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 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 / 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 / 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 Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data 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 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 / 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 Ecology / Metabarcoding/eDNA through Obitools Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite 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 / CUT&RUN 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 / 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 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 / Secretome Prediction Single Cell / Inferring single cell trajectories with Monocle3 Single Cell / Converting between common single cell data formats 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 / Differential abundance testing of small RNAs 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	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 / 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) 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 / 16S Microbial analysis with Nanopore data Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Sequence analysis / Mapping Sequence analysis / Quality and contamination control in bacterial isolate using Illumina MiSeq Data 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 / Whole transcriptome analysis of Arabidopsis thaliana Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / RNA-RNA interactome data analysis Transcriptomics / 1: RNA-Seq reads to counts Transcriptomics / Differential abundance testing of small RNAs 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 Introduction to Galaxy Analyses / NGS data logistics 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 / 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	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 / RAD-Seq Reference-based data analysis 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 / 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
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 / 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 / Bacterial Genome Annotation 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
bgruening/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 / Proteogenomics 1: Database Creation Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Reference-based RNA-Seq data analysis
Remove beginning1	Foundations of Data Science / Data Manipulation Olympics Ecology / Biodiversity data exploration Ecology / Regional GAM Epigenetics / Infinium Human Methylation BeadChip Using Galaxy and Managing your Data / Workflow Reports 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 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
bgruening/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 / Obis marine indicators Ecology / Species distribution modeling Introduction to Galaxy Analyses / NGS data logistics 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 / 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 / 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
nml/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 Introduction to Galaxy Analyses / NGS data logistics Microbiome / Clinical Metaproteomics 3: Verification Microbiome / 16S Microbial Analysis with mothur (short) Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Clinical Metaproteomics 3: Verification Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data
lparsons/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 Epigenetics / ATAC-Seq data analysis Epigenetics / CUT&RUN 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
iuc/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 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
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 / 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 Transcriptomics / Reference-based RNA-Seq data analysis
iuc/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) 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 / 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
bgruening/tp_sort_header_tool	Assembly / Making sense of a newly assembled genome Foundations of Data Science / Data Manipulation Olympics 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 Proteomics / Mass spectrometry imaging: Loading and exploring MSI data Proteomics / Label-free data analysis using MaxQuant Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / 3: RNA-seq genes to pathways Transcriptomics / Small Non-coding RNA Clustering using BlockClust
devteam/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 / 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
galaxyp/regexColumn1	Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools Foundations of Data Science / Data Manipulation Olympics Ecology / Ecoregionalization workflow tutorial Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite Ecology / Biodiversity data exploration 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 / 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
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 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 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
devteam/Add_a_column1	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Foundations of Data Science / Data Manipulation Olympics 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 / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Label-free data analysis using MaxQuant Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / 3: RNA-seq genes to pathways Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
iuc/datamash_ops	Assembly / Making sense of a newly assembled genome Climate / Getting your hands-on climate data 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 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 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
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 / 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 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
bgruening/tp_replace_in_line	Assembly / Making sense of a newly assembled genome 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 Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / 2: RNA-seq counts to genes Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC
bgruening/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 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 / CLIP-Seq data analysis from pre-processing to motif detection Transcriptomics / Genome-wide alternative splicing analysis Variant Analysis / M. tuberculosis Variant Analysis
bgruening/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 Ecology / Species distribution modeling 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 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
iuc/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 Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 3: Verification Proteomics / Metaproteomics tutorial Proteomics / metaQuantome 1: Data creation Proteomics / Proteogenomics 1: Database Creation Proteomics / Proteogenomics 2: Database Search Proteomics / Proteogenomics 3: Novel peptide analysis Transcriptomics / RNA-RNA interactome data analysis
iuc/quast	Assembly / Genome Assembly Quality Control Assembly / Genome assembly using PacBio data 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 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
iuc/anndata_inspect	Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets 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 / 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
iuc/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 Funannotate Genome Annotation / Genome annotation with Helixer
iuc/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
bgruening/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 / 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/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 Genome Annotation / Identification of AMR genes in an assembled bacterial genome Microbiome / Assembly of metagenomic sequencing data Sequence analysis / Mapping
bgruening/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 Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters 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
bgruening/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 / 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 / Combining single cell datasets after pre-processing Single Cell / Converting NCBI Data to the AnnData Format
bgruening/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 / 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
galaxyp/fasta_merge_files_and_filter_unique_sequences	Microbiome / Clinical Metaproteiomics 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 Metaproteiomics 1: Database-Generation Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 3: Verification Proteomics / Protein FASTA Database Handling Proteomics / Proteogenomics 1: Database Creation
bgruening/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 / 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 Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
iuc/anndata_manipulate	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 / 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
pjbriggs/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 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
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	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
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 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
galaxyp/regex1	Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite Ecology / Marine Omics identifying biosynthetic gene clusters Ecology / Preparing genomic data for phylogeny reconstruction Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / metaQuantome 1: Data creation 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
galaxyp/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
iuc/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
__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 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
iuc/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 Statistics and machine learning / Clustering in Machine Learning
crs4/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 / 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
Count1	Foundations of Data Science / Data Manipulation Olympics Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite 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
iuc/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
iuc/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 / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Single Cell / Pre-processing of Single-Cell RNA Data Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / 1: RNA-Seq reads to counts
devteam/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
imgteam/unzip	Ecology / Ecoregionalization workflow tutorial Ecology / Metabarcoding/eDNA through Obitools Imaging / Analyse HeLa fluorescence siRNA screen Imaging / Introduction to Image Analysis using Galaxy Imaging / Object tracking using CellProfiler Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus Single Cell / Converting NCBI Data to the AnnData Format
galaxyp/dbbuilder	Microbiome / Clinical Metaproteiomics 1: Database-Generation Microbiome / Clinical Metaproteomics 2: Discovery Microbiome / Clinical Metaproteomics 3: Verification Proteomics / Clinical Metaproteiomics 1: Database-Generation Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 3: Verification Proteomics / Protein FASTA Database Handling
galaxyp/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 / Peptide and Protein ID using OpenMS tools
devteam/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
iuc/datamash_transpose	Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite 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 Transcriptomics / Visualization of RNA-Seq results with heatmap2
iuc/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	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
bgruening/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/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 / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Microbiome / Antibiotic resistance detection
devteam/tab2fasta	Genome Annotation / Comparative gene analysis in unannotated genomes Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Proteomics / Protein FASTA Database Handling Proteomics / Proteogenomics 1: Database Creation Proteomics / Proteogenomics 2: Database Search Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
iuc/filter_tabular	Assembly / Assembly of metagenomic sequencing data Ecology / Ecoregionalization workflow tutorial Microbiome / Clinical Metaproteomics 2: Discovery Microbiome / Assembly of metagenomic sequencing data Proteomics / Clinical Metaproteomics 2: Discovery Proteomics / Proteogenomics 1: Database Creation
devteam/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 / Proteogenomics 1: Database Creation
galaxyp/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/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
iuc/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	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)
devteam/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
bgruening/tp_tail_tool	Epigenetics / DNA Methylation data analysis Genome Annotation / Bacterial Genome Annotation Introduction to Galaxy Analyses / From peaks to genes 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
devteam/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	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
bgruening/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	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	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	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
devteam/gffread	Genome Annotation / Genome annotation with Maker Genome Annotation / Genome annotation with Maker (short) Genome Annotation / Genome annotation with Helixer Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc Transcriptomics / Genome-wide alternative splicing analysis
bgruening/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/tp_split_on_column	Foundations of Data Science / Data Manipulation Olympics 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 Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data
Paste1	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 / Combining single cell datasets after pre-processing Single Cell / Converting NCBI Data to the AnnData Format
iuc/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
iuc/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/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	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
iuc/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
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
iuc/hisat2	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
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)
iuc/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
bgruening/tp_head_tool	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
bgruening/trim_galore	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
bgruening/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_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/table_compute	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 Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution Single Cell / Removing the effects of the cell cycle Transcriptomics / Reference-based RNA-Seq data analysis
iuc/rna_star	Genome Annotation / Genome annotation with Funannotate 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/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
iuc/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 / Differential abundance testing of small RNAs
iuc/collection_element_identifiers	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 Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Reference-based RNA-Seq data analysis
__MERGE_COLLECTION__	Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters 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
__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
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 / JupyterLab in Galaxy Genome Annotation / Secondary metabolite discovery
iuc/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
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 Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data
bgruening/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
lecorguille/abims_xcms_xcmsSet	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) Metabolomics / Mass spectrometry : GC-MS analysis with metaMS package Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
lecorguille/xcms_merge	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) Metabolomics / Mass spectrometry : GC-MS analysis with metaMS package Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
lecorguille/abims_xcms_group	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) Metabolomics / Mass spectrometry : GC-MS analysis with metaMS package Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
lecorguille/abims_xcms_fillPeaks	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) Metabolomics / Mass spectrometry : GC-MS analysis with metaMS package Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
lecorguille/msnbase_readmsdata	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) Metabolomics / Mass spectrometry : GC-MS analysis with metaMS package Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
ebi-gxa/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 / Combining single cell datasets after pre-processing
iuc/annotatemyids	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
iuc/scanpy_inspect	Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 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
ecology/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
interactive_tool_panoply	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
iuc/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
bgruening/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
iuc/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
rnateam/rbc_mafft	Evolution / Phylogenetics - Back to basics Genome Annotation / Comparative gene analysis in unannotated genomes Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
iuc/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
iuc/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/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/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
iuc/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/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
galaxyp/uniprotxml_downloader	Microbiome / Clinical Metaproteiomics 1: Database-Generation Microbiome / Clinical Metaproteomics 3: Verification Proteomics / Clinical Metaproteiomics 1: Database-Generation Proteomics / Clinical Metaproteomics 3: Verification
iuc/stringtie	Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc Proteomics / Proteogenomics 1: Database Creation Transcriptomics / De novo transcriptome reconstruction with RNA-Seq Transcriptomics / Genome-wide alternative splicing analysis
devteam/ncbi_blastp_wrapper	Foundations of Data Science / Learning about one gene across biological resources and formats Genome Annotation / Functional annotation of protein sequences Proteomics / Proteogenomics 3: Novel peptide analysis Sequence analysis / NCBI BLAST+ against the MAdLand
galaxyp/unipept	Microbiome / Clinical Metaproteomics 5: Data Interpretation Proteomics / Clinical Metaproteomics 5: Data Interpretation Proteomics / Metaproteomics tutorial Proteomics / metaQuantome 1: Data creation
bgruening/deeptools_plot_fingerprint	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_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	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
nilesh/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_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	Epigenetics / ATAC-Seq data analysis Epigenetics / CUT&RUN data analysis 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 Statistics and machine learning / Clustering in Machine Learning
bgruening/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	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/freebayes	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
devteam/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
iuc/jcvi_gff_stats	Genome Annotation / Genome annotation with Maker Genome Annotation / Genome annotation with Maker (short) Genome Annotation / Genome annotation with Helixer
bgruening/interproscan	Ecology / Marine Omics identifying biosynthetic gene clusters Genome Annotation / Genome annotation with Funannotate Genome Annotation / Functional annotation of protein sequences
ecology/spocc_occ	Climate / Getting your hands-on earth data Ecology / Cleaning GBIF data for the use in Ecology Ecology / Species distribution modeling
iuc/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
iuc/snpEff_download	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
devteam/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/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	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
wc_gnu	Foundations of Data Science / Data Manipulation Olympics Ecology / Metabarcoding/eDNA through Obitools Introduction to Galaxy Analyses / Data Manipulation Olympics
tabular_to_csv	Foundations of Data Science / Data Manipulation Olympics Ecology / Species distribution modeling Introduction to Galaxy Analyses / Data Manipulation Olympics
bgruening/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	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
lecorguille/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
iuc/volcanoplot	Genome Annotation / CRISPR screen analysis Transcriptomics / Visualization of RNA-Seq results with Volcano Plot Transcriptomics / Visualization of RNA-Seq results with Volcano Plot in R
ebi-gxa/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 Single Cell / Combining single cell datasets after pre-processing
iuc/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
bgruening/music_construct_eset	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
ebi-gxa/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
ebi-gxa/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
iuc/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	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	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_compute_graph	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
iuc/scanpy_cluster_reduce_dimension	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/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
iuc/scanpy_normalize	Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 Single Cell / Analysis of plant scRNA-Seq Data with Scanpy Single Cell / Clustering 3K PBMCs with Scanpy
iuc/scanpy_filter	Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 Single Cell / Analysis of plant scRNA-Seq Data with Scanpy Single Cell / Clustering 3K PBMCs with Scanpy
wig_to_bigWig	Epigenetics / ATAC-Seq data analysis Epigenetics / CUT&RUN data analysis Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
devteam/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)
ecology/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
interactive_tool_odv	Climate / Analyse Argo data Climate / Ocean Data View (ODV) Climate / Ocean's variables study
devteam/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
bgruening/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
chemteam/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/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	Computational chemistry / Protein-ligand docking Computational chemistry / Data management in Medicinal Chemistry FAIR Data, Workflows, and Research / Data management in Medicinal Chemistry
iuc/compose_text_param	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_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
devteam/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
param_value_from_file	Metabolomics / Predicting EI+ mass spectra with QCxMS Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing 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/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
__UNZIP_COLLECTION__	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 Microbiome / Taxonomic Profiling and Visualization of Metagenomic Data Sequence analysis / Removal of human reads from SARS-CoV-2 sequencing data
iuc/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/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
iuc/snippy	Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Variant Analysis / Microbial Variant Calling Variant Analysis / M. tuberculosis Variant Analysis
iuc/megahit	Assembly / Assembly of metagenomic sequencing data Microbiome / Assembly of metagenomic sequencing data Microbiome / Binning of metagenomic sequencing data
iuc/unicycler	Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads Assembly / Unicycler Assembly Microbiome / Antibiotic resistance detection
iuc/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
devteam/ncbi_blastn_wrapper	Assembly / Decontamination of a genome assembly Ecology / Metabarcoding/eDNA through Obitools Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
devteam/fasta_compute_length	Assembly / Making sense of a newly assembled genome Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
devteam/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/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/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
iuc/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
iuc/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
bgruening/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
CONVERTER_gz_to_uncompressed	Assembly / ERGA post-assembly QC Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
galaxyp/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
iuc/gffcompare	Proteomics / Proteogenomics 1: Database Creation Transcriptomics / De novo transcriptome reconstruction with RNA-Seq Transcriptomics / Genome-wide alternative splicing analysis
galaxyp/msstatstmt	Microbiome / Clinical Metaproteomics 5: Data Interpretation Proteomics / Clinical Metaproteomics 5: Data Interpretation Proteomics / MaxQuant and MSstats for the analysis of TMT data
addValue	Ecology / RAD-Seq Reference-based data analysis Proteomics / Protein FASTA Database Handling Transcriptomics / Genome-wide alternative splicing analysis
bgruening/bg_uniq	Assembly / Assembly of metagenomic sequencing data Microbiome / Assembly of metagenomic sequencing data Proteomics / Secretome Prediction
Convert characters1	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Ecology / RAD-Seq Reference-based data analysis Proteomics / Secretome Prediction
iuc/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	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_infer_experiment	Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / 1: RNA-Seq reads to counts
iuc/goseq	Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / 3: RNA-seq genes to pathways
iuc/ggplot2_heatmap2	Proteomics / MaxQuant and MSstats for the analysis of label-free data Transcriptomics / Reference-based RNA-Seq data analysis Transcriptomics / Visualization of RNA-Seq results with heatmap2
__FILTER_FROM_FILE__	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Reference-based RNA-Seq data analysis
bgruening/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	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	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	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	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	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	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	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	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	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	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	Microbiome / Analyses of metagenomics data - The global picture Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
crs4/prokka	Assembly / Chloroplast genome assembly Assembly / Unicycler Assembly Genome Annotation / Genome annotation with Prokka
galaxyp/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/histogram_rpy	Proteomics / Statistical analysis of DIA data Proteomics / Label-free data analysis using MaxQuant Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
devteam/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	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/intens_check	Metabolomics / Mass spectrometry: LC-MS data processing Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
galaxyp/eggnog_mapper	Genome Annotation / Genome annotation with Funannotate Genome Annotation / Functional annotation of protein sequences
gga/iframe	Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes) Genome Annotation / Refining Genome Annotations with Apollo (eukaryotes)
gga/create_or_update	Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes) Genome Annotation / Refining Genome Annotations with Apollo (eukaryotes)
iuc/tbl2gff3	Genome Annotation / Identification of AMR genes in an assembled bacterial genome Genome Annotation / Bacterial Genome Annotation
iuc/bakta	Genome Annotation / Identification of AMR genes in an assembled bacterial genome Genome Annotation / Bacterial Genome Annotation
iuc/maker_map_ids	Genome Annotation / Genome annotation with Maker Genome Annotation / Genome annotation with Maker (short)
iuc/maker	Genome Annotation / Genome annotation with Maker Genome Annotation / Genome annotation with Maker (short)
iuc/recentrifuge	Ecology / Checking expected species and contamination in bacterial isolate Sequence analysis / Quality and contamination control in bacterial isolate using Illumina MiSeq Data
iuc/funannotate_predict	Ecology / Preparing genomic data for phylogeny reconstruction Genome Annotation / Genome annotation with Funannotate
bgruening/repeatmasker_wrapper	Ecology / Preparing genomic data for phylogeny reconstruction Genome Annotation / Masking repeats with RepeatMasker
ecology/obis_data	Climate / Getting your hands-on earth data Ecology / Obis marine indicators
iuc/stacks_procrad	Ecology / RAD-Seq de-novo data analysis Ecology / RAD-Seq Reference-based data analysis
iuc/stacks_populations	Ecology / RAD-Seq de-novo data analysis Ecology / RAD-Seq Reference-based data analysis
iuc/stacks_denovomap	Ecology / RAD-Seq de-novo data analysis Ecology / RAD-Seq to construct genetic maps
peterjc/seq_filter_by_id	Ecology / Metabarcoding/eDNA through Obitools Single Cell / Understanding Barcodes
devteam/fastq_groomer	Ecology / Metabarcoding/eDNA through Obitools Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
__RELABEL_FROM_FILE__	Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC
devteam/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
iuc/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
iuc/gemini_query	Variant Analysis / Calling variants in diploid systems Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
mbernt/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	Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
iuc/gemini_inheritance	Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
iuc/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	Introduction to Galaxy Analyses / NGS data logistics Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
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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_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
bgruening/sklearn_generalized_linear	Statistics and machine learning / Classification in Machine Learning Statistics and machine learning / Regression in Machine Learning
melpetera/generic_filter	Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS data processing
melpetera/Batch_correction	Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS data processing
lecorguille/xcms_plot_chromatogram	Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
lecorguille/abims_CAMERA_annotateDiffreport	Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
ethevenot/quality_metrics	Metabolomics / Mass spectrometry: LC-MS analysis Metabolomics / Mass spectrometry: LC-MS data processing
galaxyp/cardinal_mz_images	Metabolomics / Mass spectrometry imaging: Examining the spatial distribution of analytes Metabolomics / Mass spectrometry imaging: Finding differential analytes
gene2exon1	Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy Transcriptomics / Genome-wide alternative splicing analysis
iuc/stringtie_merge	Transcriptomics / De novo transcriptome reconstruction with RNA-Seq Transcriptomics / Genome-wide alternative splicing analysis
galaxyp/filter_by_fasta_ids	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana
bgruening/salmon	Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana Transcriptomics / Differential abundance testing of small RNAs
iuc/limma_voom	Transcriptomics / Pathway analysis with the MINERVA Platform Transcriptomics / 2: RNA-seq counts to genes
bgruening/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	Single Cell / Converting between common single cell data formats Single Cell / Pre-processing of 10X Single-Cell RNA Datasets
ebi-gxa/monocle3_create	Single Cell / Inferring single cell trajectories with Monocle3 Single Cell / Converting between common single cell data formats
iuc/goenrichment	Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data Transcriptomics / GO Enrichment Analysis
ebi-gxa/dropletutils_read_10x	Single Cell / Generating a single cell matrix using Alevin Single Cell / Converting between common single cell data formats
ebi-gxa/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	Single Cell / Scanpy Parameter Iterator Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
iuc/scanpy_remove_confounders	Single Cell / Analysis of plant scRNA-Seq Data with Scanpy Single Cell / Clustering 3K PBMCs with Scanpy
iuc/meme_chip	Epigenetics / CUT&RUN data analysis Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/Extract genomic DNA 1	Epigenetics / CUT&RUN data analysis Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/pe_histogram	Epigenetics / ATAC-Seq data analysis Epigenetics / CUT&RUN data analysis
bgruening/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)
bgruening/replace_column_with_key_value_file	Epigenetics / DNA Methylation data analysis Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2
interactive_tool_copernicus_notebook	Climate / Sentinel 5P data visualisation Ecology / From NDVI data with OpenEO to time series visualisation with Holoviews
ecology/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	Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools Ecology / Visualization of Climate Data using NetCDF xarray Map Plotting
climate/climate_stripes	Climate / Getting your hands-on climate data Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools
ecology/argo_getdata	Climate / Analyse Argo data Climate / Getting your hands-on earth data
ecology/xarray_select	Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools
devteam/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	Climate / Getting your hands-on earth data Contributing to the Galaxy Training Material / Creating a new tutorial
bgruening/ctb_im_rxn_maker	Computational chemistry / Data management in Medicinal Chemistry FAIR Data, Workflows, and Research / Data management in Medicinal Chemistry
chemteam/mdanalysis_cosine_analysis	Computational chemistry / Analysis of molecular dynamics simulations Computational chemistry / High Throughput Molecular Dynamics and Analysis
chemteam/gmx_solvate	Computational chemistry / High Throughput Molecular Dynamics and Analysis Computational chemistry / Running molecular dynamics simulations using GROMACS
chemteam/gmx_sim	Computational chemistry / High Throughput Molecular Dynamics and Analysis Computational chemistry / Running molecular dynamics simulations using GROMACS
chemteam/gmx_setup	Computational chemistry / High Throughput Molecular Dynamics and Analysis Computational chemistry / Running molecular dynamics simulations using GROMACS
chemteam/gmx_em	Computational chemistry / High Throughput Molecular Dynamics and Analysis Computational chemistry / Running molecular dynamics simulations using GROMACS
chemteam/gmx_editconf	Computational chemistry / High Throughput Molecular Dynamics and Analysis Computational chemistry / Running molecular dynamics simulations using GROMACS
chemteam/bio3d_rmsf	Computational chemistry / Analysis of molecular dynamics simulations Computational chemistry / High Throughput Molecular Dynamics and Analysis
chemteam/bio3d_rmsd	Computational chemistry / Analysis of molecular dynamics simulations Computational chemistry / High Throughput Molecular Dynamics and Analysis
chemteam/bio3d_pca	Computational chemistry / Analysis of molecular dynamics simulations Computational chemistry / High Throughput Molecular Dynamics and Analysis
bgruening/ctb_np-likeness-calculator	Computational chemistry / Protein-ligand docking Genome Annotation / Secondary metabolite discovery
bgruening/ctb_chemfp_mol2fps	Computational chemistry / Protein-ligand docking Genome Annotation / Secondary metabolite discovery
iuc/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
bgruening/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
__FILTER_FAILED_DATASETS__	Metabolomics / Predicting EI+ mass spectra with QCxMS Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
__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/mothur_venn	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_tree_shared	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_summary_single	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_sub_sample	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_remove_seqs	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_remove_lineage	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_remove_groups	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_rarefaction_single	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_heatmap_sim	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_dist_shared	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_dist_seqs	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_count_groups	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_cluster	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
iuc/mothur_chimera_vsearch	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
devteam/XY_Plot_1	Microbiome / 16S Microbial Analysis with mothur (extended) Microbiome / 16S Microbial Analysis with mothur (short)
nml/staramr_search	Genome Annotation / Identification of AMR genes in an assembled bacterial genome Microbiome / Antibiotic resistance detection
rnateam/bg_sortmerna	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/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	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/humann_renorm_table	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/humann_rename_table	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/humann_regroup_table	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/humann	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/graphlan_annotate	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/graphlan	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/export2graphlan	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
bebatut/combine_metaphlan2_humann2	Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
iuc/tb_profiler_profile	Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Variant Analysis / M. tuberculosis Variant Analysis
iuc/tb_variant_filter	Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters Variant Analysis / M. tuberculosis Variant Analysis
iuc/iqtree	Evolution / Phylogenetics - Back to basics Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data
iuc/fasttree	Evolution / Phylogenetics - Back to basics Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
nml/metaspades	Assembly / Assembly of metagenomic sequencing data Microbiome / Assembly of metagenomic sequencing data
iuc/ngsutils_bam_filter	Assembly / Assembly of metagenomic sequencing data Microbiome / Assembly of metagenomic sequencing data
iuc/megahit_contig2fastg	Assembly / Assembly of metagenomic sequencing data Microbiome / Assembly of metagenomic sequencing data
iuc/coverm_contig	Assembly / Assembly of metagenomic sequencing data Microbiome / Assembly of metagenomic sequencing data
devteam/bamtools	Assembly / Assembly of metagenomic sequencing data Microbiome / Assembly of metagenomic sequencing data
iuc/medaka_consensus_pipeline	Assembly / Large genome assembly and polishing Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
bgruening/racon	Assembly / Large genome assembly and polishing Microbiome / Antibiotic resistance detection
barchart_gnuplot	Assembly / Large genome assembly and polishing Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
devteam/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
iuc/chromeister	Assembly / Genome Assembly Quality Control Genome Annotation / From small to large-scale genome comparison
iuc/gfa_to_fa	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step Microbiome / Antibiotic resistance detection
iuc/pretext_snapshot	Assembly / ERGA post-assembly QC Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
iuc/pretext_map	Assembly / ERGA post-assembly QC Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
iuc/bellerophon	Assembly / ERGA post-assembly QC Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
bgruening/cp_save_images	Imaging / Object tracking using CellProfiler Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_measure_object_size_shape	Imaging / Object tracking using CellProfiler Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_measure_object_intensity	Imaging / Object tracking using CellProfiler Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_identify_primary_objects	Imaging / Object tracking using CellProfiler Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_export_to_spreadsheet	Imaging / Object tracking using CellProfiler Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_common	Imaging / Object tracking using CellProfiler Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_cellprofiler	Imaging / Object tracking using CellProfiler Imaging / Nucleoli segmentation and feature extraction using CellProfiler
imgteam/ip_binary_to_labelimage	Imaging / Analyse HeLa fluorescence siRNA screen Imaging / Introduction to Image Analysis using Galaxy
imgteam/ip_filter_standard	Imaging / Analyse HeLa fluorescence siRNA screen Imaging / Introduction to Image Analysis using Galaxy
imgteam/ip_threshold	Imaging / Analyse HeLa fluorescence siRNA screen Imaging / Introduction to Image Analysis using Galaxy
galaxyp/pepquery2	Microbiome / Clinical Metaproteomics 3: Verification Proteomics / Clinical Metaproteomics 3: Verification
galaxyp/metanovo	Microbiome / Clinical Metaproteiomics 1: Database-Generation Proteomics / Clinical Metaproteiomics 1: Database-Generation
galaxyp/cardinal_data_exporter	Metabolomics / Mass spectrometry imaging: Examining the spatial distribution of analytes Proteomics / Mass spectrometry imaging: Loading and exploring MSI data
galaxyp/ident_params	Microbiome / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 2: Discovery
galaxyp/fasta_cli	Microbiome / Clinical Metaproteomics 2: Discovery Proteomics / Clinical Metaproteomics 2: Discovery
galaxyp/metaquantome_viz	Proteomics / metaQuantome 2: Function Proteomics / metaQuantome 3: Taxonomy
galaxyp/metaquantome_stat	Proteomics / metaQuantome 2: Function Proteomics / metaQuantome 3: Taxonomy
galaxyp/metaquantome_sample	Proteomics / metaQuantome 2: Function Proteomics / metaQuantome 3: Taxonomy
galaxyp/metaquantome_filter	Proteomics / metaQuantome 2: Function Proteomics / metaQuantome 3: Taxonomy
galaxyp/metaquantome_expand	Proteomics / metaQuantome 2: Function Proteomics / metaQuantome 3: Taxonomy
galaxyp/metaquantome_db	Proteomics / metaQuantome 2: Function Proteomics / metaQuantome 3: Taxonomy
proteore/Jvenn	Proteomics / Biomarker candidate identification Proteomics / Annotating a protein list identified by LC-MS/MS experiments
proteore/retrieve_from_hpa	Proteomics / Biomarker candidate identification Proteomics / Annotating a protein list identified by LC-MS/MS experiments
proteore/IDconverter	Proteomics / Biomarker candidate identification Proteomics / Annotating a protein list identified by LC-MS/MS experiments
proteore/MQoutputfilter	Proteomics / Biomarker candidate identification Proteomics / Annotating a protein list identified by LC-MS/MS experiments
proteore/rna_abbased_data	Proteomics / Biomarker candidate identification Proteomics / Annotating a protein list identified by LC-MS/MS experiments
galaxyp/XTandemAdapter	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/TextExporter	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/PeptideIndexer	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/IDScoreSwitcher	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/IDPosteriorErrorProbability	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/FileInfo	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/FidoAdapter	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/FalseDiscoveryRate	Proteomics / Peptide and Protein ID using OpenMS tools Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
bgruening/uniprot	Proteomics / MaxQuant and MSstats for the analysis of label-free data Proteomics / Secretome Prediction
jay/pdaug_sequence_property_based_descriptors	Proteomics / Machine Learning Modeling of Anticancer Peptides Proteomics / Peptide Library Data Analysis
jay/pdaug_merge_dataframes	Proteomics / Machine Learning Modeling of Anticancer Peptides Proteomics / Peptide Library Data Analysis
jay/pdaug_basic_plots	Proteomics / Machine Learning Modeling of Anticancer Peptides Proteomics / Peptide Library Data Analysis
jay/pdaug_addclasslabel	Proteomics / Machine Learning Modeling of Anticancer Peptides Proteomics / Peptide Library Data Analysis
iuc/sqlite_to_tabular	Proteomics / Metaproteomics tutorial Proteomics / Proteogenomics 1: Database Creation
comp1	Introduction to Galaxy Analyses / Galaxy Basics for genomics Proteomics / Secretome Prediction
iuc/gtftobed12	Transcriptomics / Genome-wide alternative splicing analysis Transcriptomics / Reference-based RNA-Seq data analysis
bgruening/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	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	Microbiome / Analyses of metagenomics data - The global picture Microbiome / 16S Microbial Analysis with mothur (extended)
iuc/mothur_align_seqs	Microbiome / Analyses of metagenomics data - The global picture Microbiome / 16S Microbial Analysis with mothur (extended)
devteam/picard_MergeSamFiles	Genome Annotation / Genome annotation with Funannotate Variant Analysis / Calling variants in non-diploid systems
devteam/ncbi_blastx_wrapper	Sequence analysis / NCBI BLAST+ against the MAdLand
interactive_tool_qgis	Ecology / QGIS Web Feature Services
bgruening/graphicsmagick_image_convert	Using Galaxy and Managing your Data / Creating high resolution images of Galaxy Workflows
iuc/vapor	Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data
iuc/bamtools_split_ref	Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data
iuc/cnv_vcf2json	Variant Analysis / Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons
iuc/cnv_phenopacket	Variant Analysis / Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons
iuc/beacon2_import	Variant Analysis / Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons
iuc/chopin2	Statistics and machine learning / Supervised Learning with Hyperdimensional Computing
marie-tremblay-metatoul/normalization	Metabolomics / Mass spectrometry: LC-MS data processing
ethevenot/Multivariate	Metabolomics / Mass spectrometry: LC-MS data processing
ebi-gxa/seurat_scale_data	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_run_umap	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_run_pca	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_plot	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_normalise_data	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_find_variable_genes	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_find_neighbours	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_find_markers	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_find_clusters	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
ebi-gxa/seurat_filter_cells	Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat
iuc/checkm_lineage_wf	Microbiome / Binning of metagenomic sequencing data
iuc/fastq_dump	Using Galaxy and Managing your Data / SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis
iuc/jq	Using Galaxy and Managing your Data / SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis
devteam/fastq_to_fasta_python	Using Galaxy and Managing your Data / SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis
melpetera/idchoice	Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
lecorguille/abims_xcms_summary	Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
lecorguille/xcms_export_samplemetadata	Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS
devteam/data_manager_fetch_genome_all_fasta_dbkey	Galaxy Server administration / Reference Data with Data Managers
devteam/bwa_mem_index_builder_data_manager	Galaxy Server administration / Reference Data with Data Managers
iuc/pycoqc	Sequence analysis / Quality Control
iuc/fastqe	Sequence analysis / Quality Control
iuc/seqtk_trimfq	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
iuc/seqtk_mergepe	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
iuc/qiime_align_seqs	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
iuc/mothur_degap_seqs	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
ecology/aligned_to_consensus	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
ecology/ab1_fastq_converter	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
devteam/cshl_fastx_reverse_complement	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
devteam/cshl_fastq_to_fasta	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
devteam/fastq_masker_by_quality	Sequence analysis / Clean and manage Sanger sequences from raw files to aligned consensus
richard-burhans/ncbi_fcs_adaptor	Sequence analysis / Screening assembled genomes for contamination using NCBI FCS
iuc/ncbi_fcs_gx	Sequence analysis / Screening assembled genomes for contamination using NCBI FCS
iuc/gecko	Genome Annotation / From small to large-scale genome comparison
iuc/compleasm	Genome Annotation / Genome annotation with Helixer
genouest/helixer	Genome Annotation / Genome annotation with Helixer
iuc/red	Genome Annotation / Masking repeats with RepeatMasker
iuc/bedtools_maskfastabed	Genome Annotation / Masking repeats with RepeatMasker
csbl/repeatmodeler	Genome Annotation / Masking repeats with RepeatMasker
iuc/ncbi_acc_download	Genome Annotation / Secondary metabolite discovery
iuc/bp_genbank2gff3	Genome Annotation / Secondary metabolite discovery
cpt/edu.tamu.cpt.gff3.customGbkToGff	Genome Annotation / Secondary metabolite discovery
bgruening/ctb_simsearch	Genome Annotation / Secondary metabolite discovery
bgruening/openbabel_remDuplicates	Genome Annotation / Secondary metabolite discovery
bgruening/antismash	Genome Annotation / Secondary metabolite discovery
iuc/funannotate_compare	Genome Annotation / Genome annotation with Funannotate
iuc/funannotate_annotate	Genome Annotation / Genome annotation with Funannotate
iuc/aegean_parseval	Genome Annotation / Genome annotation with Funannotate
iuc/rapidnj	Genome Annotation / Comparative gene analysis in unannotated genomes
iuc/orfipy	Genome Annotation / Comparative gene analysis in unannotated genomes
bgruening/bg_diamond_view	Genome Annotation / Comparative gene analysis in unannotated genomes
bgruening/bg_diamond_makedb	Genome Annotation / Comparative gene analysis in unannotated genomes
iuc/snap_training	Genome Annotation / Genome annotation with Maker
bgruening/augustus_training	Genome Annotation / Genome annotation with Maker
gga/list_organism	Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes)
gga/create_account	Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes)
iuc/feelnc	Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc
Extract_features1	Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc
iuc/plasmidfinder	Genome Annotation / Bacterial Genome Annotation
iuc/isescan	Genome Annotation / Bacterial Genome Annotation
iuc/integron_finder	Genome Annotation / Bacterial Genome Annotation
simon-gladman/fasta-stats	Genome Annotation / Genome annotation with Maker (short)
iuc/mageck_test	Genome Annotation / CRISPR screen analysis
iuc/mageck_mle	Genome Annotation / CRISPR screen analysis
iuc/mageck_count	Genome Annotation / CRISPR screen analysis
ecology/cb_ivr	Ecology / Champs blocs indicators
ecology/cb_div	Ecology / Champs blocs indicators
ecology/cb_dissim	Ecology / Champs blocs indicators
cb_qecb	Ecology / Champs blocs indicators
cb_ivr	Ecology / Champs blocs indicators
cb_eco	Ecology / Champs blocs indicators
ecology/ecoregion_taxa_seeker	Ecology / Ecoregionalization workflow tutorial
ecology/ecoregion_GeoNearestNeighbor	Ecology / Ecoregionalization workflow tutorial
ecology/ecoregion_eco_map	Ecology / Ecoregionalization workflow tutorial
ecology/ecoregion_cluster_estimate	Ecology / Ecoregionalization workflow tutorial
ecology/ecoregion_clara_cluster	Ecology / Ecoregionalization workflow tutorial
ecology/ecoregion_brt_analysis	Ecology / Ecoregionalization workflow tutorial
ecology/pampa_presabs	Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite
ecology/pampa_plotglm	Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite
ecology/pampa_glmsp	Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite
ecology/pampa_glmcomm	Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite
ecology/pampa_communitymetrics	Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite
interactive_tool_metashrimps	Ecology / Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS
ecology/tool_anonymization	Ecology / Biodiversity data exploration
ecology/ecology_stat_presence_abs	Ecology / Biodiversity data exploration
ecology/ecology_presence_abs_abund	Ecology / Biodiversity data exploration
ecology/ecology_link_between_var	Ecology / Biodiversity data exploration
ecology/ecology_homogeneity_normality	Ecology / Biodiversity data exploration
ecology/ecology_beta_diversity	Ecology / Biodiversity data exploration
mnhn65mo/tab2csv_R	Ecology / Regional GAM
mnhn65mo/flight-curve	Ecology / Regional GAM
mnhn65mo/csv2tab_R	Ecology / Regional GAM
ecology/regionalgam_plot_trend	Ecology / Regional GAM
ecology/regionalgam_gls	Ecology / Regional GAM
ecology/regionalgam_glmmpql	Ecology / Regional GAM
ecology/regionalgam_flight_curve	Ecology / Regional GAM
ecology/regionalgam_autocor_acf	Ecology / Regional GAM
ecology/regionalgam_ab_index	Ecology / Regional GAM
mergeCols1	Ecology / Regional GAM
kellrott/regex_replace	Ecology / RAD-Seq Reference-based data analysis
iuc/stacks_refmap	Ecology / RAD-Seq Reference-based data analysis
devteam/bwa_wrapper	Ecology / RAD-Seq Reference-based data analysis
iuc/prodigal	Ecology / Marine Omics identifying biosynthetic gene clusters
ecology/sanntis_marine	Ecology / Marine Omics identifying biosynthetic gene clusters
ecology/SanntiS_marine	Ecology / Marine Omics identifying biosynthetic gene clusters
interactive_tool_wallace	Ecology / Species distribution modeling
padge/phykit_alignment_based	Ecology / Preparing genomic data for phylogeny reconstruction
padge/clipkit	Ecology / Preparing genomic data for phylogeny reconstruction
iuc/proteinortho_grab_proteins	Ecology / Preparing genomic data for phylogeny reconstruction
iuc/proteinortho	Ecology / Preparing genomic data for phylogeny reconstruction
bgruening/glimmer_gbk_to_orf	Ecology / Preparing genomic data for phylogeny reconstruction
ecology/srs_spectral_indices	Ecology / Sentinel 2 biodiversity
ecology/srs_process_data	Ecology / Sentinel 2 biodiversity
ecology/srs_preprocess_s2	Ecology / Sentinel 2 biodiversity
ecology/srs_pca	Ecology / Sentinel 2 biodiversity
ecology/srs_global_indices	Ecology / Sentinel 2 biodiversity
ecology/srs_diversity_maps	Ecology / Sentinel 2 biodiversity
interactive_tool_metashark	Ecology / Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities
ecology/gdal_ogr2ogr	Ecology / Cleaning GBIF data for the use in Ecology
ecology/obisindicators	Ecology / Obis marine indicators
iuc/stacks_genotypes	Ecology / RAD-Seq to construct genetic maps
interactive_tool_holoviz	Ecology / From NDVI data with OpenEO to time series visualisation with Holoviews
iuc/obi_uniq	Ecology / Metabarcoding/eDNA through Obitools
iuc/obi_tab	Ecology / Metabarcoding/eDNA through Obitools
iuc/obi_stat	Ecology / Metabarcoding/eDNA through Obitools
iuc/obi_ngsfilter	Ecology / Metabarcoding/eDNA through Obitools
iuc/obi_illumina_pairend	Ecology / Metabarcoding/eDNA through Obitools
iuc/obi_grep	Ecology / Metabarcoding/eDNA through Obitools
iuc/obi_clean	Ecology / Metabarcoding/eDNA through Obitools
iuc/obi_annotate	Ecology / Metabarcoding/eDNA through Obitools
climate/cdo_operations	Ecology / Visualization of Climate Data using NetCDF xarray Map Plotting
iuc/ena_upload	Using Galaxy and Managing your Data / Submitting sequence data to ENA
ieguinoa/ena_webin_cli	Using Galaxy and Managing your Data / Submitting sequence data to ENA
bgruening/tp_tac	Using Galaxy and Managing your Data / Creating, Editing and Importing Galaxy Workflows
iuc/galaxy_intermine_exchange	Using Galaxy and Managing your Data / InterMine integration with Galaxy
intermine	Using Galaxy and Managing your Data / InterMine integration with Galaxy
tduigou/rpthermo	Synthetic Biology / Evaluating and ranking a set of pathways based on multiple metrics
tduigou/rpscore	Synthetic Biology / Evaluating and ranking a set of pathways based on multiple metrics
tduigou/rpranker	Synthetic Biology / Evaluating and ranking a set of pathways based on multiple metrics
iuc/rpfba	Synthetic Biology / Evaluating and ranking a set of pathways based on multiple metrics
tduigou/selenzy-wrapper	Synthetic Biology / Designing plasmids encoding predicted pathways by using the BASIC assembly method
tduigou/rpbasicdesign	Synthetic Biology / Designing plasmids encoding predicted pathways by using the BASIC assembly method
tduigou/dnabot	Synthetic Biology / Designing plasmids encoding predicted pathways by using the BASIC assembly method
tduigou/rrparser	Synthetic Biology / Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
tduigou/rpextractsink	Synthetic Biology / Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
tduigou/rpcompletion	Synthetic Biology / Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
tduigou/rp2paths	Synthetic Biology / Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
tduigou/retropath2	Synthetic Biology / Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
tduigou/get_sbml_model	Synthetic Biology / Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
wolma/mimodd_vcf_filter	Variant Analysis / Mapping and molecular identification of phenotype-causing mutations
wolma/mimodd_varreport	Variant Analysis / Mapping and molecular identification of phenotype-causing mutations
wolma/mimodd_varextract	Variant Analysis / Mapping and molecular identification of phenotype-causing mutations
wolma/mimodd_varcall	Variant Analysis / Mapping and molecular identification of phenotype-causing mutations
wolma/mimodd_map	Variant Analysis / Mapping and molecular identification of phenotype-causing mutations
iuc/control_freec	Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC
bgruening/tp_text_file_with_recurring_lines	Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC
iuc/varscan_somatic	Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
iuc/gemini_annotate	Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
bgruening/bg_column_arrange_by_header	Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs
iuc/nextclade	Variant Analysis / Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
iuc/gene_iobio_display_generation_iframe	Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
iuc/pyega3	Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
iuc/bcftools_merge	Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
CONVERTER_uncompressed_to_gz	Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP
iuc/tbvcfreport	Variant Analysis / M. tuberculosis Variant Analysis
iuc/mosdepth	Variant Analysis / M. tuberculosis Variant Analysis
iuc/jvarkit_wgscoverageplotter	Variant Analysis / M. tuberculosis Variant Analysis
devteam/EMBOSS:%20seqret84	Variant Analysis / M. tuberculosis Variant Analysis
devteam/EMBOSS: seqret84	Variant Analysis / M. tuberculosis Variant Analysis
iuc/gemini_db_info	Variant Analysis / Calling variants in diploid systems
devteam/vcfallelicprimitives	Variant Analysis / Calling variants in diploid systems
wolma/mimodd_info	Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
iuc/fatovcf	Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
iuc/samtools_merge	Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
iuc/ivar_trim	Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data
devteam/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
muon-spectroscopy-computational-project/pm_uep_opt	Materials Science / Finding the muon stopping site with pymuon-suite in Galaxy
muon-spectroscopy-computational-project/pm_muairss_read	Materials Science / Finding the muon stopping site with pymuon-suite in Galaxy
bgruening/plotly_parallel_coordinates_plot	Statistics and machine learning / Age prediction using machine learning
bgruening/sklearn_nn_classifier	Statistics and machine learning / Classification in Machine Learning
vijay/pancancer_within_disease_analysis	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_visualize_decisions	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_targene_summary_figures	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_targene_pharmacology	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_targene_cell_line_predictions	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_pathway_count_heatmaps	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_map_mutation_class	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_external_sample_status_prediction	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_compare_within_models	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_classifier	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_apply_weights	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
vijay/pancancer_alternative_genes_pathwaymapper	Statistics and machine learning / PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
iuc/iwtomics_testandplot	Statistics and machine learning / Interval-Wise Testing for omics data
iuc/iwtomics_plotwithscale	Statistics and machine learning / Interval-Wise Testing for omics data
iuc/iwtomics_loadandplot	Statistics and machine learning / Interval-Wise Testing for omics data
toolshed.g2.bx.psu.edu/paulo_lyra_jr	Statistics and machine learning / Train and Test a Deep learning image classifier with Galaxy-Ludwig
paulo_lyra_jr/ludwig_experiment	Statistics and machine learning / Train and Test a Deep learning image classifier with Galaxy-Ludwig
iuc/pubmed_by_queries	Statistics and machine learning / Text-mining with the SimText toolset
iuc/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
galaxyp/cardinal_spectra_plots	Metabolomics / Mass spectrometry imaging: Examining the spatial distribution of analytes
galaxyp/cardinal_filtering	Metabolomics / Mass spectrometry imaging: Examining the spatial distribution of analytes
recetox/waveica	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
recetox/riassigner	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
recetox/ramclustr_define_experiment	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
recetox/ramclustr	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
recetox/matchms_similarity	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
recetox/matchms_formatter	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
recetox/matchms_filtering	Metabolomics / Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
fgiacomoni/wsdl_hmdb	Metabolomics / Mass spectrometry: LC-MS analysis
ethevenot/Univariate	Metabolomics / Mass spectrometry: LC-MS analysis
recetox/xtb_molecular_optimization	Metabolomics / Predicting EI+ mass spectra with QCxMS
recetox/qcxms_production_run	Metabolomics / Predicting EI+ mass spectra with QCxMS
recetox/qcxms_neutral_run	Metabolomics / Predicting EI+ mass spectra with QCxMS
recetox/qcxms_getres	Metabolomics / Predicting EI+ mass spectra with QCxMS
bgruening/ctb_im_conformers	Metabolomics / Predicting EI+ mass spectra with QCxMS
galaxyp/maldi_quant_preprocessing	Metabolomics / Mass spectrometry imaging: Finding differential analytes
galaxyp/maldi_quant_peak_detection	Metabolomics / Mass spectrometry imaging: Finding differential analytes
galaxyp/cardinal_segmentations	Metabolomics / Mass spectrometry imaging: Finding differential analytes
galaxyp/cardinal_preprocessing	Metabolomics / Mass spectrometry imaging: Finding differential analytes
galaxyp/cardinal_combine	Metabolomics / Mass spectrometry imaging: Finding differential analytes
galaxyp/cardinal_classification	Metabolomics / Mass spectrometry imaging: Finding differential analytes
bgruening/join_files_on_column_fuzzy	Metabolomics / Mass spectrometry imaging: Finding differential analytes
iuc/chira_quantify	Transcriptomics / RNA-RNA interactome data analysis
iuc/chira_merge	Transcriptomics / RNA-RNA interactome data analysis
iuc/chira_map	Transcriptomics / RNA-RNA interactome data analysis
iuc/chira_extract	Transcriptomics / RNA-RNA interactome data analysis
iuc/chira_collapse	Transcriptomics / RNA-RNA interactome data analysis
iuc/bedtools_bamtofastq	Transcriptomics / Differential abundance testing of small RNAs
devteam/samtool_filter2	Transcriptomics / Differential abundance testing of small RNAs
devteam/fastq_manipulation	Transcriptomics / Differential abundance testing of small RNAs
nilesh/rseqc_junction_saturation	Transcriptomics / Genome-wide alternative splicing analysis
nilesh/rseqc_junction_annotation	Transcriptomics / Genome-wide alternative splicing analysis
nilesh/rseqc_inner_distance	Transcriptomics / Genome-wide alternative splicing analysis
iuc/rna_quast	Transcriptomics / Genome-wide alternative splicing analysis
iuc/isoformswitchanalyzer	Transcriptomics / Genome-wide alternative splicing analysis
bgruening/tp_uniq_tool	Transcriptomics / Genome-wide alternative splicing analysis
bgruening/pfamscan	Transcriptomics / Genome-wide alternative splicing analysis
bgruening/cpat	Transcriptomics / Genome-wide alternative splicing analysis
iuc/fgsea	Transcriptomics / 3: RNA-seq genes to pathways
iuc/egsea	Transcriptomics / 3: RNA-seq genes to pathways
rnateam/rcas	Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
rnateam/peakachu	Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/umi_tools_dedup	Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/bedtools_slopbed	Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/bedtools_genomecoveragebed_bedgraph	Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
iuc/bctools_extract_alignment_ends	Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
rnateam/targetfinder	Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana
rnateam/rbc_mirdeep2_quantifier	Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana
rnateam/rbc_mirdeep2_mapper	Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana
peterjc/sample_seqs	Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana
iuc/heinz_visualization	Transcriptomics / Network analysis with Heinz
iuc/heinz_scoring	Transcriptomics / Network analysis with Heinz
iuc/heinz_bum	Transcriptomics / Network analysis with Heinz
iuc/heinz	Transcriptomics / Network analysis with Heinz
iuc/goslimmer	Transcriptomics / GO Enrichment Analysis
rnateam/blockclust	Transcriptomics / Small Non-coding RNA Clustering using BlockClust
rnateam/blockbuster	Transcriptomics / Small Non-coding RNA Clustering using BlockClust
devteam/samtools_sort	Transcriptomics / Small Non-coding RNA Clustering using BlockClust
iuc/trinotate	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_samples_qccheck	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_run_de_analysis	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_filter_low_expr_transcripts	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_define_clusters_by_cutting_tree	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_contig_exn50_statistic	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_analyze_diff_expr	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_align_and_estimate_abundance	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity_abundance_estimates_to_matrix	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/trinity	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/transdecoder	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
iuc/describe_samples	Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis
ebi-gxa/monocle3_topmarkers	Single Cell / Inferring single cell trajectories with Monocle3
ebi-gxa/monocle3_reduceDim	Single Cell / Inferring single cell trajectories with Monocle3
ebi-gxa/monocle3_preprocess	Single Cell / Inferring single cell trajectories with Monocle3
ebi-gxa/monocle3_plotCells	Single Cell / Inferring single cell trajectories with Monocle3
ebi-gxa/monocle3_partition	Single Cell / Inferring single cell trajectories with Monocle3
ebi-gxa/monocle3_orderCells	Single Cell / Inferring single cell trajectories with Monocle3
ebi-gxa/monocle3_learnGraph	Single Cell / Inferring single cell trajectories with Monocle3
ebi-gxa/monocle3_diffExp	Single Cell / Inferring single cell trajectories with Monocle3
ebi-gxa/hca_matrix_downloader	Single Cell / Importing files from public atlases
iuc/scater_plot_pca	Single Cell / Single-cell quality control with scater
iuc/scater_plot_dist_scatter	Single Cell / Single-cell quality control with scater
iuc/scater_filter	Single Cell / Single-cell quality control with scater
iuc/scater_create_qcmetric_ready_sce	Single Cell / Single-cell quality control with scater
iuc/umi_tools_count	Single Cell / Pre-processing of Single-Cell RNA Data
bgruening/music_compare	Single Cell / Comparing inferred cell compositions using MuSiC deconvolution
bgruening/music_inspect_eset	Single Cell / Bulk RNA Deconvolution with MuSiC
bgruening/music_deconvolution	Single Cell / Bulk RNA Deconvolution with MuSiC
ebi-gxa/scanpy_run_paga	Single Cell / Inferring single cell trajectories with Scanpy
ebi-gxa/scanpy_run_fdg	Single Cell / Inferring single cell trajectories with Scanpy
ebi-gxa/scanpy_run_dpt	Single Cell / Inferring single cell trajectories with Scanpy
ebi-gxa/scanpy_run_diffmap	Single Cell / Inferring single cell trajectories with Scanpy
ebi-gxa/scanpy_plot_trajectory	Single Cell / Inferring single cell trajectories with Scanpy
usegalaxy.eu/repos	Single Cell / Inferring single cell trajectories with Scanpy
ebi-gxa/scanpy_scale_data	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
ebi-gxa/scanpy_run_pca	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
ebi-gxa/scanpy_normalise_data	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
ebi-gxa/scanpy_find_variable_genes	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
ebi-gxa/scanpy_find_markers	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
ebi-gxa/scanpy_filter_genes	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
interactive_tool_cellxgene	Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy
iuc/column_remove_by_header	Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution
iuc/rna_starsolo	Single Cell / Pre-processing of 10X Single-Cell RNA Datasets
ebi-gxa/sceasy_convert	Single Cell / Converting between common single cell data formats
devteam/tabular_to_fastq	Single Cell / Converting between common single cell data formats
iuc/raceid_trajectory	Single Cell / Downstream Single-cell RNA analysis with RaceID
iuc/raceid_inspecttrajectory	Single Cell / Downstream Single-cell RNA analysis with RaceID
iuc/raceid_inspectclusters	Single Cell / Downstream Single-cell RNA analysis with RaceID
iuc/raceid_filtnormconf	Single Cell / Downstream Single-cell RNA analysis with RaceID
iuc/raceid_clustering	Single Cell / Downstream Single-cell RNA analysis with RaceID
raceid_trajectory	Single Cell / Downstream Single-cell RNA analysis with RaceID
raceid_inspecttrajectory	Single Cell / Downstream Single-cell RNA analysis with RaceID
raceid_inspectclusters	Single Cell / Downstream Single-cell RNA analysis with RaceID
raceid_filtnormconf	Single Cell / Downstream Single-cell RNA analysis with RaceID
raceid_clustering	Single Cell / Downstream Single-cell RNA analysis with RaceID
ebi-gxa/scanpy_regress_variable	Single Cell / Removing the effects of the cell cycle
iuc/gprofiler_gost	Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data
ebi-gxa/_salmon_kallisto_mtx_to_10x	Single Cell / Generating a single cell matrix using Alevin
ebi-gxa/_ensembl_gtf2gene_list	Single Cell / Generating a single cell matrix using Alevin
ebi-gxa/dropletutils_empty_drops	Single Cell / Generating a single cell matrix using Alevin
ebi-gxa/_dropletBarcodePlot	Single Cell / Generating a single cell matrix using Alevin
bgruening/alevin	Single Cell / Generating a single cell matrix using Alevin
iuc/sinto_fragments	Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets
iuc/sinto_barcode	Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets
iuc/episcanpy_preprocess	Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets
iuc/episcanpy_build_matrix	Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets
ebi-gxa/scanpy_parameter_iterator	Single Cell / Scanpy Parameter Iterator
iuc/snapatac2_preprocessing	Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2
iuc/snapatac2_plotting	Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2
iuc/snapatac2_peaks_and_motif	Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2
iuc/snapatac2_clustering	Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2
devteam/Cut1	Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2
iuc/idr	Epigenetics / CUT&RUN data analysis
toolshed.g2.bx.psu.edu/bgruening	Epigenetics / CUT&RUN data analysis
crs4/bwa_mem	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
bgruening/hicexplorer_hicplottads	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
bgruening/hicexplorer_hicplotmatrix	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
bgruening/hicexplorer_hicpca	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
bgruening/hicexplorer_hicmergematrixbins	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
bgruening/hicexplorer_hicfindtads	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
bgruening/hicexplorer_hiccorrectmatrix	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
bgruening/hicexplorer_hicbuildmatrix	Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
kpbioteam/minfi_analysis	Epigenetics / Infinium Human Methylation BeadChip
kpbioteam/clusterprofiler_go	Epigenetics / Infinium Human Methylation BeadChip
kpbioteam/clusterprofiler_bitr	Epigenetics / Infinium Human Methylation BeadChip
kpbioteam/chipeakanno_annopeaks	Epigenetics / Infinium Human Methylation BeadChip
bgruening/deeptools_correct_gc_bias	Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
rnateam/metilene	Epigenetics / DNA Methylation data analysis
iuc/bwameth	Epigenetics / DNA Methylation data analysis
bgruening/pileometh	Epigenetics / DNA Methylation data analysis
bgruening/deeptools_plot_profile	Epigenetics / DNA Methylation data analysis
interactive_tool_copernicus	Climate / Sentinel 5P data visualisation
ecology/xarray_netcdf2netcdf	Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools
interactive_tool_pangeo_notebook	Climate / Pangeo Notebook in Galaxy - Introduction to Xarray
climate/psy_maps	Climate / Getting your hands-on climate data
climate/cds_essential_variability	Climate / Getting your hands-on climate data
ecology/timeseries_extraction	Climate / Analyse Argo data
ecology/divand_full_analysis	Climate / Ocean's variables study
interactive_tool_divand	Climate / Ocean's variables study
climate/ctsm_fates	Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES)
iuc/circos_wiggle_to_scatter	Visualisation / Ploting a Microbial Genome with Circos
iuc/circos_interval_to_tile	Visualisation / Ploting a Microbial Genome with Circos
iuc/circos_interval_to_text	Visualisation / Ploting a Microbial Genome with Circos
iuc/circos_gc_skew	Visualisation / Ploting a Microbial Genome with Circos
gff2bed1	Visualisation / Ploting a Microbial Genome with Circos
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/mdanalysis_rdf	Computational chemistry / Analysis of molecular dynamics simulations
chemteam/mdanalysis_ramachandran_plot	Computational chemistry / Analysis of molecular dynamics simulations
chemteam/mdanalysis_distance	Computational chemistry / Analysis of molecular dynamics simulations
chemteam/mdanalysis_dihedral	Computational chemistry / Analysis of molecular dynamics simulations
xchem_pose_scoring	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/xchem_transfs_scoring	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/sucos_max_score	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/rxdock_rbdock	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/rxdock_rbcavity	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/rdock_rbdock	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/rdock_rbcavity	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/enumerate_charges	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/ctb_frankenstein_ligand	Computational chemistry / Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
bgruening/rdconf	Computational chemistry / Protein target prediction of a bioactive ligand with Align-it and ePharmaLib
bgruening/openbabel_addh	Computational chemistry / Protein target prediction of a bioactive ligand with Align-it and ePharmaLib
bgruening/ctb_alignit	Computational chemistry / Protein target prediction of a bioactive ligand with Align-it and ePharmaLib
chemteam/vmd_hbonds	Computational chemistry / High Throughput Molecular Dynamics and Analysis
chemteam/gmx_merge_topology_files	Computational chemistry / High Throughput Molecular Dynamics and Analysis
chemteam/gmx_energy	Computational chemistry / High Throughput Molecular Dynamics and Analysis
chemteam/bio3d_pca_visualize	Computational chemistry / High Throughput Molecular Dynamics and Analysis
chemteam/ambertools_acpype	Computational chemistry / High Throughput Molecular Dynamics and Analysis
bgruening/sdf_to_tab	Computational chemistry / Protein-ligand docking
bgruening/ctb_remIons	Computational chemistry / Protein-ligand docking
bgruening/ctb_remDuplicates	Computational chemistry / Protein-ligand docking
bgruening/ctb_obgrep	Computational chemistry / Protein-ligand docking
bgruening/ctb_filter	Computational chemistry / Protein-ligand docking
bgruening/ctb_compound_convert	Computational chemistry / Protein-ligand docking
bgruening/ctb_change_title	Computational chemistry / Protein-ligand docking
bgruening/fpocket	Computational chemistry / Protein-ligand docking
bgruening/ctb_online_data_fetch	Computational chemistry / Protein-ligand docking
bgruening/ctb_chemfp_nxn_clustering	Computational chemistry / Protein-ligand docking
bgruening/ctb_chemfp_butina_clustering	Computational chemistry / Protein-ligand docking
bgruening/prepare_receptor	Computational chemistry / Protein-ligand docking
bgruening/prepare_box	Computational chemistry / Protein-ligand docking
bgruening/docking	Computational chemistry / Protein-ligand docking
iuc/krakentools_beta_diversity	Microbiome / Calculating α and β diversity from microbiome taxonomic data
iuc/krakentools_alpha_diversity	Microbiome / Calculating α and β diversity from microbiome taxonomic data
iuc/samtools_depth	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/samtools_coverage	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/mlst	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/krakentools_extract_kraken_reads	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/ggplot2_heatmap	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/clair3	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/bedtools_getfastabed	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/bamtools_split_mapped	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/abricate	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
bgruening/tp_multijoin_tool	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
__FILTER_EMPTY_DATASETS__	Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
iuc/mothur_taxonomy_to_krona	Microbiome / 16S Microbial Analysis with mothur (extended)
iuc/mothur_seq_error	Microbiome / 16S Microbial Analysis with mothur (extended)
iuc/mothur_make_contigs	Microbiome / 16S Microbial Analysis with mothur (extended)
iuc/mothur_get_groups	Microbiome / 16S Microbial Analysis with mothur (extended)
iuc/phyloseq_from_dada2	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_seqCounts	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_removeBimeraDenovo	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_plotQualityProfile	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_mergePairs	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_makeSequenceTable	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_learnErrors	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_filterAndTrim	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/dada2_dada	Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2
iuc/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
earlhaminst/lotus2	Microbiome / Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2
iuc/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/datamash_reverse	Microbiome / 16S Microbial analysis with Nanopore data
iuc/PlasFlow	Microbiome / Antibiotic resistance detection
iuc/miniasm	Microbiome / Antibiotic resistance detection
mvdbeek/addName	Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters
iuc/snp_sites	Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters
iuc/snp_dists	Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters
iuc/raxml	Evolution / Tree thinking for tuberculosis evolution and epidemiology
iuc/shovill	Assembly / Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data
iuc/pilon	Assembly / Chloroplast genome assembly
iuc/seqtk_sample	Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
iuc/polypolish	Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
iuc/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/compress_file	Assembly / Assembly of the mitochondrial genome from PacBio HiFi reads
bgruening/mitohifi	Assembly / Assembly of the mitochondrial genome from PacBio HiFi reads
iuc/parse_mito_blast	Assembly / Decontamination of a genome assembly
devteam/ncbi_dustmasker_wrapper	Assembly / Decontamination of a genome assembly
simon-gladman/velvetoptimiser	Assembly / De Bruijn Graph Assembly
nml/spades	Assembly / De Bruijn Graph Assembly
iuc/circos_interval_to_tiles	Assembly / Making sense of a newly assembled genome
iuc/circos_aln_to_links	Assembly / Making sense of a newly assembled genome
iuc/bedtools_complementbed	Assembly / Making sense of a newly assembled genome
devteam/lastz_wrapper_2	Assembly / Making sense of a newly assembled genome
iuc/yahs	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
iuc/salsa	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
iuc/purge_dups	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
bgruening/hifiasm	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
bgruening/bionano_scaffold	Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
galaxy-australia/smudgeplot	Assembly / ERGA post-assembly QC
bgruening/blobtoolkit	Assembly / ERGA post-assembly QC
interactive_tool_blobtoolkit	Assembly / ERGA post-assembly QC
bgruening/cp_track_objects	Imaging / Object tracking using CellProfiler
bgruening/cp_tile	Imaging / Object tracking using CellProfiler
bgruening/cp_overlay_outlines	Imaging / Object tracking using CellProfiler
bgruening/cp_color_to_gray	Imaging / Object tracking using CellProfiler
iuc/idr_download_by_ids	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_relate_objects	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_measure_texture	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_measure_image_quality	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_measure_image_intensity	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_measure_image_area_occupied	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_measure_granularity	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_mask_image	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_image_math	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_gray_to_color	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_enhance_or_suppress_features	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_display_data_on_image	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
bgruening/cp_convert_objects_to_image	Imaging / Nucleoli segmentation and feature extraction using CellProfiler
imgteam/ip_2d_filter_segmentation_by_features	Imaging / Analyse HeLa fluorescence siRNA screen
imgteam/ip_2d_feature_extraction	Imaging / Analyse HeLa fluorescence siRNA screen
imgteam/ip_overlay_images	Imaging / Introduction to Image Analysis using Galaxy
imgteam/ip_imageinfo	Imaging / Introduction to Image Analysis using Galaxy
imgteam/ip_count_objects	Imaging / Introduction to Image Analysis using Galaxy
imgteam/ip_histogram_equalization	Imaging / Introduction to Image Analysis using Galaxy
perssond/quantification	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
perssond/unet_coreograph	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
perssond/basic_illumination	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
perssond/ashlar	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
imgteam/ip_convertimage	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
goeckslab/vitessce_spatial	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
goeckslab/scimap_phenotyping	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
goeckslab/scimap_mcmicro_to_anndata	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
goeckslab/rename_tiff_channels	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
goeckslab/mesmer	Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME
imgteam/ip_spot_detection_2d	Imaging / Tracking of mitochondria and capturing mitoflashes
imgteam/ip_points_association_nn	Imaging / Tracking of mitochondria and capturing mitoflashes
imgteam/ip_curve_fitting	Imaging / Tracking of mitochondria and capturing mitoflashes
jay/pdaug_ml_models	Proteomics / Machine Learning Modeling of Anticancer Peptides
galaxyp/flashlfq	Proteomics / metaQuantome 1: Data creation
proteore/reactome_analysis	Proteomics / Annotating a protein list identified by LC-MS/MS experiments
proteore/cluter_profiler	Proteomics / Annotating a protein list identified by LC-MS/MS experiments
galaxyp/translate_bed	Proteomics / Proteogenomics 1: Database Creation
galaxyp/gffcompare_to_bed	Proteomics / Proteogenomics 1: Database Creation
galaxyp/custom_pro_db	Proteomics / Proteogenomics 1: Database Creation
galaxyp/bed_to_protein_map	Proteomics / Proteogenomics 1: Database Creation
galaxyp/mz_to_sqlite	Proteomics / Proteogenomics 2: Database Search
galaxyp/ProteinQuantifier	Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/MultiplexResolver	Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/IDMapper	Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/IDConflictResolver	Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
galaxyp/FeatureFinderMultiplex	Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
PeakPickerHiRes	Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker
FileConverter	Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker
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/encyclopedia_searchtolib	Proteomics / EncyclopeDIA
galaxyp/encyclopedia_quantify	Proteomics / EncyclopeDIA
galaxyp/DecoyDatabase	Proteomics / Protein FASTA Database Handling
galaxyp/peptide_genomic_coordinate	Proteomics / Proteogenomics 3: Novel peptide analysis
galaxyp/pep_pointer	Proteomics / Proteogenomics 3: Novel peptide analysis
galaxyp/TargetedFileConverter	Proteomics / Library Generation for DIA Analysis
galaxyp/OpenSwathDecoyGenerator	Proteomics / Library Generation for DIA Analysis
galaxyp/OpenSwathAssayGenerator	Proteomics / Library Generation for DIA Analysis
galaxyp/diapysef	Proteomics / Library Generation for DIA Analysis
proteore/prot_features	Proteomics / Biomarker candidate identification
proteore/retr_pepatlas1	Proteomics / Biomarker candidate identification
galaxyp/PeakPickerHiRes	Proteomics / Peptide and Protein ID using OpenMS tools
galaxyp/MSGFPlusAdapter	Proteomics / Peptide and Protein ID using OpenMS tools
galaxyp/IDMerger	Proteomics / Peptide and Protein ID using OpenMS tools
galaxyp/IDFilter	Proteomics / Peptide and Protein ID using OpenMS tools
galaxyp/ConsensusID	Proteomics / Peptide and Protein ID using OpenMS tools
galaxyp/pyprophet_score	Proteomics / DIA Analysis using OpenSwathWorkflow
galaxyp/pyprophet_protein	Proteomics / DIA Analysis using OpenSwathWorkflow
galaxyp/pyprophet_peptide	Proteomics / DIA Analysis using OpenSwathWorkflow
galaxyp/pyprophet_merge	Proteomics / DIA Analysis using OpenSwathWorkflow
galaxyp/pyprophet_export	Proteomics / DIA Analysis using OpenSwathWorkflow
galaxyp/OpenSwathWorkflow	Proteomics / DIA Analysis using OpenSwathWorkflow
peterjc/wolf_psort	Proteomics / Secretome Prediction
term_id_vs_term_name	Proteomics / Secretome Prediction
get_subontology_from	Proteomics / Secretome Prediction
jay/pdaug_tsvtofasta	Proteomics / Peptide Library Data Analysis
jay/pdaug_peptide_sequence_analysis	Proteomics / Peptide Library Data Analysis
jay/pdaug_peptide_data_access	Proteomics / Peptide Library Data Analysis
jay/pdaug_fishers_plot	Proteomics / Peptide Library Data Analysis
iuc/bedtools_mergebed	Epigenetics / Formation of the Super-Structures on the Inactive X
iuc/transit_gumbel	Genome Annotation / Essential genes detection with Transposon insertion sequencing
iuc/gff_to_prot	Genome Annotation / Essential genes detection with Transposon insertion sequencing
devteam/bowtie_wrapper	Genome Annotation / Essential genes detection with Transposon insertion sequencing
bgruening/bg_find_subsequences	Genome Annotation / Essential genes detection with Transposon insertion sequencing
nick/sequence_content_trimmer	Variant Analysis / Calling very rare variants
nick/make_families	Variant Analysis / Calling very rare variants
nick/dunovo	Variant Analysis / Calling very rare variants
nick/correct_barcodes	Variant Analysis / Calling very rare variants
nick/align_families	Variant Analysis / Calling very rare variants
nick/allele_counts_1	Variant Analysis / Calling very rare variants
blankenberg/naive_variant_caller	Variant Analysis / Calling very rare variants
iuc/pathview	Transcriptomics / Reference-based RNA-Seq data analysis
iuc/length_and_gc_content	Transcriptomics / Reference-based RNA-Seq data analysis
iuc/dexseq_count	Transcriptomics / Reference-based RNA-Seq data analysis
iuc/dexseq	Transcriptomics / Reference-based RNA-Seq data analysis
iuc/deg_annotate	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	Statistics and machine learning / Clustering in Machine Learning
devteam/velveth	Assembly / An Introduction to Genome Assembly
devteam/velvetg	Assembly / An Introduction to Genome Assembly
saskia-hiltemann/krona-text	Microbiome / Analyses of metagenomics data - The global picture
iuc/mothur_make_group	Microbiome / Analyses of metagenomics data - The global picture
iuc/metaphlan2krona	Microbiome / Analyses of metagenomics data - The global picture
iuc/metaphlan2	Microbiome / Analyses of metagenomics data - The global picture
iuc/humann2_renorm_table	Microbiome / Analyses of metagenomics data - The global picture
iuc/humann2_regroup_table	Microbiome / Analyses of metagenomics data - The global picture
iuc/humann2	Microbiome / Analyses of metagenomics data - The global picture
devteam/cshl_fastq_quality_filter	Introduction to Galaxy Analyses / A short introduction to Galaxy
devteam/get_flanks1	Introduction to Galaxy Analyses / From peaks to genes
CONVERTER_interval_to_bed_0	Introduction to Galaxy Analyses / From peaks to genes
devteam/vcffilter2	Variant Analysis / Calling variants in non-diploid systems
devteam/vcf2tsv	Variant Analysis / Calling variants in non-diploid systems