Expertise: High Performance Computing, Scientific workflow developement, Software Engineering, astronomy
Tools: Galaxy, Jupyter notebook, Python, Workflows, Git
Teams: IBISBA Workflows, EOSC-Life WP3, NGFF Tools, Euro-BioImaging, AI4Life OC
Organizations: Unspecified, EMBL-EBI, Euro-BioImaging

Expertise: image analysis
Teams: Galaxy Training Network
Organizations: Erasmus University Medical Centre

Expertise: Genomics, amplicon analysis, Microbiology
Tools: Galaxy
Post-doc at ErasmusMC, Galaxy Training Network (GTN) Lead
Expertise: Bioinformatics, Computer Science, Data Management, Genetics, Genomics, Machine Learning, Metagenomics, NGS, Scientific workflow developement, Software Engineering
Tools: Databases, Galaxy, Genomics, Jupyter notebook, Machine Learning, Nextflow, nf-core, PCR, Perl, Python, R, rtPCR, Snakemake, Transcriptomics, Virology, Web, Web services, Workflows
Dad, husband and PhD. Scientist, technologist and engineer. Bibliophile. Philomath. Passionate about science, medicine, research, computing and all things geeky!
Teams: Bioinformatics Innovation Lab
Organizations: Pondicherry University

Expertise: Bioinformatics, Systems Biology, Machine Learning
Tools: Galaxy, Cytoscape, Databases, Jupyter notebook, R, Python
Ph.D. Student at Department of Bioinformatics, Pondicherry University
Teams: GalaxyProject SARS-CoV-2
Organizations: Earlham Institute

Expertise: Bioinformatics
Tools: Galaxy
Research Director @ INRAe
Associated Tutorial
This workflows is part of the tutorial Deep Learning (Part 2) - Recurrent neural networks (RNN), available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Kaivan Kamali
Tutorial Author(s): [Kaivan ...
Final output is a table of Taxa and how many sequences aligned with them. This table can be used to then visualize via a pie chart.
Associated Tutorial
This workflows is part of the tutorial Taxonomic Analysis of eDNA, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Age prediction using machine learning
Associated Tutorial
This workflows is part of the tutorial Age prediction using machine learning, available in the GTN
Thanks to...
Tutorial Author(s): Ekaterina Polkh, [Anup ...
Age prediction using machine learning
Associated Tutorial
This workflows is part of the tutorial Age prediction using machine learning, available in the GTN
Thanks to...
Tutorial Author(s): Ekaterina Polkh, [Anup ...
Basics of machine learning
Associated Tutorial
This workflows is part of the tutorial Basics of machine learning, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Anup ...
Interval-Wise Testing for omics data
Associated Tutorial
This workflows is part of the tutorial Interval-Wise Testing for omics data, available in the GTN
Thanks to...
Tutorial Author(s): Marzia A Cremona, Fabio Cumbo ...
Visualization of RNA-Seq results with heatmap2
Associated Tutorial
This workflows is part of the tutorial Visualization of RNA-Seq results with heatmap2, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Tutorial ...
Identify upregulated miRNAS and analyze potential targets in downregulated genes.
Associated Tutorial
This workflows is part of the tutorial Whole transcriptome analysis of Arabidopsis thaliana, available in the GTN
Thanks to...
Tutorial Author(s): Cristóbal Gallardo, ...
roscoff hackathon
Associated Tutorial
This workflows is part of the tutorial De novo transcriptome assembly, annotation, and differential expression analysis, available in the GTN
Thanks to...
Tutorial Author(s): Anthony Bretaudeau, [Gildas Le ...
Reference-based RNA-Seq data analysis
Associated Tutorial
This workflows is part of the tutorial Reference-based RNA-Seq data analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Bérénice Batut, ...
Associated Tutorial
This workflows is part of the tutorial From NDVI data with OpenEO to time series visualisation with Holoviews, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Marie Jossé
**Tutorial ...
Reference-based RNA-Seq data analysis
Associated Tutorial
This workflows is part of the tutorial Reference-based RNA-Seq data analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Bérénice Batut, ...
Associated Tutorial
This workflows is part of the tutorial From NDVI data with OpenEO to time series visualisation with Holoviews, available in the GTN
Thanks to...
Workflow Author(s): Marie Jossé
Tutorial Author(s): Marie Josse
Tutorial Contributor(s): [Helena ...
Reference-based RNA-Seq data analysis
Associated Tutorial
This workflows is part of the tutorial Reference-based RNA-Seq data analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Uses ...
Regional GAM
Associated Tutorial
This workflows is part of the tutorial Regional GAM, available in the GTN
Thanks to...
Tutorial Author(s): Clara Urfer, Elisa Michon, [Yvan Le ...
Visualization of RNA-Seq results with Volcano Plot
Associated Tutorial
This workflows is part of the tutorial Visualization of RNA-Seq results with Volcano Plot, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes ...
Associated Tutorial
This workflows is part of the tutorial RNA-Seq data analysis, clustering and visualisation tutorial, available in the GTN
Thanks to...
Tutorial Author(s): Peter-Bram 't Hoen, [Casper de ...
Regional GAM
Associated Tutorial
This workflows is part of the tutorial Regional GAM, available in the GTN
Thanks to...
Tutorial Author(s): Clara Urfer, Elisa Michon, [Yvan Le ...
Regional GAM
Associated Tutorial
This workflows is part of the tutorial Regional GAM, available in the GTN
Thanks to...
Tutorial Author(s): Clara Urfer, Elisa Michon, [Yvan Le ...
CLIP-Seq data analysis from pre-processing to motif detection
Associated Tutorial
This workflows is part of the tutorial CLIP-Seq data analysis from pre-processing to motif detection, available in the GTN
Thanks to...
Tutorial Author(s): Florian Heyl, [Daniel ...
Regional GAM
Associated Tutorial
This workflows is part of the tutorial Regional GAM, available in the GTN
Thanks to...
Tutorial Author(s): Clara Urfer, Elisa Michon, [Yvan Le ...
RNA-seq counts to genes
Associated Tutorial
This workflows is part of the tutorial 2: RNA-seq counts to genes, available in the GTN
Thanks to...
Tutorial Author(s): Maria Doyle, Belinda Phipson, ...
Metabarcoding/eDNA through Obitools
Associated Tutorial
This workflows is part of the tutorial Metabarcoding/eDNA through Obitools, available in the GTN
Thanks to...
Tutorial Author(s): Coline Royaux, [Olivier ...
Running molecular dynamics simulations using NAMD
Associated Tutorial
This workflows is part of the tutorial Running molecular dynamics simulations using NAMD, available in the GTN
Thanks to...
Tutorial Author(s): Christopher Barnett, ...
Running molecular dynamics simulations using NAMD
Associated Tutorial
This workflows is part of the tutorial Running molecular dynamics simulations using NAMD, available in the GTN
Thanks to...
Tutorial Author(s): Christopher Barnett, ...
RNA-seq genes to pathways
Associated Tutorial
This workflows is part of the tutorial 3: RNA-seq genes to pathways, available in the GTN
Thanks to...
Tutorial Author(s): Maria Doyle, Belinda Phipson ...
From Obis data to Biodiversity indicators
Associated Tutorial
This workflows is part of the tutorial Obis marine indicators, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Marie Jossé
Tutorial Author(s): ...
Analysis of molecular dynamics simulations
Associated Tutorial
This workflows is part of the tutorial Analysis of molecular dynamics simulations, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Tutorial ...
rna-seq-reads-to-counts
Associated Tutorial
This workflows is part of the tutorial 1: RNA-Seq reads to counts, available in the GTN
Thanks to...
Tutorial Author(s): Maria Doyle, Belinda Phipson, ...
Compute and analyze biodiversity metrics with PAMPA toolsuite
Associated Tutorial
This workflows is part of the tutorial Compute and analyze biodiversity metrics with PAMPA toolsuite, available in the GTN
Thanks to...
Tutorial Author(s): Coline Royaux, ...
Analysis of MD trajectories using MDAnalysis, generating a Ramachandran plot and various timeseries.
Associated Tutorial
This workflows is part of the tutorial Analysis of molecular dynamics simulations, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Biodiversity data exploration
Associated Tutorial
This workflows is part of the tutorial Biodiversity data exploration, available in the GTN
Thanks to...
Tutorial Author(s): Olivier Norvez, Marie Josse, ...
RNA-Seq reads to counts
Associated Tutorial
This workflows is part of the tutorial 1: RNA-Seq reads to counts, available in the GTN
Thanks to...
Tutorial Author(s): Maria Doyle, Belinda Phipson, ...
Protein target prediction of a bioactive ligand with Align-it and ePharmaLib
Associated Tutorial
This workflows is part of the tutorial Protein target prediction of a bioactive ligand with Align-it and ePharmaLib, available in the GTN
Thanks to...
Workflow Author(s): Aurélien F. A. Moumbock, Albert-Ludwigs-Universität Freiburg ...
Compute indicators for Champs blocs
Associated Tutorial
This workflows is part of the tutorial Champs blocs indicators, available in the GTN
Thanks to...
Tutorial Author(s): Marie Josse, Yvan Le Bras ...
High Throughput Molecular Dynamics and Analysis
Associated Tutorial
This workflows is part of the tutorial High Throughput Molecular Dynamics and Analysis, available in the GTN
Thanks to...
Tutorial Author(s): Simon Bray, [Tharindu ...
Analyze differential isoform expression
Associated Tutorial
This workflows is part of the tutorial Genome-wide alternative splicing analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
High Throughput Molecular Dynamics and Analysis
Associated Tutorial
This workflows is part of the tutorial High Throughput Molecular Dynamics and Analysis, available in the GTN
Thanks to...
Tutorial Author(s): Simon Bray, [Tharindu ...
Species distribution modeling
Associated Tutorial
This workflows is part of the tutorial Species distribution modeling, available in the GTN
Thanks to...
Tutorial Author(s): Elisa Michon, Yvan Le Bras, ...
De novo transcriptome reconstruction with RNA-Seq
Associated Tutorial
This workflows is part of the tutorial De novo transcriptome reconstruction with RNA-Seq, available in the GTN
Thanks to...
Tutorial Author(s): Mallory Freeberg, [Mo ...
Analyse Bulk RNA-Seq data in preparation for downstream Pathways analysis with MINERVA
Associated Tutorial
This workflows is part of the tutorial Pathway analysis with the MINERVA Platform, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
RAD-Seq to construct genetic maps
Associated Tutorial
This workflows is part of the tutorial RAD-Seq to construct genetic maps, available in the GTN
Thanks to...
Tutorial Author(s): Yvan Le Bras
[![gtn star logo followed by the word ...
Reproduce the tutorial analysis at https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html
Associated Tutorial
This workflows is part of the tutorial Mapping and molecular identification of phenotype-causing mutations, available in the GTN
Thanks to...
**Tutorial ...
RNA-RNA interactome analysis using ChiRA tool suite
Associated Tutorial
This workflows is part of the tutorial RNA-RNA interactome data analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): ...
Associated Tutorial
This workflows is part of the tutorial Ecoregionalization workflow tutorial, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Uses Galaxy Workflow Comments ...
Downloads data from NCBI assuming the correct data input format. (I.e. it should be two columns, with a header, Run and Group, where Run is an SRR identifier.)
Associated Tutorial
This workflows is part of the tutorial Pathway analysis with the MINERVA Platform, available in the GTN
Features
- Includes [Galaxy Workflow ...
Identification of somatic and germline variants from tumor and normal sample pairs tutorial
Associated Tutorial
This workflows is part of the tutorial Identification of somatic and germline variants from tumor and normal sample pairs, available in the GTN
Features
- Includes [Galaxy Workflow ...
Network analysis with Heinz
Associated Tutorial
This workflows is part of the tutorial Network analysis with Heinz, available in the GTN
Thanks to...
Tutorial Author(s): Chao Zhang
[![gtn star logo followed by the word ...
This workflow completes the second part of the sRNA-seq tutorial from transcript quantification through differential abundance testing.
Associated Tutorial
This workflows is part of the tutorial Differential abundance testing of small RNAs, available in the GTN
Thanks to...
Tutorial Author(s): [Mallory ...
This portion of the workflow produces sets of feature Counts ready for analysis by limma/etc.
Associated Tutorial
This workflows is part of the tutorial Pathway analysis with the MINERVA Platform, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Checking expected species and contamination in bacterial isolate
Associated Tutorial
This workflows is part of the tutorial Checking expected species and contamination in bacterial isolate, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
This workflow completes the first part of the small RNA-seq tutorial from read pre-processing to trimming.e
Associated Tutorial
This workflows is part of the tutorial Differential abundance testing of small RNAs, available in the GTN
Thanks to...
Tutorial Author(s): Mallory Freeberg ...
Exome sequencing data analysis for diagnosing a genetic disease; short version starting from pre-mapped reads
Associated Tutorial
This workflows is part of the tutorial Exome sequencing data analysis for diagnosing a genetic disease, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Small Non-coding RNA Clustering using BlockClust
Associated Tutorial
This workflows is part of the tutorial Small Non-coding RNA Clustering using BlockClust, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
...
Cleaning GBIF data for the use in Ecology
Associated Tutorial
This workflows is part of the tutorial Cleaning GBIF data for the use in Ecology, available in the GTN
Thanks to...
Tutorial Author(s): Yvan Le Bras, [Simon ...
Associated Tutorial
This workflows is part of the tutorial Sentinel 2 biodiversity, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Marie Josse
Tutorial Author(s): [Marie ...
Exome sequencing data analysis for diagnosing a genetic disease
Associated Tutorial
This workflows is part of the tutorial Exome sequencing data analysis for diagnosing a genetic disease, available in the GTN
Features
- Includes Galaxy Workflow Tests
...
RAD-Seq Reference-based data analysis
Associated Tutorial
This workflows is part of the tutorial RAD-Seq Reference-based data analysis, available in the GTN
Thanks to...
Tutorial Author(s): Yvan Le Bras
Tutorial Contributor(s): [Verena ...
RAD-Seq de-novo data analysis
Associated Tutorial
This workflows is part of the tutorial RAD-Seq de-novo data analysis, available in the GTN
Thanks to...
Tutorial Author(s): Yvan Le Bras
Tutorial Contributor(s): [Verena ...
GO Enrichment Analysis Tutorial
Associated Tutorial
This workflows is part of the tutorial GO Enrichment Analysis, available in the GTN
Thanks to...
Tutorial Author(s): IGC Bioinformatics Unit, Maria Doyle ...
Run this on raw duplex sequencing reads to produce duplex consensus sequences.
Associated Tutorial
This workflows is part of the tutorial Calling very rare variants, available in the GTN
Thanks to...
Tutorial Author(s): Anton Nekrutenko, [Nick ...
Mapping
Associated Tutorial
This workflows is part of the tutorial Mapping, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Joachim Wolff, ...
RAD-Seq Reference-based data analysis
Associated Tutorial
This workflows is part of the tutorial RAD-Seq Reference-based data analysis, available in the GTN
Thanks to...
Tutorial Author(s): Yvan Le Bras
Tutorial Contributor(s): [Verena ...
Secondary metabolite biosynthetic gene cluster (SMBGC) Annotation using Neural Networks Trained on Interpro Signatures
Associated Tutorial
This workflows is part of the tutorial Marine Omics identifying biosynthetic gene clusters, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Run this on the trimmed consensus reads (DCS or SSCS) from Du Novo.
Associated Tutorial
This workflows is part of the tutorial Calling very rare variants, available in the GTN
Thanks to...
Tutorial Author(s): Anton Nekrutenko, [Nick ...
Calling variants in non-diploid systems
Associated Tutorial
This workflows is part of the tutorial Calling variants in non-diploid systems, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Mapping
Associated Tutorial
This workflows is part of the tutorial Mapping, available in the GTN
Thanks to...
Tutorial Author(s): Joachim Wolff, Bérénice Batut, [Helena ...
Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring
Associated Tutorial
This workflows is part of the tutorial Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring, available in the GTN
Thanks to...
Tutorial Author(s): Simon Bray ...
This workflow begins from a set of genome assemblies of different samples, strains, species. The genome is first annotated with Funnanotate. Predicted proteins are furtner annotated with Busco. Next, 'ProteinOrtho' finds orthologs across the samples and makes orthogroups. Orthogroups where all samples are represented are extracted. Orthologs in each orthogroup are aligned with ClustalW. The alignments are cleaned with ClipKIT and the concatenation matrix is built using PhyKit. This can be used ...
Calling variants in diploid systems
Associated Tutorial
This workflows is part of the tutorial Calling variants in diploid systems, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Visualization of Climate Data using NetCDF Xarray Map Plotting
Associated Tutorial
This workflows is part of the tutorial Visualization of Climate Data using NetCDF xarray Map Plotting, available in the GTN
Thanks to...
Workflow Author(s): Soumya Jha
Tutorial Author(s): Soumya Jha ...
Removal of human reads from SARS-CoV-2 sequencing data
Associated Tutorial
This workflows is part of the tutorial Removal of human reads from SARS-CoV-2 sequencing data, available in the GTN
Thanks to...
Tutorial Author(s): Wolfgang Maier
[![gtn star ...
Workflow includes data import, format conversion and some basic medicinal chemistry analyses.
Associated Tutorial
This workflows is part of the tutorial Data management in Medicinal Chemistry, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
This workflow is created as part of a tutorial listed on GTN. The workflow shows the steps in human copy number variance detection using the Contrl_FREEC tool.
Associated Tutorial
This workflows is part of the tutorial Somatic Variant Discovery from WES Data Using Control-FREEC, available in the GTN
Features
- Includes [Galaxy ...
Associated Tutorial
This workflows is part of the tutorial Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Associated Tutorial
This workflows is part of the tutorial Assembly of the mitochondrial genome from PacBio HiFi reads, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): VGP, Galaxy
**Tutorial ...
CTB Unittest workflow
Associated Tutorial
This workflows is part of the tutorial Protein-ligand docking, available in the GTN
Thanks to...
Tutorial Author(s): Simon Bray
[![gtn star logo followed by the word ...
Predict variants and drug resistance from M. tuberculosis sequence samples (Illumina)
Associated Tutorial
This workflows is part of the tutorial M. tuberculosis Variant Analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
...
Running molecular dynamics simulations using GROMACS
Associated Tutorial
This workflows is part of the tutorial Running molecular dynamics simulations using GROMACS, available in the GTN
Features
- Includes Galaxy Workflow Tests
...
Genome assembly quality control using PacBio data and with reference genome
Associated Tutorial
This workflows is part of the tutorial Genome Assembly Quality Control, available in the GTN
Thanks to...
Workflow Author(s): Erwan Corre, Stéphanie Robin, Anthony Bretaudeau, Alexandre Cormier, Laura Leroi
Tutorial Author(s): ...
Quality and contamination control in bacterial isolate using Illumina MiSeq Data
Associated Tutorial
This workflows is part of the tutorial Quality and contamination control in bacterial isolate using Illumina MiSeq Data, available in the GTN
Features
- Includes [Galaxy Workflow ...
Analysis of variation within individual COVID-19 samples (Paired End Illumina). Does not use paured
Associated Tutorial
This workflows is part of the tutorial From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis, available in the GTN
Thanks to...
Tutorial Author(s): [Marius van den ...
Associated Tutorial
This workflows is part of the tutorial Deep Learning (Part 3) - Convolutional neural networks (CNN), available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Kaivan Kamali
Tutorial Author(s): [Kaivan ...
ERGA post-assembly QC
Associated Tutorial
This workflows is part of the tutorial ERGA post-assembly QC, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report ...
Quality Control
Associated Tutorial
This workflows is part of the tutorial Quality Control, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Bérénice Batut, ...
Making sense of a newly assembled genome
Associated Tutorial
This workflows is part of the tutorial Making sense of a newly assembled genome, available in the GTN
Thanks to...
Tutorial Author(s): Anton Nekrutenko, [Delphine ...
Microbial Variant Calling
Associated Tutorial
This workflows is part of the tutorial Microbial Variant Calling, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Anna ...
Introduction to Deep Learning
Associated Tutorial
This workflows is part of the tutorial Introduction to deep learning, available in the GTN
Thanks to...
Tutorial Author(s): Anup Kumar, Alireza Khanteymoori ...
Trio Analysis using Synthetic Datasets from RD-Connect GPAP
Associated Tutorial
This workflows is part of the tutorial Trio Analysis using Synthetic Datasets from RD-Connect GPAP, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks
...
Associated Tutorial
This workflows is part of the tutorial Assembly of metagenomic sequencing data, available in the GTN
Thanks to...
Tutorial Author(s): Polina Polunina, Bérénice Batut ...
Associated Tutorial
This workflows is part of the tutorial Clean and manage Sanger sequences from raw files to aligned consensus, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Coline Royaux ...
Regression in Machine Learning
Associated Tutorial
This workflows is part of the tutorial Regression in Machine Learning, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Anup Kumar
**Tutorial ...
From a reference and a primer scheme generate two masked half-genome references for ITR-aware pox virus sequencing data analysis.
Associated Tutorial
This workflows is part of the tutorial Pox virus genome analysis from tiled-amplicon sequencing data, available in the GTN
Features
- Includes [Galaxy Workflow ...
Associated Tutorial
This workflows is part of the tutorial Clean and manage Sanger sequences from raw files to aligned consensus, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Coline Royaux ...
Associated Tutorial
This workflows is part of the tutorial Assembly of metagenomic sequencing data, available in the GTN
Thanks to...
Tutorial Author(s): Polina Polunina, Bérénice Batut ...
Creating a new tutorial
Associated Tutorial
This workflows is part of the tutorial Creating a new tutorial, available in the GTN
Thanks to...
Tutorial Author(s): Bérénice Batut, Helena Rasche, ...
This standard workflow determines SNV positions from baculovirus isolates using bcftools.
Associated Tutorial
This workflows is part of the tutorial Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates, available in the GTN
Features
- Includes [Galaxy Workflow ...
Primer design of related virus gene sequences.
Associated Tutorial
This workflows is part of the tutorial Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Retrieve climate data from Copernicus
Associated Tutorial
This workflows is part of the tutorial Creating a new tutorial, available in the GTN
Thanks to...
Tutorial Author(s): Bérénice Batut, Helena Rasche, ...
De Bruijn Graph Assembly
Associated Tutorial
This workflows is part of the tutorial De Bruijn Graph Assembly, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Simon ...
The workflow containes the step to perpare the data for and run Galaxy Infinium Human Methylation BeadChip tool that represents many popular algorithms for detecting somatic genetic alterations from genome and exome data
Associated Tutorial
This workflows is part of the tutorial Infinium Human Methylation BeadChip, available in the GTN
Features
...
V 16 - including updated diff-tool
Associated Tutorial
This workflows is part of the tutorial Text-Mining Differences in Chinese Newspaper Articles, available in the GTN
Features
- Includes a Galaxy Workflow Report
- Uses [Galaxy Workflow ...
tutorial
Associated Tutorial
This workflows is part of the tutorial An Introduction to Genome Assembly, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Simon ...
Genome Assembly using PacBio data and Flye or Hifiasm assembler
Associated Tutorial
This workflows is part of the tutorial Genome assembly using PacBio data, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): ...
Identification of the binding sites of the Estrogen receptor
Associated Tutorial
This workflows is part of the tutorial Identification of the binding sites of the Estrogen receptor, available in the GTN
Thanks to...
Tutorial Author(s): Friederike Dündar, ...
Identification of the binding sites of the Estrogen receptor
Associated Tutorial
This workflows is part of the tutorial Identification of the binding sites of the Estrogen receptor, available in the GTN
Thanks to...
Tutorial Author(s): Friederike Dündar, ...
Image classification with fruit 360 dataset
Associated Tutorial
This workflows is part of the tutorial Image classification in Galaxy with fruit 360 dataset, available in the GTN
Thanks to...
Workflow Author(s): Kaivan Kamali
Tutorial Author(s): Kaivan Kamali ...
Assembly with preprocessing and SRA download
Associated Tutorial
This workflows is part of the tutorial Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads, available in the GTN
Thanks to...
Tutorial Author(s): Wolfgang Maier ...
Assembly
Associated Tutorial
This workflows is part of the tutorial Chloroplast genome assembly, available in the GTN
Thanks to...
Tutorial Author(s): Anna Syme
[![gtn star logo followed by the word ...
Associated Tutorial
This workflows is part of the tutorial Formation of the Super-Structures on the Inactive X, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Friederike Dündar, ...
Deep Learning image classifier model
Associated Tutorial
This workflows is part of the tutorial Train and Test a Deep learning image classifier with Galaxy-Ludwig, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Workflow ...
Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
Associated Tutorial
This workflows is part of the tutorial Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data), available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Assembly with preprocessing
Associated Tutorial
This workflows is part of the tutorial Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads, available in the GTN
Thanks to...
Tutorial Author(s): Wolfgang Maier
[![gtn ...
Associated Tutorial
This workflows is part of the tutorial Large genome assembly and polishing, available in the GTN
Features
- Includes a Galaxy Workflow Report
- Uses subworkflows ...
Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
Associated Tutorial
This workflows is part of the tutorial Hi-C analysis of Drosophila melanogaster cells using HiCExplorer, available in the GTN
Thanks to...
Tutorial Author(s): Joachim Wolff, ...
Clustering in Machine Learning
Associated Tutorial
This workflows is part of the tutorial Clustering in Machine Learning, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Alireza ...
Associated Tutorial
This workflows is part of the tutorial Large genome assembly and polishing, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Anna Syme
Tutorial Author(s): [Anna ...
VGP assembly tutorial
Associated Tutorial
This workflows is part of the tutorial Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step, available in the GTN
Thanks to...
Tutorial Author(s): Delphine Lariviere, [Alex ...
Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
Associated Tutorial
This workflows is part of the tutorial Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1), available in the GTN
Features
- Includes [Galaxy Workflow ...
PanCancer Aberrant Pathway Activity Analysis: PI3K example
Associated Tutorial
This workflows is part of the tutorial PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis, available in the GTN
Thanks to...
Tutorial Author(s): Vijay, [Daniel ...
Associated Tutorial
This workflows is part of the tutorial Large genome assembly and polishing, available in the GTN
Thanks to...
Workflow Author(s): Anna Syme
Tutorial Author(s): Anna Syme
[![gtn star logo followed by the word ...
In this workflow the similarity among set of search queries (e.g. genes) is analyzed based on the associated vocabulary in PubMed. The last tool is an interactive tool that enables the inspection of the data.
Associated Tutorial
This workflows is part of the tutorial Text-mining with the SimText toolset, available in the GTN
Thanks to...
...
Genome Assembly of MRSA using Illumina MiSeq Data
Associated Tutorial
This workflows is part of the tutorial Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data, available in the GTN
Features
- Includes Galaxy Workflow Tests
...
Data Manipulation Olympics
Associated Tutorial
This workflows is part of the tutorial Data Manipulation Olympics, available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, Yongbin Li ...
Generates LORIS LLR6 model
Associated Tutorial
This workflows is part of the tutorial Building the LORIS LLR6 PanCancer Model Using PyCaret, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Paulo Cilas ...
Associated Tutorial
This workflows is part of the tutorial Large genome assembly and polishing, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Anna Syme
Tutorial Author(s): [Anna ...
Unicycler Assembly
Associated Tutorial
This workflows is part of the tutorial Unicycler Assembly, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Anton Nekrutenko, ...
This workflow predict in-silico mass spectra using semi-empirical quantum physics method.
Associated Tutorial
This workflows is part of the tutorial Predicting EI+ mass spectra with QCxMS, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Machine learning: classification and regression
Associated Tutorial
This workflows is part of the tutorial Machine learning: classification and regression, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Tutorial ...
Associated Tutorial
This workflows is part of the tutorial Decontamination of a genome assembly, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report ...
Associated Tutorial
This workflows is part of the tutorial Large genome assembly and polishing, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Anna Syme
Tutorial Author(s): [Anna ...
Mass spectrometry imaging: Examining the spatial distribution of analytes
Associated Tutorial
This workflows is part of the tutorial Mass spectrometry imaging: Examining the spatial distribution of analytes, available in the GTN
Thanks to...
Tutorial Author(s): Melanie Föll, ...
Machine learning: classification and regression
Associated Tutorial
This workflows is part of the tutorial Machine learning: classification and regression, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Tutorial ...
This workflow can be used to assign multi-element molecular formulas to ultrahigh resolution mass spectra.
Associated Tutorial
This workflows is part of the tutorial Molecular formula assignment and mass recalibration with MFAssignR package, available in the GTN
Features
- Includes [Galaxy Workflow ...
Workflow includes data import, format conversion and some basic medicinal chemistry analyses.
Associated Tutorial
This workflows is part of the tutorial Data management in Medicinal Chemistry, available in the GTN
Features
- Includes Galaxy Workflow Tests
...
Associated Tutorial
This workflows is part of the tutorial Large genome assembly and polishing, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Anna Syme
Tutorial Author(s): [Anna ...
Mass spectrometry imaging: Finding differential analytes
Associated Tutorial
This workflows is part of the tutorial Mass spectrometry imaging: Finding differential analytes, available in the GTN
Thanks to...
Tutorial Author(s): Melanie Föll
[![gtn ...
Classification in Machine Learning
Associated Tutorial
This workflows is part of the tutorial Classification in Machine Learning, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Associated Tutorial
This workflows is part of the tutorial Large genome assembly and polishing, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Anna Syme
Tutorial Author(s): [Anna ...
Associated Tutorial
This workflows is part of the tutorial Finding the muon stopping site with pymuon-suite in Galaxy, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Muon ...
Mass spectrometry: LC-MS analysis
Associated Tutorial
This workflows is part of the tutorial Mass spectrometry: LC-MS analysis, available in the GTN
Thanks to...
Tutorial Author(s): Mélanie Petera, Gildas Le Corguillé, ...
Associated Tutorial
This workflows is part of the tutorial Deep Learning (Part 1) - Feedforward neural networks (FNN), available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Kaivan Kamali
Tutorial Author(s): [Kaivan ...
Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
Associated Tutorial
This workflows is part of the tutorial Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools, available in the GTN
Thanks to...
**Tutorial ...
XCMS and RAMClustR based workflow for data processing and annotation using library matching via matchms.
Associated Tutorial
This workflows is part of the tutorial Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms), available in the GTN
Features
- Includes [Galaxy Workflow ...
Associated Tutorial
This workflows is part of the tutorial Large genome assembly and polishing, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Anna Syme
Tutorial Author(s): [Anna ...
Associated Tutorial
This workflows is part of the tutorial A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy, available in the GTN
Thanks to...
Tutorial Author(s): Anup Kumar
Tutorial Contributor(s): [Saskia ...
Associated Tutorial
This workflows is part of the tutorial Large genome assembly and polishing, available in the GTN
Features
- Includes a Galaxy Workflow Report
- Uses subworkflows ...
Design plasmids encoding predicted pathways by using the BASIC assembly method.
Associated Tutorial
This workflows is part of the tutorial Designing plasmids encoding predicted pathways by using the BASIC assembly method, available in the GTN
Thanks to...
Tutorial Author(s): [Kenza ...
Estimate a phylogenetic tree from whole genome sequencing data for M. tuberculosis
Associated Tutorial
This workflows is part of the tutorial Tree thinking for tuberculosis evolution and epidemiology, available in the GTN
Thanks to...
Tutorial Author(s): Christoph Stritt, ...
Associated Tutorial
This workflows is part of the tutorial Evaluating Reference Data for Bulk RNA Deconvolution, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Downstream Single-cell RNA Plant analysis with ScanPy
Associated Tutorial
This workflows is part of the tutorial Analysis of plant scRNA-Seq Data with Scanpy, available in the GTN
Thanks to...
Tutorial Author(s): Mehmet Tekman, [Beatriz ...
From Fastqs to VCFs and BAMs
Associated Tutorial
This workflows is part of the tutorial Identifying tuberculosis transmission links: from SNPs to transmission clusters, available in the GTN
Thanks to...
Tutorial Author(s): Galo A. Goig, [Daniela ...
Evaluating and ranking a set of pathways based on multiple metrics
Associated Tutorial
This workflows is part of the tutorial Evaluating and ranking a set of pathways based on multiple metrics, available in the GTN
Thanks to...
Tutorial Author(s): Kenza Bazi-Kabbaj, ...
Associated Tutorial
This workflows is part of the tutorial Evaluating Reference Data for Bulk RNA Deconvolution, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Associated Tutorial
This workflows is part of the tutorial Filter, plot, and explore single cell RNA-seq data with Seurat, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): ...
atac-seq
Associated Tutorial
This workflows is part of the tutorial ATAC-Seq data analysis, available in the GTN
Thanks to...
Tutorial Author(s): Lucille Delisle, Maria Doyle, [Florian ...
Given a set of VCF files and the reference genome used to do the mapping and SNP calling, create a multifasta file containing the genomes of all samples and calculate the matrix of pairwise SNP distances
Associated Tutorial
This workflows is part of the tutorial Identifying tuberculosis transmission links: from SNPs to transmission clusters, available in the GTN ...
Associated Tutorial
This workflows is part of the tutorial Evaluating Reference Data for Bulk RNA Deconvolution, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
DNA Methylation data analysis
Associated Tutorial
This workflows is part of the tutorial DNA Methylation data analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Joachim ...
Associated Tutorial
This workflows is part of the tutorial Converting NCBI Data to the AnnData Format, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report ...
Starting from the BAM files produced by snippy, generate a table that summarizes the drug-resistance profile for each sample
Associated Tutorial
This workflows is part of the tutorial Identifying tuberculosis transmission links: from SNPs to transmission clusters, available in the GTN
Thanks to...
Tutorial Author(s): [Galo A. ...
Associated Tutorial
This workflows is part of the tutorial Evaluating Reference Data for Bulk RNA Deconvolution, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
CUT&RUN workflow used in GTN
Associated Tutorial
This workflows is part of the tutorial CUT&RUN data analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Tree building for "Phylogenetics - Back to basics"
Associated Tutorial
This workflows is part of the tutorial Phylogenetics - Back to basics, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Helena ...
This is the workflow for the Clustering 3K PBMCs with Seurat tutorial if you are using the separate preprocessing tools (NormalizeData, FindVariableFeatures, ScaleData).
Associated Tutorial
This workflows is part of the tutorial Clustering 3K PBMCs with Seurat, available in the GTN
Features
- Includes [Galaxy Workflow ...
This Workflow takes a dataset collection of single-cell ATAC-seq fragments and performs:
- preprocessing
- filtering
- concatenation
- dimension reduction
- batch correction
- leiden clustering
Associated Tutorial
This workflows is part of the tutorial Multi-sample batch correction with Harmony and SnapATAC2, available in the GTN ...
Associated Tutorial
This workflows is part of the tutorial Secondary metabolite discovery, available in the GTN
Thanks to...
Tutorial Author(s): Paul Zierep
[![gtn star logo followed by the word ...
Workflow for the first half of the "Bulk RNA Deconvolution with MuSiC" tutorial.
Associated Tutorial
This workflows is part of the tutorial Bulk RNA Deconvolution with MuSiC, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy ...
Pseudobulk Analysis Workflow for Tutorial
Associated Tutorial
This workflows is part of the tutorial Pseudobulk Analysis with Decoupler and EdgeR, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
This is the workflow for the Clustering 3K PBMCs with Seurat tutorial if you use SCTransform for preprocessing.
Associated Tutorial
This workflows is part of the tutorial Clustering 3K PBMCs with Seurat, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Workflow for the second half of the "Bulk RNA Deconvolution with MuSiC" tutorial.
Implements the "Estimation of cell type proportions with pre-grouping of cell types" section
Associated Tutorial
This workflows is part of the tutorial Bulk RNA Deconvolution with MuSiC, available in the GTN
Features
- Includes [Galaxy Workflow ...
Refining Genome Annotations with Apollo
Associated Tutorial
This workflows is part of the tutorial Refining Genome Annotations with Apollo (prokaryotes), available in the GTN
Thanks to...
Tutorial Author(s): Anthony Bretaudeau, [Helena ...
This workflow generates from only an EBI SCXA reference the metadata for creating an ESet object
Associated Tutorial
This workflows is part of the tutorial Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution, available in the GTN
Thanks to...
Workflow Author(s): Wendi Bacon, ...
Associated Tutorial
This workflows is part of the tutorial Removing the effects of the cell cycle, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report ...
Workflow of Tutorial "Single-cell ATAC-seq standard processing with SnapATAC2". This workflow takes a fragment file as input and performs the standard steps of scATAC-seq analysis: filtering, dimension reduction, embedding and visualization of marker genes with SnapATAC2. In an alternative step, the fragment file can also be generated from a BAM file.
Associated Tutorial
This workflows is part of the tutorial [Single-cell ATAC-seq standard processing with ...
Genome annotation with Maker (short)
Associated Tutorial
This workflows is part of the tutorial Genome annotation with Maker (short), available in the GTN
Thanks to...
Tutorial Author(s): Anthony Bretaudeau
[![gtn star logo followed by the ...
This workflow creates an ESet object from scRNA metadata file and EBI SCXA retrieveal
Associated Tutorial
This workflows is part of the tutorial Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution, available in the GTN
Features
- Uses ...
Associated Tutorial
This workflows is part of the tutorial Pre-processing of 10X Single-Cell RNA Datasets, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Downstream Single-cell RNA analysis with RaceID
Associated Tutorial
This workflows is part of the tutorial Downstream Single-cell RNA analysis with RaceID, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
A workflow designed to compare chromosomes and study large-scale rearrangements using CHROMEISTER
Associated Tutorial
This workflows is part of the tutorial From small to large-scale genome comparison, available in the GTN
Thanks to...
Tutorial Author(s): Esteban Perez-Wohlfeil ...
Introduction to Genomics and Galaxy
Associated Tutorial
This workflows is part of the tutorial Introduction to Genomics and Galaxy, available in the GTN
Thanks to...
Tutorial Author(s): Dave Clements, [Cristóbal ...
Workflow associated with this training: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html
Associated Tutorial
This workflows is part of the tutorial Combining single cell datasets after pre-processing, available in the GTN
Features
- Includes ...
A workflow designed to compare two sequences using GECKO, extract repeats and perform multiple sequence alignment
Associated Tutorial
This workflows is part of the tutorial From small to large-scale genome comparison, available in the GTN
Thanks to...
Tutorial Author(s): Esteban Perez-Wohlfeil ...
This workflow creates bulk ESet objects from uploaded raw matrix & metadata files
Associated Tutorial
This workflows is part of the tutorial Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution, available in the GTN
Features
- Uses subworkflows ...
NGS data logistics
Associated Tutorial
This workflows is part of the tutorial NGS data logistics, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Masking repeats in a genome using RepeatMasker
Associated Tutorial
This workflows is part of the tutorial Masking repeats with RepeatMasker, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Anthony ...
Updated March 2024
Associated Tutorial
This workflows is part of the tutorial Combining single cell datasets after pre-processing, available in the GTN
Thanks to...
Workflow Author(s): Julia Jakiela, Wendi Bacon
Tutorial Author(s): Wendi Bacon ...
This workflow is for the training material: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_alevin/tutorial.html
Associated Tutorial
This workflows is part of the tutorial Generating a single cell matrix using Alevin, available in the GTN
Features
- Includes a [Galaxy Workflow ...
introduction
Associated Tutorial
This workflows is part of the tutorial Galaxy Basics for everyone, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Anne ...
Creates input file for Filter, Plot, Explore tutorial
Associated Tutorial
This workflows is part of the tutorial Importing files from public atlases, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
CRISPR screen analysis
Associated Tutorial
This workflows is part of the tutorial CRISPR screen analysis, available in the GTN
Thanks to...
Tutorial Author(s): Maria Doyle, Kenji Fujihara, ...
This workflow generates a single cell matrix using Alevin.
Associated Tutorial
This workflows is part of the tutorial Generating a single cell matrix using Alevin, available in the GTN
Thanks to...
Workflow Author(s): Julia Jakiela, Wendi Bacon
Tutorial Author(s): Wendi Bacon, ...
Associated Tutorial
This workflows is part of the tutorial Introduction to Image Analysis using Galaxy, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Till Korten, Leonid Kostrykin
**Tutorial ...
AnnData to CDS format conversion (manually using Galaxy buttons). This workflow does not include renaming the column containing gene symbols.
Associated Tutorial
This workflows is part of the tutorial Converting between common single cell data formats, available in the GTN
Features
- Includes [Galaxy Workflow ...
Associated Tutorial
This workflows is part of the tutorial Inferring single cell trajectories with Scanpy, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Marisa Loach
Tutorial Author(s): ...
Essential genes detection with Transposon insertion sequencing
Associated Tutorial
This workflows is part of the tutorial Essential genes detection with Transposon insertion sequencing, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks
...
The present workflow allows to perform 2D spots/blobs detection on specific channel and stack of an image. Images will be directly fetched from IDR by including the IDs. A pre-processing steps with histogram normalization is performed before the blobs detection.
Associated Tutorial
This workflows is part of the tutorial Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines, ...
AnnData to Seurat format conversion (manually using Galaxy buttons)
Associated Tutorial
This workflows is part of the tutorial Converting between common single cell data formats, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks
...
Structural and functional genome annotation with Funannotate
Associated Tutorial
This workflows is part of the tutorial Genome annotation with Funannotate, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Workflow ...
Associated Tutorial
This workflows is part of the tutorial Using BioImage.IO models for image analysis in Galaxy, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Trajectory analysis using Monocle3, starting from AnnData
Associated Tutorial
This workflows is part of the tutorial Inferring single cell trajectories with Monocle3, available in the GTN
Features
- Includes Galaxy Workflow Tests
...
AnnData to SCE format conversion (manually using Galaxy buttons)
Associated Tutorial
This workflows is part of the tutorial Converting between common single cell data formats, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks
...
Generic workflow to perform Voronoi segmentation. Input requirements:
- Image: -- Preferably lighter objects on a darker background for the mask to work well. -- Format: .tiff, stored in planar RGB format, not interleaved (http://avitevet.com/uncategorized/when-to-use-it-interleaved-vs-planar-image-data-storage/).
- Seeds: -- White seeds on a black background -- Format: .tiff
Associated Tutorial
This workflows is part of the tutorial [Voronoi ...
Functional annotation of protein sequences
Associated Tutorial
This workflows is part of the tutorial Functional annotation of protein sequences, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): ...
Preparing and filtering gene and cell annotations files and expression matrix to be passed as input for Monocle
Associated Tutorial
This workflows is part of the tutorial Inferring single cell trajectories with Monocle3, available in the GTN
Thanks to...
Tutorial Author(s): [Julia ...
Workflow based on clustering 3K PBMCs with Scanpy tutorial
Associated Tutorial
This workflows is part of the tutorial Clustering 3K PBMCs with Scanpy, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Workflows for comparison of genes in annotated genomes
Associated Tutorial
This workflows is part of the tutorial Comparative gene analysis in unannotated genomes, available in the GTN
Thanks to...
Workflow Author(s): Anton Nekrutenko
Tutorial Author(s): Anton Nekrutenko ...
Workflow to assess nuclei segmentation by applying different Gaussian filtering values during image pre-processing.
Associated Tutorial
This workflows is part of the tutorial Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy, available in the GTN
Features
- Includes [Galaxy Workflow ...
Trajectory analysis using Monocle3, starting from 3 input files: expression matrix, gene and cell annotations
Associated Tutorial
This workflows is part of the tutorial Inferring single cell trajectories with Monocle3, available in the GTN
Thanks to...
Tutorial Author(s): [Julia ...
Associated Tutorial
This workflows is part of the tutorial GO Enrichment Analysis on Single-Cell RNA-Seq Data, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report ...
Bacterial Genome Annotation
Associated Tutorial
This workflows is part of the tutorial Bacterial Genome Annotation, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Bérénice Batut, ...
End-to-End Tissue Microarray Analysis with Galaxy-ME
Associated Tutorial
This workflows is part of the tutorial End-to-End Tissue Microarray Image Analysis with Galaxy-ME, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks
...
Analyse HeLa fluorescence siRNA screen
Associated Tutorial
This workflows is part of the tutorial Analyse HeLa fluorescence siRNA screen, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Uses ...
Associated Tutorial
This workflows is part of the tutorial Scanpy Parameter Iterator, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Julia Jakiela
Tutorial Author(s): [Julia ...
Single-cell quality control with scater
Associated Tutorial
This workflows is part of the tutorial Single-cell quality control with scater, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Associated Tutorial
This workflows is part of the tutorial Analyse HeLa fluorescence siRNA screen, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Till Korten, Leonid Kostrykin
Tutorial Author(s): ...
This workflow uses Braker3 to annotate a genome.
Associated Tutorial
This workflows is part of the tutorial Genome annotation with Braker3, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Associated Tutorial
This workflows is part of the tutorial Understanding Barcodes, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report ...
Associated Tutorial
This workflows is part of the tutorial Pre-processing of 10X Single-Cell ATAC-seq Datasets, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Pavankumar Videm
**Tutorial ...
Genome annotation with Maker
Associated Tutorial
This workflows is part of the tutorial Genome annotation with Maker, available in the GTN
Thanks to...
Workflow Author(s): Anthony Bretaudeau, French National Institute for Agriculture, Food, and Environment (INRAE)
Tutorial Author(s): [Anthony ...
Nucleoli segmentation and feature extraction using CellProfiler
Associated Tutorial
This workflows is part of the tutorial Nucleoli segmentation and feature extraction using CellProfiler, available in the GTN
Thanks to...
Tutorial Author(s): Beatriz Serrano-Solano, ...
example cellprofiler pipeline
Associated Tutorial
This workflows is part of the tutorial Object tracking using CellProfiler, available in the GTN
Thanks to...
Tutorial Author(s): Yi Sun, [Beatriz ...
Associated Tutorial
This workflows is part of the tutorial Pre-processing of 10X Single-Cell ATAC-seq Datasets, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Pavankumar Videm
**Tutorial ...
Workflow for this training: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html
Associated Tutorial
This workflows is part of the tutorial Filter, plot and explore single-cell RNA-seq data with Scanpy, available in the GTN
Features
- Includes [Galaxy Workflow ...
This workflow allows you to annotate a genome with Helixer and evaluate the quality of the annotation using BUSCO and Genome Annotation statistics. GFFRead is also used to predict protein sequences derived from this annotation, and BUSCO and OMArk are used to assess proteome quality.
Associated Tutorial
This workflows is part of the tutorial Genome annotation with Helixer, available ...
This workflow is developed for automatic detection and measuring of mitoflashes in time-lapse microscopy images.
In addition, this workflow can be used for detection and tracking of other spot-like organelles with small motion.
If this workflow helped with the analysis of your data, please do not forget to cite: https://doi.org/10.1097/j.pain.0000000000002642
Associated Tutorial
This workflows is part of the tutorial [Tracking of mitochondria and capturing ...
This workflow runs 3 comparisons using MuSiC Deconvolution compare: where datasets cell compositions are inferred from a reference containing healthy and diseased cells; where diseased are inferred from disease and healthy from healthy; and where both diseased and healthy are inferred from a healthy reference.
Associated Tutorial
This workflows is part of the tutorial Comparing inferred cell compositions using MuSiC deconvolution, ...
Genome annotation with Prokka
Associated Tutorial
This workflows is part of the tutorial Genome annotation with Prokka, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Anna Syme, Torsten ...
Nanopore datasets analysis - Phylogenetic Identification - antibiotic resistance genes detection and contigs building
Associated Tutorial
This workflows is part of the tutorial Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition, available in the GTN
Features
- Includes ...
Filter, Plot and Explore Single-cell RNA-seq Data
Associated Tutorial
This workflows is part of the tutorial Filter, plot and explore single-cell RNA-seq data with Scanpy, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks
...
Pre-processing of Single-Cell RNA Data
Associated Tutorial
This workflows is part of the tutorial Pre-processing of Single-Cell RNA Data, available in the GTN
Thanks to...
Tutorial Author(s): Mehmet Tekman, [Bérénice ...
Galaxy 101
Associated Tutorial
This workflows is part of the tutorial Galaxy Basics for genomics, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report ...
Microbiome - QC and Contamination Filtering
Associated Tutorial
This workflows is part of the tutorial Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Pre-processing of Single-Cell RNA Data
Associated Tutorial
This workflows is part of the tutorial Pre-processing of Single-Cell RNA Data, available in the GTN
Features
- Uses subworkflows
Thanks to...
Tutorial Author(s): [Mehmet ...
Updated tool versions Aug 24 2022
Associated Tutorial
This workflows is part of the tutorial Filter, plot and explore single-cell RNA-seq data with Scanpy, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy ...
introduction
Associated Tutorial
This workflows is part of the tutorial How to reproduce published Galaxy analyses, available in the GTN
Thanks to...
Tutorial Author(s): Melanie Föll, Anne Fouilloux ...
Identification of AMR genes in an assembled bacterial genome
Associated Tutorial
This workflows is part of the tutorial Identification of AMR genes in an assembled bacterial genome, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Pathogens of all samples report generation and visualization
Associated Tutorial
This workflows is part of the tutorial Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition, available in the GTN
Features
- Includes a [Galaxy Workflow ...
Downstream Single-cell RNA Plant analysis with ScanPy
Associated Tutorial
This workflows is part of the tutorial Analysis of plant scRNA-Seq Data with Scanpy, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Data Manipulation Olympics
Associated Tutorial
This workflows is part of the tutorial Data Manipulation Olympics, available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, Yongbin Li ...
Long non-coding RNAs (lncRNAs) annotation with FEELnc
Associated Tutorial
This workflows is part of the tutorial Long non-coding RNAs (lncRNAs) annotation with FEELnc, available in the GTN
Thanks to...
Workflow Author(s): Stéphanie Robin
Tutorial Author(s): Stéphanie Robin ...
Microbiome - Taxonomy Profiling
Associated Tutorial
This workflows is part of the tutorial Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Interpreting MaxQuant data using MSstats involves applying a rigorous statistical framework to glean meaningful insights from quantitative proteomic datasets
Associated Tutorial
This workflows is part of the tutorial Clinical Metaproteomics 5: Data Interpretation, available in the GTN
Thanks to...
Workflow Author(s): ...
A short introduction to Galaxy
Associated Tutorial
This workflows is part of the tutorial A short introduction to Galaxy, available in the GTN
Thanks to...
Tutorial Author(s): Anna Syme, Nicola Soranzo ...
Associated Tutorial
This workflows is part of the tutorial Assembly of metagenomic sequencing data, available in the GTN
Thanks to...
Tutorial Author(s): Polina Polunina, Bérénice Batut ...
Microbiome - Variant calling and Consensus Building
Associated Tutorial
This workflows is part of the tutorial Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Galaxy Introduction Peaks2Genes - Part 1
Associated Tutorial
This workflows is part of the tutorial From peaks to genes, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Anne ...
Antibiotic resistance detection
Associated Tutorial
This workflows is part of the tutorial Antibiotic resistance detection, available in the GTN
Thanks to...
Tutorial Author(s): Willem de Koning, [Saskia ...
Analyses of metagenomics data - The global picture
Associated Tutorial
This workflows is part of the tutorial Analyses of metagenomics data - The global picture, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Tutorial ...
Introduction to Genomics and Galaxy
Associated Tutorial
This workflows is part of the tutorial Introduction to Genomics and Galaxy, available in the GTN
Thanks to...
Tutorial Author(s): Dave Clements, [Cristóbal ...
Generating a large database and then reducing it to a compact database using Metanovo
Associated Tutorial
This workflows is part of the tutorial Clinical Metaproteomics 1: Database-Generation, available in the GTN
Thanks to...
Workflow Author(s): Subina Mehta
Tutorial Author(s): [Subina ...
16S rRNA analysis with Nanopore reads
Associated Tutorial
This workflows is part of the tutorial 16S Microbial analysis with Nanopore data, available in the GTN
Thanks to...
Tutorial Author(s): Cristóbal Gallardo
[![gtn star logo followed by the ...
Analyses of metagenomics data - The global picture
Associated Tutorial
This workflows is part of the tutorial Analyses of metagenomics data - The global picture, available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, [Bérénice ...
encyclopedia- DIA Metaproteomics
Associated Tutorial
This workflows is part of the tutorial EncyclopeDIA, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report ...
This workflow performs taxonomic profiling of metagenomic data and visualizes microbial community composition using Kraken2 and Bracken as well as MetaPhlAn.
Associated Tutorial
This workflows is part of the tutorial Taxonomic Profiling and Visualization of Metagenomic Data, available in the GTN
Features
- Includes [Galaxy Workflow ...
Quantification using the MaxQuant tool
Associated Tutorial
This workflows is part of the tutorial Clinical Metaproteomics 4: Quantitation, available in the GTN
Thanks to...
Workflow Author(s): Subina Mehta
Tutorial Author(s): Subina Mehta, ...
This workflow query metagenomic raw data against a metaplasmidome database to identify plasmids and annotate them with genes, KO, PFAM
Associated Tutorial
This workflows is part of the tutorial Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data, available in the GTN ...
Proteogenomics 3: Novel peptide analysis
Associated Tutorial
This workflows is part of the tutorial Proteogenomics 3: Novel peptide analysis, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
...
Associated Tutorial
This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Uses subworkflows ...
16S Microbial Analysis with mothur (extended)
Associated Tutorial
This workflows is part of the tutorial 16S Microbial Analysis with mothur (extended), available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, [Bérénice ...
WF3- Peptide verification/validaiton workflow
Associated Tutorial
This workflows is part of the tutorial Clinical Metaproteomics 3: Verification, available in the GTN
Thanks to...
Workflow Author(s): Subina Mehta
Tutorial Author(s): Subina Mehta, ...
DIA Analysis Training using HEK Ecoli data in OSW
Associated Tutorial
This workflows is part of the tutorial DIA Analysis using OpenSwathWorkflow, available in the GTN
Thanks to...
Tutorial Author(s): Matthias Fahrner, [Melanie ...
DIA MSstats Training msstats input tabular
Associated Tutorial
This workflows is part of the tutorial Statistical analysis of DIA data, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Matthias ...
Generating a large database and then reducing it to a compact database using Metanovo
Associated Tutorial
This workflows is part of the tutorial Clinical Metaproteomics 1: Database-Generation, available in the GTN
Thanks to...
Workflow Author(s): Subina Mehta
Tutorial Author(s): [Subina ...
Workflow for running LotuS2 tool on fungal ITS paired-end sequencing data, to identify the fungi present in the samples
Associated Tutorial
This workflows is part of the tutorial Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2, available in the GTN
Features
- Includes [Galaxy Workflow ...
metaquantome-taxonomy
Associated Tutorial
This workflows is part of the tutorial metaQuantome 3: Taxonomy, available in the GTN
Thanks to...
Tutorial Author(s): Subina Mehta, Timothy J. Griffin, ...
DIA MSstats Training export tabular
Associated Tutorial
This workflows is part of the tutorial Statistical analysis of DIA data, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Matthias ...
Annotating the novel peptides
Associated Tutorial
This workflows is part of the tutorial Neoantigen 5: Variant Annotation, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): ...
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Associated Tutorial
This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Mass spectrometry imaging: Loading and exploring MSI data
Associated Tutorial
This workflows is part of the tutorial Mass spectrometry imaging: Loading and exploring MSI data, available in the GTN
Thanks to...
Tutorial Author(s): Melanie Föll, ...
ML Modeling of Anti-cancer Peptides
Associated Tutorial
This workflows is part of the tutorial Machine Learning Modeling of Anticancer Peptides, available in the GTN
Thanks to...
Tutorial Author(s): Jayadev Joshi, [Daniel ...
metaquantome-function
Associated Tutorial
This workflows is part of the tutorial metaQuantome 2: Function, available in the GTN
Thanks to...
Tutorial Author(s): Subina Mehta, Timothy J. Griffin, ...
metaquantome-data-creation
Associated Tutorial
This workflows is part of the tutorial metaQuantome 1: Data creation, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Subina ...
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Associated Tutorial
This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Peptide and Protein ID using OpenMS tools
Associated Tutorial
This workflows is part of the tutorial Peptide and Protein ID using OpenMS tools, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, [Björn ...
Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
Associated Tutorial
This workflows is part of the tutorial Peptide and Protein Quantification via Stable Isotope Labelling (SIL), available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Label-free data analysis using MaxQuant
Associated Tutorial
This workflows is part of the tutorial Label-free data analysis using MaxQuant, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Melanie ...
Peptide and Protein ID using OpenMS tools
Associated Tutorial
This workflows is part of the tutorial Peptide and Protein ID using OpenMS tools, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, [Björn ...
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Associated Tutorial
This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Subset data on the Mediterreanean see and extract and visualise the Phosphate variable
Associated Tutorial
This workflows is part of the tutorial Ocean's variables study, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy ...
Metaproteomics tutorial
Associated Tutorial
This workflows is part of the tutorial Metaproteomics tutorial, available in the GTN
Thanks to...
Tutorial Author(s): Timothy J. Griffin, Pratik Jagtap, ...
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Associated Tutorial
This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Create a protein Fusion database through the Arriba workflow
Associated Tutorial
This workflows is part of the tutorial Neoantigen 1: Fusion-Database-Generation, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Visualize Climate data with Panoply netCDF viewer
Associated Tutorial
This workflows is part of the tutorial Getting your hands-on climate data, available in the GTN
Thanks to...
Workflow Author(s): Anne Fouilloux
Tutorial Author(s): Anne Fouilloux
[![gtn star ...
Identification of the micro-organisms in a beer using Nanopore sequencing
Associated Tutorial
This workflows is part of the tutorial Identification of the micro-organisms in a beer using Nanopore sequencing, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
From Copernicus Sentinel 5P data to panoply visualization of volcanic activity impact to atmosphere
Associated Tutorial
This workflows is part of the tutorial Sentinel 5P data visualisation, available in the GTN
Thanks to...
Workflow Author(s): Marie Jossé
Tutorial Author(s): Marie Josse ...
Generating non-reference protein database for FragPipe discovery
Associated Tutorial
This workflows is part of the tutorial Neoantigen 2: Non-Reference-Database-Generation, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Protein FASTA Database Handling
Associated Tutorial
This workflows is part of the tutorial Protein FASTA Database Handling, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, [Björn ...
Process argo data with the Pangeo Ecosystem and visualise them with Ocean Data View (ODV)
Associated Tutorial
This workflows is part of the tutorial Analyse Argo data, available in the GTN
Thanks to...
Workflow Author(s): Marie Jossé
Tutorial Author(s): Marie Josse ...
Discovery workflow with SG/PS and MaxQuant to generate microbial peptides
Associated Tutorial
This workflows is part of the tutorial Clinical Metaproteomics 2: Discovery, available in the GTN
Thanks to...
Workflow Author(s): Subina Mehta
Tutorial Author(s): Subina Mehta, ...
Protein FASTA Database Handling
Associated Tutorial
This workflows is part of the tutorial Protein FASTA Database Handling, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, [Björn ...
Interpreting MaxQuant data using MSstats involves applying a rigorous statistical framework to glean meaningful insights from quantitative proteomic datasets
Associated Tutorial
This workflows is part of the tutorial Clinical Metaproteomics 5: Data Interpretation, available in the GTN
Thanks to...
Workflow Author(s): ...
Workflow for GTN Pangeo 101 for everyone - Introduction to Xarray
Associated Tutorial
This workflows is part of the tutorial Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools, available in the GTN
Thanks to...
Workflow Author(s): Anne Fouilloux
Tutorial Author(s): Anne Fouilloux ...
Calculating diversity from bracken output
Associated Tutorial
This workflows is part of the tutorial Calculating α and β diversity from microbiome taxonomic data, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Prediction of HLA binding for verified candidates
Associated Tutorial
This workflows is part of the tutorial Neoantigen 6: Predicting HLA Binding, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
...
Associated Tutorial
This workflows is part of the tutorial Proteogenomics 2: Database Search, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Tutorial Author(s): [Subina ...
16S Microbial Analysis with mothur (short)
Associated Tutorial
This workflows is part of the tutorial 16S Microbial Analysis with mothur (short), available in the GTN
Thanks to...
Workflow Author(s): Saskia Hiltemann
Tutorial Author(s): Saskia Hiltemann, ...
Functionally Assembled Terrestrial Ecosystem Simulator (FATES)
Associated Tutorial
This workflows is part of the tutorial Functionally Assembled Terrestrial Ecosystem Simulator (FATES), available in the GTN
Thanks to...
Workflow Author(s): Anne Fouilloux
Tutorial Author(s): Anne Fouilloux, ...
Associated Tutorial
This workflows is part of the tutorial MaxQuant and MSstats for the analysis of label-free data, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Tutorial Author(s): [Melanie ...
WF3- Peptide verification/validaiton workflow
Associated Tutorial
This workflows is part of the tutorial Clinical Metaproteomics 3: Verification, available in the GTN
Thanks to...
Workflow Author(s): Subina Mehta
Tutorial Author(s): Subina Mehta, ...
Detection and quantitation of N-termini (degradomics) via N-TAILS
Associated Tutorial
This workflows is part of the tutorial Detection and quantitation of N-termini (degradomics) via N-TAILS, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, ...
16S Microbial Analysis with mothur (short)
Associated Tutorial
This workflows is part of the tutorial 16S Microbial Analysis with mothur (short), available in the GTN
Thanks to...
Workflow Author(s): Saskia Hiltemann
Tutorial Author(s): Saskia Hiltemann, ...
Workflow for GTN Pangeo Notebook in Galaxy - Introduction to Xarray
Associated Tutorial
This workflows is part of the tutorial Pangeo Notebook in Galaxy - Introduction to Xarray, available in the GTN
Thanks to...
Workflow Author(s): Anne Fouilloux
Tutorial Author(s): Anne Fouilloux ...
DIA library Training HEK Ecoli data
Associated Tutorial
This workflows is part of the tutorial Library Generation for DIA Analysis, available in the GTN
Thanks to...
Tutorial Author(s): Matthias Fahrner, Melanie Föll ...
Quantification using the MaxQuant tool
Associated Tutorial
This workflows is part of the tutorial Clinical Metaproteomics 4: Quantitation, available in the GTN
Thanks to...
Workflow Author(s): Subina Mehta
Tutorial Author(s): Subina Mehta, ...
This workflow will create a simple plot of a microbial sized genome (e.g. E. coli) using a couple of datasets like sequencing depth (bigwigs), gff3 formatted annotations, and some variants.
Associated Tutorial
This workflows is part of the tutorial Ploting a Microbial Genome with Circos, available in the GTN
Features
- Includes [Galaxy ...
16S Microbial Analysis with mothur (short)
Associated Tutorial
This workflows is part of the tutorial 16S Microbial Analysis with mothur (short), available in the GTN
Thanks to...
Workflow Author(s): Saskia Hiltemann
Tutorial Author(s): Saskia Hiltemann, ...
version 1.0, 160318, published at https://github.com/Stortebecker/secretome_prediction
Associated Tutorial
This workflows is part of the tutorial Secretome Prediction, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, ...
Validate the NeoAntigen Candidates from FragPipe discovery through the PepQuery Novel search
Associated Tutorial
This workflows is part of the tutorial Neoantigen 4: PepQuery2 Verification, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Annotating a protein list identified by LC-MS/MS experiments
Associated Tutorial
This workflows is part of the tutorial Annotating a protein list identified by LC-MS/MS experiments, available in the GTN
Thanks to...
Tutorial Author(s): Valentin Loux, [Florence ...
Visualisation with Circos
Associated Tutorial
This workflows is part of the tutorial Visualisation with Circos, available in the GTN
Thanks to...
Workflow Author(s): Helena Rasche, Saskia Hiltemann
Tutorial Author(s): Saskia Hiltemann, [Helena ...
Visualisation with Circos
Associated Tutorial
This workflows is part of the tutorial Visualisation with Circos, available in the GTN
Thanks to...
Workflow Author(s): Helena Rasche, Saskia Hiltemann
Tutorial Author(s): Saskia Hiltemann, [Helena ...
16S Microbial Analysis with mothur (short)
Associated Tutorial
This workflows is part of the tutorial 16S Microbial Analysis with mothur (short), available in the GTN
Thanks to...
Workflow Author(s): Saskia Hiltemann
Tutorial Author(s): Saskia Hiltemann, ...
Merging Fusion and non-normal databases + Discovery peptidomics using FragPipe
Associated Tutorial
This workflows is part of the tutorial Neoantigen 3: Database merge and FragPipe discovery, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Annotating a protein list identified by LC-MS/MS experiments
Associated Tutorial
This workflows is part of the tutorial Annotating a protein list identified by LC-MS/MS experiments, available in the GTN
Thanks to...
Tutorial Author(s): Valentin Loux, [Florence ...
Submitting SARS-CoV-2 sequences to ENA
Associated Tutorial
This workflows is part of the tutorial Submitting sequence data to ENA, available in the GTN
Thanks to...
Tutorial Author(s): Miguel Roncoroni, [Bert ...
16S Microbial Analysis with mothur (short)
Associated Tutorial
This workflows is part of the tutorial 16S Microbial Analysis with mothur (short), available in the GTN
Thanks to...
Workflow Author(s): Saskia Hiltemann
Tutorial Author(s): Saskia Hiltemann, ...
Associated Tutorial
This workflows is part of the tutorial Proteogenomics 1: Database Creation, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Tutorial Author(s): [Subina ...
Predict binding using IEDB and check novelty peptides with PepQuery
Associated Tutorial
This workflows is part of the tutorial Neoantigen 7: IEDB binding PepQuery Validated Neopeptides, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
introduction
Associated Tutorial
This workflows is part of the tutorial Workflow Reports, available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann
Tutorial Contributor(s): Helena Rasche, ...
16S Microbial Analysis with mothur (short)
Associated Tutorial
This workflows is part of the tutorial 16S Microbial Analysis with mothur (short), available in the GTN
Thanks to...
Workflow Author(s): Saskia Hiltemann
Tutorial Author(s): Saskia Hiltemann, ...
Biomarker candidate identification
Associated Tutorial
This workflows is part of the tutorial Biomarker candidate identification, available in the GTN
Thanks to...
Tutorial Author(s): Florence Combes, [David ...
introduction
Associated Tutorial
This workflows is part of the tutorial Workflow Reports, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Tutorial Author(s): [Saskia ...
MaxQuant and MSstats for the analysis of TMT data
Associated Tutorial
This workflows is part of the tutorial MaxQuant and MSstats for the analysis of TMT data, available in the GTN
Thanks to...
Tutorial Author(s): Klemens Fröhlich, [Melanie ...
16S Microbial Analysis with mothur (short)
Associated Tutorial
This workflows is part of the tutorial 16S Microbial Analysis with mothur (short), available in the GTN
Thanks to...
Workflow Author(s): Saskia Hiltemann
Tutorial Author(s): Saskia Hiltemann, ...
Peptide and Protein ID using SearchGUI and PeptideShaker
Associated Tutorial
This workflows is part of the tutorial Peptide and Protein ID using SearchGUI and PeptideShaker, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, ...
Intermine import/export
Associated Tutorial
This workflows is part of the tutorial InterMine integration with Galaxy, available in the GTN
Thanks to...
Tutorial Author(s): Daniela Butano, Yo Yehudi ...
Workflows: Using Workflow Parameters
Associated Tutorial
This workflows is part of the tutorial Using Workflow Parameters, available in the GTN
Thanks to...
Tutorial Author(s): Marius van den Beek, Helena Rasche ...
workflow-editor
Associated Tutorial
This workflows is part of the tutorial Creating, Editing and Importing Galaxy Workflows, available in the GTN
Features
- Uses subworkflows
Thanks to...
Tutorial Author(s): [Marius van den ...
Building an amplicon sequence variant (ASV) table from 16S data using DADA2
Associated Tutorial
This workflows is part of the tutorial Building an amplicon sequence variant (ASV) table from 16S data using DADA2, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Peptide and Protein ID using SearchGUI and PeptideShaker
Associated Tutorial
This workflows is part of the tutorial Peptide and Protein ID using SearchGUI and PeptideShaker, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, ...
Discovery workflow with SG/PS and MaxQuant to generate microbial peptides
Associated Tutorial
This workflows is part of the tutorial Clinical Metaproteomics 2: Discovery, available in the GTN
Thanks to...
Workflow Author(s): Subina Mehta
Tutorial Author(s): Subina Mehta, ...
workflow-editor
Associated Tutorial
This workflows is part of the tutorial Creating, Editing and Importing Galaxy Workflows, available in the GTN
Thanks to...
Tutorial Author(s): Marius van den Beek
[![gtn star logo followed by the word ...
Peptide Library Data Analysis
Associated Tutorial
This workflows is part of the tutorial Peptide Library Data Analysis, available in the GTN
Thanks to...
Tutorial Author(s): Jayadev Joshi, [Daniel ...
Associated Tutorial
This workflows is part of the tutorial Assembly of metagenomic sequencing data, available in the GTN
Thanks to...
Tutorial Author(s): Polina Polunina, Bérénice Batut ...
workflow-automation
Associated Tutorial
This workflows is part of the tutorial Automating Galaxy workflows using the command line, available in the GTN
Thanks to...
Workflow Author(s): Wolfgang Maier
Tutorial Author(s): Simon Bray, [Wolfgang ...
Associated Tutorial
This workflows is part of the tutorial Multiomics data analysis using MultiGSEA, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report ...
EOSC4Cancer_D2.2
Galaxy workflow used for EOSC4Cancer D2.2 - Analytical methods for data extraction, processing and sharing using biomedical images - demonstrator
Link to deliverable report on Zenodo:
Type: Galaxy
Creators: Jeanne Chèneby, Hakim Achterberg, Dario Longo, Francesco Gammaraccio, Robin Navest
Submitter: Robin Navest
This Galaxy workflow streamlines comprehensive copy number variation (CNV) analysis by integrating CNVkit’s robust detection capabilities with an efficient conversion step using cnv-vcf2json to format results into Beacon JSON. Designed for computational biologists and bioinformaticians, the workflow standardizes CNV identification and output formatting to enhance interoperability with Beacon networks. It is specifically optimized for use with mapped BAM files from the EGAD00001008392 synthetic ...
PAIRED-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.
IMPORTANT:
- For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
- SELECT THE MOST ADAPTED VADR MODEL for annotation (see vadr parameters).
SINGLE-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.
IMPORTANT:
- For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
- SELECT the mot ADAPTED VADR MODEL for annotation (see vadr parameters).
Workflow for tracking objects in Cell Profiler: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html
Performs Long Read assembly using PacBio data and Hifiasm. Part of VGP assembly pipeline. This workflow generate a phased assembly.
Performs scaffolding using HiC Data. Part of VGP assembly pipeline. The scaffolding can be performed on long read assembly contigs or on scaffolds (e.g.: Bionano scaffolds).
Performs scaffolding using Bionano Data. Part of VGP assembly pipeline.
Purge Phased assembly of duplications and overlaps. Include purge steps for Primary and Alternate assemblies.
Performs Long Read assembly using PacBio data and Hifiasm. Part of VGP assembly pipeline. This workflow generate a phased assembly.
Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.
Workflow to take DataOne data packages (raw datasets + metadata written in Ecological Metadata Standard) as input and create a DwC occurence.csv file almost ready to put in a Dawrin core Archive using eml-annotations at the attribute level
This workflow has been created as part of Demonstrator 6 of the project EOSC-Life (within WP3) and is focused on reusing publicly available RNAi screens to gain insights into the nucleolus biology. The workflow downloads images from the Image Data Resource (IDR), performs object segmentation (of nuclei and nucleoli) and feature extraction of the images and objects identified.
Abstract CWL Automatically generated from the Galaxy workflow file: Workflow with Copernicus Essential Climate Variable - select and plot
Alignment, assembly and annotation of RNQSEQ reads using TOPHAT (without filtering out host reads).
Detects SNPs and INDELs using VARSCAN2.
Collection of de-novo genome assembly workflows written for implementation in Galaxy
Input data should be Oxford Nanopore raw reads plus Illumina WGS reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output one scaffolded collapsed assembly and the complete QC analyses
Please run the workflows in order: WF0 (there are two, one for ONT, and another one for Illumina that can be used independently for the WGS and HiC reads), WF1, WF2, WF3, WF4
Maintainers: Diego De Panis
Number of items: 6
Tags: Assembly, Bioinformatics, Galaxy, Genomics, Genome assembly, ONT, illumina, Hi-C
Collection of de-novo genome assembly workflows written for implementation in Galaxy
Input data should be Oxford Nanopore raw reads plus Illumina WGS reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output one scaffolded collapsed assembly and the complete QC analyses
Please run the workflows in order: WF0 (there are two, one for ONT, and another one for Illumina that can be used independently for the WGS and HiC reads), WF1, WF2, WF3, WF4
Maintainers: Diego De Panis
Number of items: 6
Tags: Assembly, Bioinformatics, Galaxy, Genomics, Genome assembly, ONT, illumina, Hi-C
Collection of de-novo genome assembly workflows written for implementation in Galaxy
Input data should be PacBio HiFi reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output two scaffolded haplotype assemblies and the complete QC analyses
Please run the workflows in order: WF0 (there are two, one for HiFi and one for Illumina HiC), WF1, WF2, WF3, WF4
Maintainers: Tom Brown, Diego De Panis
Number of items: 6
Tags: Assembly, Bioinformatics, Galaxy, Genomics, Genome assembly, HiFi, Hi-C
The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data. Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, ...