	Ecology / Phylodiversity analysis quick tutorial
ecology/phylo_index/phylo_index	Ecology / Phylodiversity analysis quick tutorial
ecology/estimate_endem/estimate_endem	Ecology / Phylodiversity analysis quick tutorial
ecology/crsconverter/crsconverter	Ecology / Phylodiversity analysis quick tutorial
interactive_tool_metashark	Ecology / Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities
iuc/ena_upload/ena_upload	Using Galaxy and Managing your Data / Submitting sequence data to ENA
ieguinoa/ena_webin_cli/ena_consensus_submit	Using Galaxy and Managing your Data / Submitting sequence data to ENA
iuc/intermine_galaxy_exchange/galaxy_intermine_exchange	Using Galaxy and Managing your Data / InterMine integration with Galaxy
intermine	Using Galaxy and Managing your Data / InterMine integration with Galaxy
bgruening/text_processing/tp_tac	Using Galaxy and Managing your Data / Creating, Editing and Importing Galaxy Workflows
iuc/rapidnj/rapidnj	Genome Annotation / Comparative gene analysis in unannotated genomes
iuc/orfipy/orfipy	Genome Annotation / Comparative gene analysis in unannotated genomes
bgruening/diamond/bg_diamond_view	Genome Annotation / Comparative gene analysis in unannotated genomes
bgruening/diamond/bg_diamond_makedb	Genome Annotation / Comparative gene analysis in unannotated genomes
iuc/plasmidfinder/plasmidfinder	Genome Annotation / Bacterial Genome Annotation
iuc/isescan/isescan	Genome Annotation / Bacterial Genome Annotation
iuc/integron_finder/integron_finder	Genome Annotation / Bacterial Genome Annotation
gga/apollo_list_organism/list_organism	Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes)
gga/apollo_create_account/create_account	Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes)
simon-gladman/fasta_stats/fasta-stats	Genome Annotation / Genome annotation with Maker (short)
iuc/bp_genbank2gff3/bp_genbank2gff3	Genome Annotation / Secondary metabolite discovery
cpt/cpt_gbk_to_gff/edu.tamu.cpt.gff3.customGbkToGff	Genome Annotation / Secondary metabolite discovery
bgruening/simsearch/ctb_simsearch	Genome Annotation / Secondary metabolite discovery
bgruening/openbabel_remduplicates/openbabel_remDuplicates	Genome Annotation / Secondary metabolite discovery
bgruening/antismash/antismash	Genome Annotation / Secondary metabolite discovery
iuc/red/red	Genome Annotation / Masking repeats with RepeatMasker
csbl/repeatmodeler/repeatmodeler	Genome Annotation / Masking repeats with RepeatMasker
iuc/funannotate_compare/funannotate_compare	Genome Annotation / Genome annotation with Funannotate
iuc/funannotate_annotate/funannotate_annotate	Genome Annotation / Genome annotation with Funannotate
iuc/aegean_parseval/aegean_parseval	Genome Annotation / Genome annotation with Funannotate
iuc/mageck_test/mageck_test	Genome Annotation / CRISPR screen analysis
iuc/mageck_mle/mageck_mle	Genome Annotation / CRISPR screen analysis
iuc/mageck_count/mageck_count	Genome Annotation / CRISPR screen analysis
iuc/feelnc/feelnc	Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc
Extract_features1	Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc
iuc/gecko/gecko	Genome Annotation / From small to large-scale genome comparison
iuc/snap_training/snap_training	Genome Annotation / Genome annotation with Maker
bgruening/augustus_training/augustus_training	Genome Annotation / Genome annotation with Maker
iuc/circos/circos_interval_to_tiles	Assembly / Making sense of a newly assembled genome
iuc/circos/circos_aln_to_links	Assembly / Making sense of a newly assembled genome
iuc/bedtools/bedtools_complementbed	Assembly / Making sense of a newly assembled genome
devteam/lastz/lastz_wrapper_2	Assembly / Making sense of a newly assembled genome
iuc/yahs/yahs	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
iuc/salsa/salsa	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
iuc/purge_dups/purge_dups	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
bgruening/bionano_scaffold/bionano_scaffold	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
iuc/seqtk/seqtk_sample	Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
simon-gladman/velvetoptimiser/velvetoptimiser	Assembly / De Bruijn Graph Assembly
nml/spades/spades	Assembly / De Bruijn Graph Assembly
iuc/shovill/shovill	Assembly / Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data
iuc/parse_mito_blast/parse_mito_blast	Assembly / Decontamination of a genome assembly
devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper	Assembly / Decontamination of a genome assembly
iuc/compress_file/compress_file	Assembly / Assembly of the mitochondrial genome from PacBio HiFi reads
bgruening/mitohifi/mitohifi	Assembly / Assembly of the mitochondrial genome from PacBio HiFi reads
iuc/pilon/pilon	Assembly / Chloroplast genome assembly
galaxy-australia/smudgeplot/smudgeplot	Assembly / ERGA post-assembly QC
bgruening/blobtoolkit/blobtoolkit	Assembly / ERGA post-assembly QC
interactive_tool_blobtoolkit	Assembly / ERGA post-assembly QC
iuc/polypolish/polypolish	Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
iuc/filtlong/filtlong	Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
CONVERTER_bz2_to_uncompressed	Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
iuc/iwtomics_testandplot/iwtomics_testandplot	Statistics and machine learning / Interval-Wise Testing for omics data
iuc/iwtomics_plotwithscale/iwtomics_plotwithscale	Statistics and machine learning / Interval-Wise Testing for omics data
iuc/iwtomics_loadandplot/iwtomics_loadandplot	Statistics and machine learning / Interval-Wise Testing for omics data
bgruening/sklearn_nn_classifier/sklearn_nn_classifier	Statistics and machine learning / Classification in Machine Learning
paulo_lyra_jr/pycaret_model_comparison/PyCaret_Model_Comparison	Statistics and machine learning / Building the LORIS LLR6 PanCancer Model Using PyCaret
iuc/pick_value/pick_value	Statistics and machine learning / Modeling Breast Cancer Subtypes with Flexynesis
bgruening/tabpfn/tabpfn	Statistics and machine learning / Modeling Breast Cancer Subtypes with Flexynesis
bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot	Statistics and machine learning / Age prediction using machine learning
iuc/pubmed_by_queries/pubmed_by_queries	Statistics and machine learning / Text-mining with the SimText toolset
iuc/pmids_to_pubtator_matrix/pmids_to_pubtator_matrix	Statistics and machine learning / Text-mining with the SimText toolset
interactive_tool_simtext_app	Statistics and machine learning / Text-mining with the SimText toolset
vijay/pancancer_within_disease_analysis/pancancer_within_disease_analysis	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_visualize_decisions/pancancer_visualize_decisions	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_targene_summary_figures/pancancer_targene_summary_figures	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_targene_pharmacology/pancancer_targene_pharmacology	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_targene_cell_line_predictions/pancancer_targene_cell_line_predictions	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_pathway_count_heatmaps/pancancer_pathway_count_heatmaps	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_map_mutation_class/pancancer_map_mutation_class	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_external_sample_status_prediction/pancancer_external_sample_status_prediction	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_compare_within_models/pancancer_compare_within_models	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_classifier/pancancer_classifier	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_apply_weights/pancancer_apply_weights	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_alternative_genes_pathwaymapper/pancancer_alternative_genes_pathwaymapper	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
paulo_lyra_jr/ludwig_applications/ludwig_experiment	Statistics and machine learning / Train and Test a Deep learning image classifier with Galaxy-Ludwig
bgruening/flexynesis_cbioportal_import/flexynesis_cbioportal_import	Statistics and machine learning / Prepare Data from CbioPortal for Flexynesis Integration
setup	Computational chemistry / Running molecular dynamics simulations using NAMD
namd_nvt	Computational chemistry / Running molecular dynamics simulations using NAMD
namd_npt	Computational chemistry / Running molecular dynamics simulations using NAMD
minimizer	Computational chemistry / Running molecular dynamics simulations using NAMD
chemteam/vmd_hbonds/vmd_hbonds	Computational chemistry / High Throughput Molecular Dynamics and Analysis
chemteam/gmx_merge_topology_files/gmx_merge_topology_files	Computational chemistry / High Throughput Molecular Dynamics and Analysis
chemteam/gmx_energy/gmx_energy	Computational chemistry / High Throughput Molecular Dynamics and Analysis
chemteam/bio3d_pca_visualize/bio3d_pca_visualize	Computational chemistry / High Throughput Molecular Dynamics and Analysis
chemteam/ambertools_acpype/ambertools_acpype	Computational chemistry / High Throughput Molecular Dynamics and Analysis
xchem_pose_scoring	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/xchem_transfs_scoring/xchem_transfs_scoring	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/sucos_max_score/sucos_max_score	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/rxdock_rbdock/rxdock_rbdock	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/rxdock_rbcavity/rxdock_rbcavity	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/rdock_rbdock/rdock_rbdock	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/rdock_rbcavity/rdock_rbcavity	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/enumerate_charges/enumerate_charges	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
chemteam/mdanalysis_rdf/mdanalysis_rdf	Computational chemistry / Analysis of molecular dynamics simulations
chemteam/mdanalysis_ramachandran_plot/mdanalysis_ramachandran_plot	Computational chemistry / Analysis of molecular dynamics simulations
chemteam/mdanalysis_distance/mdanalysis_distance	Computational chemistry / Analysis of molecular dynamics simulations
chemteam/mdanalysis_dihedral/mdanalysis_dihedral	Computational chemistry / Analysis of molecular dynamics simulations
bgruening/sdf_to_tab/sdf_to_tab	Computational chemistry / Protein-ligand docking
bgruening/openbabel/ctb_remIons	Computational chemistry / Protein-ligand docking
bgruening/openbabel/ctb_remDuplicates	Computational chemistry / Protein-ligand docking
bgruening/openbabel/ctb_obgrep	Computational chemistry / Protein-ligand docking
bgruening/openbabel/ctb_filter	Computational chemistry / Protein-ligand docking
bgruening/openbabel/ctb_compound_convert	Computational chemistry / Protein-ligand docking
bgruening/openbabel/ctb_change_title	Computational chemistry / Protein-ligand docking
bgruening/fpocket/fpocket	Computational chemistry / Protein-ligand docking
bgruening/chemical_data_sources/ctb_online_data_fetch	Computational chemistry / Protein-ligand docking
bgruening/chemfp/ctb_chemfp_nxn_clustering	Computational chemistry / Protein-ligand docking
bgruening/chemfp/ctb_chemfp_butina_clustering	Computational chemistry / Protein-ligand docking
bgruening/autodock_vina_prepare_receptor/prepare_receptor	Computational chemistry / Protein-ligand docking
bgruening/autodock_vina_prepare_box/prepare_box	Computational chemistry / Protein-ligand docking
bgruening/autodock_vina/docking	Computational chemistry / Protein-ligand docking
bgruening/rdconf/rdconf	Computational chemistry / Protein target prediction of a bioactive ligand with Align-it and ePharmaLib
bgruening/openbabel_addh/openbabel_addh	Computational chemistry / Protein target prediction of a bioactive ligand with Align-it and ePharmaLib
bgruening/align_it/ctb_alignit	Computational chemistry / Protein target prediction of a bioactive ligand with Align-it and ePharmaLib
iuc/bedtools/bedtools_mergebed	Epigenetics / Formation of the Super-Structures on the Inactive X
iuc/bbgbigwig/bbgtobigwig	Epigenetics / Formation of the Super-Structures on the Inactive X
fubar/jbrowse2/jbrowse2	Epigenetics / Formation of the Super-Structures on the Inactive X
iuc/transit_gumbel/transit_gumbel	Genome Annotation / Essential genes detection with Transposon insertion sequencing
iuc/gff_to_prot/gff_to_prot	Genome Annotation / Essential genes detection with Transposon insertion sequencing
devteam/bowtie_wrappers/bowtie_wrapper	Genome Annotation / Essential genes detection with Transposon insertion sequencing
bgruening/find_subsequences/bg_find_subsequences	Genome Annotation / Essential genes detection with Transposon insertion sequencing
nick/sequence_content_trimmer/sequence_content_trimmer	Variant Analysis / Calling very rare variants
nick/dunovo/make_families	Variant Analysis / Calling very rare variants
nick/dunovo/dunovo	Variant Analysis / Calling very rare variants
nick/dunovo/correct_barcodes	Variant Analysis / Calling very rare variants
nick/dunovo/align_families	Variant Analysis / Calling very rare variants
nick/allele_counts/allele_counts_1	Variant Analysis / Calling very rare variants
blankenberg/naive_variant_caller/naive_variant_caller	Variant Analysis / Calling very rare variants
iuc/pathview/pathview	Transcriptomics / Reference-based RNA-Seq data analysis
iuc/dexseq/dexseq_count	Transcriptomics / Reference-based RNA-Seq data analysis
iuc/dexseq/dexseq	Transcriptomics / Reference-based RNA-Seq data analysis
__TAG_FROM_FILE__	Transcriptomics / Reference-based RNA-Seq data analysis
ChangeCase	Transcriptomics / Reference-based RNA-Seq data analysis
bgruening/sklearn_numeric_clustering/sklearn_numeric_clustering	Statistics and machine learning / Clustering in Machine Learning
devteam/velvet/velveth	Assembly / An Introduction to Genome Assembly
devteam/velvet/velvetg	Assembly / An Introduction to Genome Assembly
saskia-hiltemann/krona_text/krona-text	Microbiome / Analyses of metagenomics data - The global picture
iuc/mothur_make_group/mothur_make_group	Microbiome / Analyses of metagenomics data - The global picture
iuc/metaphlan2krona/metaphlan2krona	Microbiome / Analyses of metagenomics data - The global picture
iuc/metaphlan2/metaphlan2	Microbiome / Analyses of metagenomics data - The global picture
iuc/humann2_renorm_table/humann2_renorm_table	Microbiome / Analyses of metagenomics data - The global picture
iuc/humann2_regroup_table/humann2_regroup_table	Microbiome / Analyses of metagenomics data - The global picture
iuc/humann2/humann2	Microbiome / Analyses of metagenomics data - The global picture
devteam/fastq_quality_filter/cshl_fastq_quality_filter	Introduction to Galaxy Analyses / A short introduction to Galaxy
devteam/get_flanks/get_flanks1	Introduction to Galaxy Analyses / From peaks to genes
CONVERTER_interval_to_bed_0	Introduction to Galaxy Analyses / From peaks to genes