Structural genome annotation with Helixer
Associated Tutorial
This workflows is part of the tutorial Genome annotation with Helixer, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Romane Libouban ...
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 ...
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, ...
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, ...
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): ...
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, ...
Generating a large database and then reducing it to a compact database using Metanovo
Associated Tutorial
This workflows is part of the tutorial Clinical Metaproteiomics 1: Database-Generation, available in the GTN
Thanks to...
Workflow Author(s): Subina Mehta
Tutorial Author(s): [Subina ...
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 ...
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 ...
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 ...
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 ...
Visualisation with Circos
Associated Tutorial
This workflows is part of the tutorial Circos: Nature workflow, available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, Helena Rasche, ...
workflow-editor
Associated Tutorial
This workflows is part of the tutorial Tutorial workflow, available in the GTN
Thanks to...
Tutorial Author(s): Marius van den Beek
[![gtn star logo followed by the word ...
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
Thanks
...
Submitting SARS-CoV-2 sequences to ENA
Associated Tutorial
This workflows is part of the tutorial GTN_ENA_upload_workflow, available in the GTN
Thanks to...
Tutorial Author(s): Miguel Roncoroni, [Bert ...
Small Non-coding RNA Clustering using BlockClust
Associated Tutorial
This workflows is part of the tutorial Blockclust 1.1.0 Clustering, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): ...
Analyse Bulk RNA-Seq data in preparation for downstream Pathways analysis with MINERVA
Associated Tutorial
This workflows is part of the tutorial mRNA-Seq BY-COVID Pipeline: Analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Classification in Machine Learning
Associated Tutorial
This workflows is part of the tutorial ml_classification, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Alireza ...
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 BY-COVID: Data Download, available in the GTN
Features
- Includes [Galaxy Workflow ...
Reference-based RNA-Seq data analysis
Associated Tutorial
This workflows is part of the tutorial QC + Mapping + Counting (single+paired) - Ref Based RNA Seq - Transcriptomics - GTN, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks
...
Regression in Machine Learning
Associated Tutorial
This workflows is part of the tutorial ml_regression, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Alireza ...
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 mRNA-Seq BY-COVID Pipeline: Counts, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Reference-based RNA-Seq data analysis
Associated Tutorial
This workflows is part of the tutorial DEG Part - Ref Based RNA Seq - Transcriptomics - GTN, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): ...
Associated Tutorial
This workflows is part of the tutorial gpu_jupytool, available in the GTN
Thanks to...
Tutorial Author(s): Anup Kumar
Training workflow
Associated Tutorial
This workflows is part of the tutorial Genome-wide alternative splicing analysis: human, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): ...
Reference-based RNA-Seq data analysis
Associated Tutorial
This workflows is part of the tutorial QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Uses ...
Image classification with fruit 360 dataset
Associated Tutorial
This workflows is part of the tutorial fruit_360, available in the GTN
Thanks to...
Tutorial Author(s): Kaivan Kamali
Workflow Author(s): Kaivan Kamali
[![gtn star logo followed by the word ...
RNA-seq counts to genes
Associated Tutorial
This workflows is part of the tutorial RNA Seq Counts To Genes, available in the GTN
Thanks to...
Tutorial Author(s): Maria Doyle, Belinda Phipson, ...
Basics of machine learning
Associated Tutorial
This workflows is part of the tutorial Machine Learning, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Anup ...
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 ...
Identify upregulated miRNAS and analyze potential targets in downregulated genes.
Associated Tutorial
This workflows is part of the tutorial Plant bulk RNA-Seq workflow, available in the GTN
Thanks to...
Tutorial Author(s): Cristóbal Gallardo, ...
Interval-Wise Testing for omics data
Associated Tutorial
This workflows is part of the tutorial Workflow Constructed From History 'IWTomics Workflow', available in the GTN
Thanks to...
Tutorial Author(s): Marzia A Cremona, [Fabio ...
RNA-seq genes to pathways
Associated Tutorial
This workflows is part of the tutorial RNA Seq Genes To Pathways (imported from uploaded file), available in the GTN
Thanks to...
Tutorial Author(s): Maria Doyle, [Belinda ...
GO Enrichment Analysis Tutorial
Associated Tutorial
This workflows is part of the tutorial GO Enrichment Workflow, available in the GTN
Thanks to...
Tutorial Author(s): IGC Bioinformatics Unit, Maria Doyle ...
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 From BAMs to drug resistance prediction with TB-profiler, available in the GTN
Thanks to...
Tutorial Author(s): [Galo A. ...
Associated Tutorial
This workflows is part of the tutorial Intro_To_CNN_v1.0.11.0, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Kaivan Kamali ...
Retrieve climate data from Copernicus
Associated Tutorial
This workflows is part of the tutorial Retrieve climate data from Copernicus, available in the GTN
Thanks to...
Tutorial Author(s): Bérénice Batut, [Helena ...
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 Simtext training workflow, available in the GTN
Thanks to...
**Tutorial ...
Visualization of RNA-Seq results with heatmap2
Associated Tutorial
This workflows is part of the tutorial Heatmap2 Workflow, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Maria ...
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 From VCFs to SNP distance matrix, available in the GTN
Thanks to...
**Tutorial ...
Creating a new tutorial
Associated Tutorial
This workflows is part of the tutorial MakeAFakeInput, available in the GTN
Thanks to...
Tutorial Author(s): Bérénice Batut, Helena Rasche, ...
Associated Tutorial
This workflows is part of the tutorial Intro_To_FNN_v1_0_10_0, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Kaivan Kamali ...
roscoff hackathon
Associated Tutorial
This workflows is part of the tutorial trinity NG, available in the GTN
Thanks to...
Tutorial Author(s): Anthony Bretaudeau, Gildas Le Corguillé, ...
From Fastqs to VCFs and BAMs
Associated Tutorial
This workflows is part of the tutorial From Fastqs to VCFs and BAMs, available in the GTN
Thanks to...
Tutorial Author(s): Galo A. Goig, Daniela Brites, ...
Workflows: Using Workflow Parameters
Associated Tutorial
This workflows is part of the tutorial Select First N Lines, available in the GTN
Thanks to...
Tutorial Author(s): Marius van den Beek, Helena Rasche ...
Network analysis with Heinz
Associated Tutorial
This workflows is part of the tutorial Workflow Constructed From History 'Heinz Workflow Trial Sep 11', available in the GTN
Thanks to...
Tutorial Author(s): Chao Zhang
[![gtn star logo ...
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 ...
introduction
Associated Tutorial
This workflows is part of the tutorial GTN Training: Workflow Reports - Galaxy 101 For Everyone, available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann
Tutorial Contributor(s): [Helena ...
Estimate a phylogenetic tree from whole genome sequencing data for M. tuberculosis
Associated Tutorial
This workflows is part of the tutorial Mtb phylogeny, available in the GTN
Thanks to...
Tutorial Author(s): Christoph Stritt, [Daniela ...
rna-seq-reads-to-counts
Associated Tutorial
This workflows is part of the tutorial QC report, available in the GTN
Thanks to...
Tutorial Author(s): Maria Doyle, Belinda Phipson, ...
Introduction to Deep Learning
Associated Tutorial
This workflows is part of the tutorial Intro_To_Deep_Learning, available in the GTN
Thanks to...
Tutorial Author(s): Anup Kumar, Alireza Khanteymoori ...
introduction
Associated Tutorial
This workflows is part of the tutorial GTN Training: Workflow Reports, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Tutorial Author(s): [Saskia ...
Tree building for "Phylogenetics - Back to basics"
Associated Tutorial
This workflows is part of the tutorial Tree Building (imported from uploaded file), available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): ...
RNA-Seq reads to counts
Associated Tutorial
This workflows is part of the tutorial RNA Seq Reads To Counts, available in the GTN
Thanks to...
Tutorial Author(s): Maria Doyle, Belinda Phipson, ...
Machine learning: classification and regression
Associated Tutorial
This workflows is part of the tutorial Classification LSVC, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Anup ...
workflow-automation
Associated Tutorial
This workflows is part of the tutorial vcf2lineage, available in the GTN
Thanks to...
Tutorial Author(s): Simon Bray, Wolfgang Maier ...
Associated Tutorial
This workflows is part of the tutorial Training Sanger sequences CHD8, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Coline ...
RNA-RNA interactome analysis using ChiRA tool suite
Associated Tutorial
This workflows is part of the tutorial RNA-RNA interactome data analysis - chira v1.4.3, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Tutorial ...
Intermine import/export
Associated Tutorial
This workflows is part of the tutorial Intermine import/export, available in the GTN
Thanks to...
Tutorial Author(s): Daniela Butano, Yo Yehudi ...
workflow-editor
Associated Tutorial
This workflows is part of the tutorial Subworkflow, available in the GTN
Features
- Uses subworkflows
Thanks to...
Tutorial Author(s): Marius van den Beek ...
Machine learning: classification and regression
Associated Tutorial
This workflows is part of the tutorial Regression GradientBoosting, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Anup ...
Associated Tutorial
This workflows is part of the tutorial Sanger1 : From AB1 to aligned consensus and primers fasta + BLAST, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Coline ...
RAD-Seq de-novo data analysis
Associated Tutorial
This workflows is part of the tutorial de novo Rad Seq, available in the GTN
Thanks to...
Tutorial Author(s): Yvan Le Bras
[![gtn star logo followed by the word ...
CLIP-Seq data analysis from pre-processing to motif detection
Associated Tutorial
This workflows is part of the tutorial Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38 , available in the GTN
Thanks to...
Tutorial Author(s): Florian Heyl, [Daniel ...
PanCancer Aberrant Pathway Activity Analysis: PI3K example
Associated Tutorial
This workflows is part of the tutorial papaa@0.1.9_PI3K_OG_model_tutorial, available in the GTN
Thanks to...
Tutorial Author(s): Vijay, [Daniel ...
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, ...
Quality Control
Associated Tutorial
This workflows is part of the tutorial GTN - Sequence Analyses - Quality Control (imported from uploaded file), available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): ...
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 sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming), available in the GTN
Thanks to...
Tutorial Author(s): [Mallory ...
Age prediction using machine learning
Associated Tutorial
This workflows is part of the tutorial Age Prediction RNA-Seq, available in the GTN
Thanks to...
Tutorial Author(s): Ekaterina Polkh, Anup Kumar ...
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 sRNA Seq Step 2: Salmon And DESeq2, available in the GTN
Thanks to...
Tutorial Author(s): Mallory Freeberg ...
Biodiversity data exploration
Associated Tutorial
This workflows is part of the tutorial Workflow 'Biodiversity data exploration tuto', available in the GTN
Thanks to...
Tutorial Author(s): Olivier Norvez, [Marie ...
Age prediction using machine learning
Associated Tutorial
This workflows is part of the tutorial Age Prediction DNA Methylation, available in the GTN
Thanks to...
Tutorial Author(s): Ekaterina Polkh, Anup Kumar ...
Associated Tutorial
This workflows is part of the tutorial scATAC-seq Count Matrix Filtering, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Pavankumar ...
Removal of human reads from SARS-CoV-2 sequencing data
Associated Tutorial
This workflows is part of the tutorial GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data, available in the GTN
Thanks to...
Tutorial Author(s): Wolfgang Maier ...
Metabarcoding/eDNA through Obitools
Associated Tutorial
This workflows is part of the tutorial Workflow constructed from history 'Tuto Obitools', available in the GTN
Thanks to...
Tutorial Author(s): Coline Royaux, [Olivier ...
Associated Tutorial
This workflows is part of the tutorial Intro_To_RNN_v1_0_10_0, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Kaivan Kamali ...
Associated Tutorial
This workflows is part of the tutorial NCBI to Anndata, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Morgan Howells ...
Analyse HeLa fluorescence siRNA screen
Associated Tutorial
This workflows is part of the tutorial analyze_screen, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Uses subworkflows ...
Associated Tutorial
This workflows is part of the tutorial feature_extraction, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Thomas Wollmann, ...
Mapping
Associated Tutorial
This workflows is part of the tutorial GTN - Sequence Analyses - Mapping - Jbrowse (imported from uploaded file), available in the GTN
Thanks to...
Tutorial Author(s): Joachim Wolff, [Bérénice ...
Cleaning GBIF data for the use in Ecology
Associated Tutorial
This workflows is part of the tutorial GBIF data Quality check and filtering workflow Feb-2020, available in the GTN
Thanks to...
Tutorial Author(s): Yvan Le Bras, [Simon ...
End-to-End Tissue Microarray Analysis with Galaxy-ME
Associated Tutorial
This workflows is part of the tutorial GTN_Exemplar_002_TMA_workflow, available in the GTN
Thanks to...
Tutorial Author(s): Cameron Watson, [Allison ...
Downstream Single-cell RNA Plant analysis with ScanPy
Associated Tutorial
This workflows is part of the tutorial scRNA Plant Analysis, available in the GTN
Thanks to...
Tutorial Author(s): Mehmet Tekman, Beatriz Serrano-Solano, ...
Mapping
Associated Tutorial
This workflows is part of the tutorial GTN - Sequence Analyses - Mapping (imported from uploaded file), available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Joachim ...
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 ...
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
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Tutorial ...
Nucleoli segmentation and feature extraction using CellProfiler
Associated Tutorial
This workflows is part of the tutorial CP_pipeline_IDR_training, available in the GTN
Thanks to...
Tutorial Author(s): Beatriz Serrano-Solano, [Jean-Karim ...
This workflow creates an ESet object from scRNA metadata file and EBI SCXA retrieveal
Associated Tutorial
This workflows is part of the tutorial MuSiC-Deconvolution: Data generation | sc | matrix + ESet, available in the GTN
Features
- Uses subworkflows ...
Visualization of Climate Data using NetCDF Xarray Map Plotting
Associated Tutorial
This workflows is part of the tutorial Xarray_Map_Plotting_Workflow, available in the GTN
Thanks to...
Tutorial Author(s): Soumya Jha
Workflow Author(s): Soumya Jha ...
Workflow based on clustering 3K PBMCs with Scanpy tutorial
Associated Tutorial
This workflows is part of the tutorial Clustering 3k PBMC with Scanpy, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): ...
Associated Tutorial
This workflows is part of the tutorial Workflow constructed from Tutorial 'Introduction to image analysis using Galaxy', available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Thomas ...
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 MuSiC-Deconvolution: Data generation | sc | metadata, available in the GTN
Thanks to...
Tutorial Author(s): Wendi Bacon, ...
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 ...
AnnData to Seurat format conversion (manually using Galaxy buttons)
Associated Tutorial
This workflows is part of the tutorial AnnData to Seurat conversion, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Tutorial ...
example cellprofiler pipeline
Associated Tutorial
This workflows is part of the tutorial CP_object_tracking_example, available in the GTN
Thanks to...
Tutorial Author(s): Yi Sun, Beatriz Serrano-Solano, ...
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 Circos for E. Coli, available in the GTN
Features
- Includes [Galaxy Workflow ...
From Obis data to Biodiversity indicators
Associated Tutorial
This workflows is part of the tutorial Marine Omics visualisation, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Marie ...
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 AnnData to Cell Data Set (CDS) conversion, available in the GTN
Features
- Includes [Galaxy Workflow ...
RAD-Seq Reference-based data analysis
Associated Tutorial
This workflows is part of the tutorial Workflow Constructed From History 'STACKS RAD: Population Genomics With Reference Genome', available in the GTN
Thanks to...
Tutorial Author(s): Yvan Le Bras ...
Visualisation with Circos
Associated Tutorial
This workflows is part of the tutorial Circos: Nature workflow, available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, Helena Rasche, ...
Visualisation with Circos
Associated Tutorial
This workflows is part of the tutorial Circos tutorial, available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, Helena Rasche, ...
AnnData to SCE format conversion (manually using Galaxy buttons)
Associated Tutorial
This workflows is part of the tutorial AnnData to SingleCellExperiment (SCE) conversion, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
...
Associated Tutorial
This workflows is part of the tutorial Cell Cycle Regression Workflow, available in the GTN
Thanks to...
Tutorial Author(s): Marisa Loach
Tutorial Contributor(s): Wendi Bacon, ...
RAD-Seq Reference-based data analysis
Associated Tutorial
This workflows is part of the tutorial Ref Based Rad Seq, available in the GTN
Thanks to...
Tutorial Author(s): Yvan Le Bras
[![gtn star logo followed by the word ...
Peptide Library Data Analysis
Associated Tutorial
This workflows is part of the tutorial Copy of PeptideDataAnalysis (imported from uploaded file), available in the GTN
Thanks to...
Tutorial Author(s): Jayadev Joshi, [Daniel ...
Associated Tutorial
This workflows is part of the tutorial Scanpy Parameter Iterator workflow full (imported from URL), available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Julia ...
Associated Tutorial
This workflows is part of the tutorial NDVI with OpenEO, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Marie Josse ...
Single-cell quality control with scater
Associated Tutorial
This workflows is part of the tutorial Scater, available in the GTN
Thanks to...
Tutorial Author(s): Graham Etherington, Nicola Soranzo ...
MaxQuant and MSstats for the analysis of label-free data
Associated Tutorial
This workflows is part of the tutorial Proteomics: MaxQuant and MSstats LFQ workflow, available in the GTN
Thanks to...
Tutorial Author(s): Melanie Föll, [Matthias ...
Associated Tutorial
This workflows is part of the tutorial NDVI with OpenEO, available in the GTN
Thanks to...
Tutorial Author(s): Marie Josse
Workflow Author(s): Marie Jossé
Funder(s): Fair-Ease, ...
Associated Tutorial
This workflows is part of the tutorial Inferring Trajectories with Scanpy Tutorial Workflow, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Marisa ...
Trajectory analysis using Monocle3, starting from 3 input files: expression matrix, gene and cell annotations
Associated Tutorial
This workflows is part of the tutorial Monocle3 workflow, available in the GTN
Thanks to...
Tutorial Author(s): Julia Jakiela ...
Proteogenomics 3: Novel peptide analysis
Associated Tutorial
This workflows is part of the tutorial GTN Proteogemics3 Novel Peptide Analysis, available in the GTN
Thanks to...
Tutorial Author(s): Subina Mehta, [Timothy J. ...
Species distribution modeling
Associated Tutorial
This workflows is part of the tutorial Species Distribution Modeling With Wallace From GBIF - Training Material, available in the GTN
Thanks to...
Tutorial Author(s): Elisa Michon, [Yvan Le ...
Bulk RNA Deconvolution with MuSiC
Associated Tutorial
This workflows is part of the tutorial MuSiC Workflow, available in the GTN
Thanks to...
Tutorial Author(s): Mehmet Tekman, Wendi Bacon ...
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 AnnData object to Monocle input files, available in the GTN
Thanks to...
Tutorial Author(s): Julia Jakiela ...
Biomarker candidate identification
Associated Tutorial
This workflows is part of the tutorial 'Biomarkers4Paris' Workflow, available in the GTN
Thanks to...
Tutorial Author(s): Florence Combes, David Christiany, ...
Regional GAM
Associated Tutorial
This workflows is part of the tutorial Abundance Index "stacked" Visualization Creation, available in the GTN
Thanks to...
Tutorial Author(s): Clara Urfer, Elisa Michon, ...
This workflow creates bulk ESet objects from uploaded raw matrix & metadata files
Associated Tutorial
This workflows is part of the tutorial MuSiC-Deconvolution: Data generation | bulk | ESet, available in the GTN
Features
- Uses subworkflows ...
Regional GAM
Associated Tutorial
This workflows is part of the tutorial Tutorial regionalGAM Complete Multispecies, available in the GTN
Thanks to...
Tutorial Author(s): Clara Urfer, Elisa Michon, ...
Trajectory analysis using Monocle3, starting from AnnData
Associated Tutorial
This workflows is part of the tutorial Trajectory analysis using Monocle3 - full tutorial workflow, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
MaxQuant and MSstats for the analysis of TMT data
Associated Tutorial
This workflows is part of the tutorial MaxQuant MSstatsTMT Training, available in the GTN
Thanks to...
Tutorial Author(s): Klemens Fröhlich, [Melanie ...
Regional GAM
Associated Tutorial
This workflows is part of the tutorial Phenology "stacked" Visualization Creation, available in the GTN
Thanks to...
Tutorial Author(s): Clara Urfer, Elisa Michon, ...
Updated March 2024
Associated Tutorial
This workflows is part of the tutorial Combining datasets after pre-processing, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Wendi ...
DIA library Training HEK Ecoli data
Associated Tutorial
This workflows is part of the tutorial DIA_lib_OSW, available in the GTN
Thanks to...
Tutorial Author(s): Matthias Fahrner, Melanie Föll ...
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 MuSiC-Deconvolution: Compare, ...
Regional GAM
Associated Tutorial
This workflows is part of the tutorial Regional GAM Workflow, available in the GTN
Thanks to...
Tutorial Author(s): Clara Urfer, Elisa Michon, [Yvan Le ...
metaquantome-function
Associated Tutorial
This workflows is part of the tutorial metaquantome-function-worklow, available in the GTN
Thanks to...
Tutorial Author(s): Subina Mehta, Timothy J. Griffin, ...
Associated Tutorial
This workflows is part of the tutorial Preprocessing of 10X scRNA-seq data, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Mehmet ...
Updated tool versions Aug 24 2022
Associated Tutorial
This workflows is part of the tutorial CS3_Filter, Plot and Explore Single-cell RNA-seq Data, available in the GTN
Thanks to...
Tutorial Author(s): Wendi Bacon
Tutorial Contributor(s): ...
Pre-processing of Single-Cell RNA Data
Associated Tutorial
This workflows is part of the tutorial CelSeq2: Multi Batch (mm10), available in the GTN
Features
- Uses subworkflows
Thanks to...
Tutorial Author(s): [Mehmet ...
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 ...
RAD-Seq to construct genetic maps
Associated Tutorial
This workflows is part of the tutorial Genetic Map Rad Seq Workflow, available in the GTN
Thanks to...
Tutorial Author(s): Yvan Le Bras
[![gtn star logo followed by the word ...
Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
Associated Tutorial
This workflows is part of the tutorial Proteomics: Peptide and Protein Quantification via stable istobe labeling, 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 CelSeq2: Single Batch (mm10), available in the GTN
Thanks to...
Tutorial Author(s): Mehmet Tekman, Bérénice Batut, ...
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 updated, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks
...
Detection and quantitation of N-termini (degradomics) via N-TAILS
Associated Tutorial
This workflows is part of the tutorial Tails Triple Dimethyl OpenMS2.1, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, [Björn ...
Associated Tutorial
This workflows is part of the tutorial Sentinel 2 example, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Marie Josse, ...
Creates input file for Filter, Plot, Explore tutorial
Associated Tutorial
This workflows is part of the tutorial EBI SCXA to AnnData (Scanpy) or Seurat Object, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Tutorial ...
Annotating a protein list identified by LC-MS/MS experiments
Associated Tutorial
This workflows is part of the tutorial ProteoRE ProteomeAnnotation Tutorial (release 2.0), available in the GTN
Thanks to...
Tutorial Author(s): Valentin Loux, [Florence ...
Associated Tutorial
This workflows is part of the tutorial scATAC-seq FASTQ to Count Matrix, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Pavankumar ...
Annotating a protein list identified by LC-MS/MS experiments
Associated Tutorial
This workflows is part of the tutorial 'Proteome Annotation', available in the GTN
Thanks to...
Tutorial Author(s): Valentin Loux, [Florence ...
Data Manipulation Olympics
Associated Tutorial
This workflows is part of the tutorial GTN Tutorial: Data manipulation Olympics - all steps and exercises, available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann
**Tutorial ...
Downstream Single-cell RNA analysis with RaceID
Associated Tutorial
This workflows is part of the tutorial RaceID Workflow, available in the GTN
Thanks to...
Tutorial Author(s): Mehmet Tekman, Alex Ostrovsky ...
Protein FASTA Database Handling
Associated Tutorial
This workflows is part of the tutorial Proteomics: database handling, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, [Björn ...
From Copernicus Sentinel 5P data to panoply visualization of volcanic activity impact to atmosphere
Associated Tutorial
This workflows is part of the tutorial Sentinel5 volcanic data, available in the GTN
Thanks to...
Tutorial Author(s): Marie Josse
**Workflow ...
Structural and functional genome annotation with Funannotate
Associated Tutorial
This workflows is part of the tutorial Funannotate, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Anthony ...
Proteogenomics Galaxy Training Network Database Creation
Associated Tutorial
This workflows is part of the tutorial GTN Proteogenomics1 Database Creation, available in the GTN
Thanks to...
Tutorial Author(s): Subina Mehta, [Timothy J. ...
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 ...
Protein FASTA Database Handling
Associated Tutorial
This workflows is part of the tutorial Proteomics: database handling including mycoplasma, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, [Björn ...
Masking repeats in a genome using RepeatMasker
Associated Tutorial
This workflows is part of the tutorial RepeatMasker, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Anthony ...
Assembly with preprocessing and SRA download
Associated Tutorial
This workflows is part of the tutorial assembly_with_preprocessing_and_sra_download, available in the GTN
Thanks to...
Tutorial Author(s): Wolfgang Maier
[![gtn star logo followed by the ...
Workflow for GTN Pangeo 101 for everyone - Introduction to Xarray
Associated Tutorial
This workflows is part of the tutorial GTN 'Pangeo 101 for everyone - Xarray', available in the GTN
Thanks to...
Tutorial Author(s): Anne Fouilloux
Workflow Author(s): Anne Fouilloux ...
ML Modeling of Anti-cancer Peptides
Associated Tutorial
This workflows is part of the tutorial PeptideML, available in the GTN
Thanks to...
Tutorial Author(s): Jayadev Joshi, Daniel Blankenberg ...
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 ...
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...
Tutorial Author(s): Marie Josse
Workflow Author(s): Marie ...
tutorial
Associated Tutorial
This workflows is part of the tutorial Intro to Genome Assembly, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Simon Gladman ...
Peptide and Protein ID using OpenMS tools
Associated Tutorial
This workflows is part of the tutorial Peptide And Protein ID Via OMS Using Two Search Engines, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, [Björn ...
Refining Genome Annotations with Apollo
Associated Tutorial
This workflows is part of the tutorial Apollo Load Test, available in the GTN
Thanks to...
Tutorial Author(s): Anthony Bretaudeau, Helena Rasche, ...
Workflow for GTN Pangeo Notebook in Galaxy - Introduction to Xarray
Associated Tutorial
This workflows is part of the tutorial Pangeo Jupyter Notebook, available in the GTN
Thanks to...
Tutorial Author(s): Anne Fouilloux
Workflow Author(s): Anne Fouilloux ...
Peptide and Protein ID using OpenMS tools
Associated Tutorial
This workflows is part of the tutorial Proteomics: Peptide and Protein ID using OpenMS, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, [Björn ...
VGP assembly tutorial
Associated Tutorial
This workflows is part of the tutorial VGP assembly: training workflow, available in the GTN
Thanks to...
Tutorial Author(s): Delphine Lariviere, Alex Ostrovsky, ...
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...
Tutorial Author(s): [Anna ...
Functionally Assembled Terrestrial Ecosystem Simulator (FATES)
Associated Tutorial
This workflows is part of the tutorial CLM-FATES_ ALP1 simulation (5 years), available in the GTN
Thanks to...
Tutorial Author(s): Anne Fouilloux, [Hui ...
Mass spectrometry imaging: Loading and exploring MSI data
Associated Tutorial
This workflows is part of the tutorial MS Imaging Loading Exploring Data, available in the GTN
Thanks to...
Tutorial Author(s): Melanie Föll, ...
Functional annotation of protein sequences
Associated Tutorial
This workflows is part of the tutorial Functional annotation, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Anthony ...
Unicycler Assembly
Associated Tutorial
This workflows is part of the tutorial Unicycler training, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Anton Nekrutenko, ...
Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
Associated Tutorial
This workflows is part of the tutorial Galaxy Workflow Galaxy Hi C, available in the GTN
Thanks to...
Tutorial Author(s): Joachim Wolff, [Fidel ...
DIA Analysis Training using HEK Ecoli data in OSW
Associated Tutorial
This workflows is part of the tutorial DIA_Analysis_OSW, available in the GTN
Thanks to...
Tutorial Author(s): Matthias Fahrner, Melanie Föll ...
CRISPR screen analysis
Associated Tutorial
This workflows is part of the tutorial Workflow constructed from history 'CRISPR tutorial Kenji', available in the GTN
Thanks to...
Tutorial Author(s): Maria Doyle, [Kenji ...
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 using Oxford Nanopore MinION (and Illumina data if available), available in the GTN
Features
- Includes Galaxy Workflow Tests ...
metaquantome-data-creation
Associated Tutorial
This workflows is part of the tutorial metaQuantome_datacreation_workflow, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Subina ...
Associated Tutorial
This workflows is part of the tutorial Combined workflows for large genome assembly - upgraded , available in the GTN
Features
- Includes a Galaxy Workflow Report
- Uses subworkflows ...
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 ...
Associated Tutorial
This workflows is part of the tutorial Assembly polishing - upgraded, available in the GTN
Features
- Includes a Galaxy Workflow Report
- Uses subworkflows ...
Workflows for comparison of genes in annotated genomes
Associated Tutorial
This workflows is part of the tutorial Comparative gene analysis, available in the GTN
Thanks to...
Tutorial Author(s): Anton Nekrutenko
Workflow Author(s): Anton Nekrutenko
[![gtn ...
Peptide and Protein ID using SearchGUI and PeptideShaker
Associated Tutorial
This workflows is part of the tutorial Peptide And Protein ID Tutorial, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, [Björn ...
Peptide and Protein ID using SearchGUI and PeptideShaker
Associated Tutorial
This workflows is part of the tutorial ProteinID SG PS Tutorial WF datasetCollection, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, [Björn ...
Associated Tutorial
This workflows is part of the tutorial Assembly with Flye - upgraded, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Tutorial Author(s): Anna Syme ...
Identification of AMR genes in an assembled bacterial genome
Associated Tutorial
This workflows is part of the tutorial mrsa AMR gene detection, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): ...
atac-seq
Associated Tutorial
This workflows is part of the tutorial ATAC-seq GTM, available in the GTN
Thanks to...
Tutorial Author(s): Lucille Delisle, Maria Doyle, [Florian ...
DIA MSstats Training export tabular
Associated Tutorial
This workflows is part of the tutorial DIA_analysis_MSstats, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Matthias ...
Associated Tutorial
This workflows is part of the tutorial kmer counting - meryl - upgraded, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Tutorial Author(s): Anna Syme ...
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
...
Genome annotation with Maker
Associated Tutorial
This workflows is part of the tutorial Genome annotation with Maker , available in the GTN
Thanks to...
Tutorial Author(s): Anthony Bretaudeau
Workflow Author(s): Anthony Bretaudeau, French ...
DIA MSstats Training msstats input tabular
Associated Tutorial
This workflows is part of the tutorial DIA_analysis_MSstats, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Matthias ...
Associated Tutorial
This workflows is part of the tutorial Data QC - upgraded, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Tutorial Author(s): Anna Syme ...
atac-seq
Associated Tutorial
This workflows is part of the tutorial ATAC-seq GTM, available in the GTN
Thanks to...
Tutorial Author(s): Florian Heyl
Tutorial Contributor(s): Helena Rasche, ...
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 GECKO pairwise comparison, available in the GTN
Thanks to...
Tutorial Author(s): Esteban Perez-Wohlfeil ...
Metaproteomics tutorial
Associated Tutorial
This workflows is part of the tutorial Metaproteomics_GTN, available in the GTN
Thanks to...
Tutorial Author(s): Timothy J. Griffin, Pratik Jagtap, ...
Associated Tutorial
This workflows is part of the tutorial Assess genome quality - upgraded, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Tutorial Author(s): Anna Syme ...
DNA Methylation data analysis
Associated Tutorial
This workflows is part of the tutorial Workflow Methylation Seq, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Joachim ...
A workflow designed to compare chromosomes and study large-scale rearrangements using CHROMEISTER
Associated Tutorial
This workflows is part of the tutorial CHROMEISTER chromosome comparison, available in the GTN
Thanks to...
Tutorial Author(s): Esteban Perez-Wohlfeil ...
metaquantome-taxonomy
Associated Tutorial
This workflows is part of the tutorial metaquantome-taxonomy-workflow, available in the GTN
Thanks to...
Tutorial Author(s): Subina Mehta, Timothy J. Griffin, ...
Associated Tutorial
This workflows is part of the tutorial Racon polish with long reads, x4 - upgraded, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Tutorial Author(s): [Anna ...
Associated Tutorial
This workflows is part of the tutorial GTN - ChIP Seq - Formation Of Super Structures On Xi, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Friederike ...
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 - Qc Mapping, available in the GTN
Thanks to...
Tutorial Author(s): Friederike Dündar, ...
Proteogenomics 2: Database Search
Associated Tutorial
This workflows is part of the tutorial GTN Proteogemics2 Database Search, available in the GTN
Thanks to...
Tutorial Author(s): Subina Mehta, [Timothy J. ...
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 - Chip Seq, available in the GTN
Thanks to...
Tutorial Author(s): Friederike Dündar, ...
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
...
Associated Tutorial
This workflows is part of the tutorial Racon polish with Illumina reads (R1 only), x2 - upgraded, available in the GTN
Thanks to...
Tutorial Author(s): Anna Syme
Workflow Author(s): Anna Syme
[![gtn star logo followed by the word ...
Design plasmids encoding predicted pathways by using the BASIC assembly method.
Associated Tutorial
This workflows is part of the tutorial Genetic Design (BASIC Assembly), available in the GTN
Thanks to...
Tutorial Author(s): Kenza Bazi-Kabbaj, ...
encyclopedia
Associated Tutorial
This workflows is part of the tutorial May19 EncyclopeDIA raw inputs, available in the GTN
Thanks to...
Tutorial Author(s): Emma Leith, Subina Mehta, ...
Associated Tutorial
This workflows is part of the tutorial Gene Cluster Product Similarity Search , available in the GTN
Thanks to...
Tutorial Author(s): Paul Zierep
[![gtn star logo followed by the word ...
Associated Tutorial
This workflows is part of the tutorial Trim and filter reads - fastp - upgraded , available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Tutorial Author(s): [Anna ...
version 1.0, 160318, published at https://github.com/Stortebecker/secretome_prediction
Associated Tutorial
This workflows is part of the tutorial Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper, available in the GTN
Thanks to...
Tutorial Author(s): [Florian Christoph ...
Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
Associated Tutorial
This workflows is part of the tutorial RetroSynthesis, available in the GTN
Thanks to...
Tutorial Author(s): Guillaume Gricourt, ...
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...
Tutorial Author(s): Stéphanie Robin
**Tutorial ...
Assembly
Associated Tutorial
This workflows is part of the tutorial Chloroplast-genome-assembly-and-annotation, available in the GTN
Thanks to...
Tutorial Author(s): Anna Syme
[![gtn star logo followed by the word ...
Label-free data analysis using MaxQuant
Associated Tutorial
This workflows is part of the tutorial Proteomics: MaxQuant workflow, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Melanie ...
Visualize Climate data with Panoply netCDF viewer
Associated Tutorial
This workflows is part of the tutorial Climate 101, available in the GTN
Thanks to...
Tutorial Author(s): Anne Fouilloux
Workflow Author(s): Anne Fouilloux
[![gtn star logo followed by the word ...
Evaluating and ranking a set of pathways based on multiple metrics
Associated Tutorial
This workflows is part of the tutorial Pathway Analysis, available in the GTN
Thanks to...
Tutorial Author(s): Kenza Bazi-Kabbaj, [Thomas ...
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, ...
Genome Assembly of MRSA using Illumina MiSeq Data
Associated Tutorial
This workflows is part of the tutorial Genome Assembly of MRSA using Illumina MiSeq Data, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): ...
High Throughput Molecular Dynamics and Analysis
Associated Tutorial
This workflows is part of the tutorial MD protein-ligand workflow (from PDB structure), available in the GTN
Thanks to...
Tutorial Author(s): Simon Bray, [Tharindu ...
16S Microbial Analysis with mothur (short)
Associated Tutorial
This workflows is part of the tutorial Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur], available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, ...
Assembly with preprocessing
Associated Tutorial
This workflows is part of the tutorial assembly_with_preprocessing, available in the GTN
Thanks to...
Tutorial Author(s): Wolfgang Maier
[![gtn star logo followed by the word ...
Genome Assembly using PacBio data and Flye assembler
Associated Tutorial
This workflows is part of the tutorial Genome Assembly using PacBio data, available in the GTN
Thanks to...
Tutorial Author(s): Anthony Bretaudeau, [Alexandre ...
Running molecular dynamics simulations using GROMACS
Associated Tutorial
This workflows is part of the tutorial GROMACS Training Workflow, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Tutorial ...
16S Microbial Analysis with mothur (short)
Associated Tutorial
This workflows is part of the tutorial Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur], available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, ...
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...
Tutorial Author(s): Anthony Bretaudeau, [Alexandre ...
ERGA post-assembly QC
Associated Tutorial
This workflows is part of the tutorial Post-assembly workflow, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Fabian ...
Analysis of MD trajectories using MDAnalysis, generating a Ramachandran plot and various timeseries.
Associated Tutorial
This workflows is part of the tutorial Analysis using MDAnalysis, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
16S Microbial Analysis with mothur (short)
Associated Tutorial
This workflows is part of the tutorial Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur], available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, ...
De Bruijn Graph Assembly
Associated Tutorial
This workflows is part of the tutorial Debruijn Graph, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Simon ...
Mass spectrometry imaging: Finding differential analytes
Associated Tutorial
This workflows is part of the tutorial MSI Finding Diff Analytes, available in the GTN
Thanks to...
Tutorial Author(s): Melanie Föll
[![gtn star logo followed by the word ...
Analysis of molecular dynamics simulations
Associated Tutorial
This workflows is part of the tutorial Simple Analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Christopher ...
16S Microbial Analysis with mothur (short)
Associated Tutorial
This workflows is part of the tutorial Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur], available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, ...
Associated Tutorial
This workflows is part of the tutorial Metagenomics assembly tutorial workflow, available in the GTN
Thanks to...
Tutorial Author(s): Polina Polunina, Bérénice Batut ...
XCMS and RAMClustR based workflow for data processing and annotation using library matching via matchms.
Associated Tutorial
This workflows is part of the tutorial GC MS using XCMS, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks
...
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 ...
16S Microbial Analysis with mothur (short)
Associated Tutorial
This workflows is part of the tutorial Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur], available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, ...
Associated Tutorial
This workflows is part of the tutorial workflow-generate-dataset-for-assembly-tutorial, available in the GTN
Thanks to...
Tutorial Author(s): Polina Polunina, Bérénice Batut ...
NGS data logistics
Associated Tutorial
This workflows is part of the tutorial NGS_tutorial, available in the GTN
Thanks to...
Tutorial Author(s): Anton Nekrutenko, Marius van den Beek, ...
Exome sequencing data analysis for diagnosing a genetic disease
Associated Tutorial
This workflows is part of the tutorial Exome Seq Training Full W Cached Ref, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Tutorial ...
Making sense of a newly assembled genome
Associated Tutorial
This workflows is part of the tutorial Ecoli Comparison, available in the GTN
Thanks to...
Tutorial Author(s): Anton Nekrutenko, Delphine Lariviere, ...
16S Microbial Analysis with mothur (short)
Associated Tutorial
This workflows is part of the tutorial Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur], available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, ...
Introduction to Genomics and Galaxy
Associated Tutorial
This workflows is part of the tutorial Galaxy Intro Strands 2, available in the GTN
Thanks to...
Tutorial Author(s): Dave Clements, Cristóbal Gallardo ...
Introduction to Genomics and Galaxy
Associated Tutorial
This workflows is part of the tutorial Galaxy Intro Strands, available in the GTN
Thanks to...
Tutorial Author(s): Dave Clements, Cristóbal Gallardo ...
Associated Tutorial
This workflows is part of the tutorial Finding the Muon Stopping Site: pymuon-suite in Galaxy, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Leandro ...
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 Seq Training Pre-Mapped W Cached Ref, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Antibiotic resistance detection
Associated Tutorial
This workflows is part of the tutorial Copy Of GTN Training - Antibiotic Resistance Detection, available in the GTN
Thanks to...
Tutorial Author(s): Willem de Koning, [Saskia ...
Galaxy 101
Associated Tutorial
This workflows is part of the tutorial Find exons with the highest number of features, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Saskia ...
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 ...
Calling variants in diploid systems
Associated Tutorial
This workflows is part of the tutorial Diploid, available in the GTN
Thanks to...
Tutorial Author(s): Anton Nekrutenko, Nicola Soranzo ...
Associated Tutorial
This workflows is part of the tutorial Metagenomics assembly tutorial workflow, available in the GTN
Thanks to...
Tutorial Author(s): Polina Polunina, Bérénice Batut ...
Galaxy Introduction Peaks2Genes - Part 1
Associated Tutorial
This workflows is part of the tutorial Galaxy Introduction Peaks2Genes - Part 1, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): ...
16S Microbial Analysis with mothur (extended)
Associated Tutorial
This workflows is part of the tutorial Training: 16S rRNA Sequencing With Mothur: Main Tutorial, available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, [Bérénice ...
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
Thanks to...
Tutorial Author(s): [Anton ...
Associated Tutorial
This workflows is part of the tutorial workflow-generate-dataset-for-assembly-tutorial, available in the GTN
Thanks to...
Tutorial Author(s): Polina Polunina, Bérénice Batut ...
introduction
Associated Tutorial
This workflows is part of the tutorial GTN Training: Galaxy 101 For Everyone, available in the GTN
Thanks to...
Tutorial Author(s): Melanie Föll, Anne Fouilloux ...
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 ...
Trio Analysis using Synthetic Datasets from RD-Connect GPAP
Associated Tutorial
This workflows is part of the tutorial Trio Analysis Tutorial, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Jasper ...
Taxonomic Profiling and Visualization of Metagenomic Data
Associated Tutorial
This workflows is part of the tutorial Taxonomic Profiling and Visualization of Metagenomic Data, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks
...
A short introduction to Galaxy
Associated Tutorial
This workflows is part of the tutorial Galaxy Intro Short, available in the GTN
Thanks to...
Tutorial Author(s): Anna Syme, Nicola Soranzo ...
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 ...
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Associated Tutorial
This workflows is part of the tutorial Workflow 1: Preprocessing, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Tutorial ...
Nanopore datasets analysis - Phylogenetic Identification - antibiotic resistance genes detection and contigs building
Associated Tutorial
This workflows is part of the tutorial Gene-based Pathogen Identification, available in the GTN
Features
- Includes [Galaxy Workflow ...
Data Manipulation Olympics
Associated Tutorial
This workflows is part of the tutorial GTN Tutorial: Data manipulation Olympics - all steps and exercises, available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann
**Tutorial ...
Run this on the trimmed consensus reads (DCS or SSCS) from Du Novo.
Associated Tutorial
This workflows is part of the tutorial Du Novo GTN Tutorial - Variant Calling, available in the GTN
Thanks to...
Tutorial Author(s): Anton Nekrutenko, [Nick ...
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Associated Tutorial
This workflows is part of the tutorial Workflow 2: Community Profile, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Tutorial ...
introduction
Associated Tutorial
This workflows is part of the tutorial GTN Training: Galaxy 101 For Everyone, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Anne ...
Run this on raw duplex sequencing reads to produce duplex consensus sequences.
Associated Tutorial
This workflows is part of the tutorial Du Novo GTN Tutorial - Make Consensus Sequences, available in the GTN
Thanks to...
Tutorial Author(s): Anton Nekrutenko, [Nick ...
Microbiome - QC and Contamination Filtering
Associated Tutorial
This workflows is part of the tutorial Nanopore Preprocessing, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Associated Tutorial
This workflows is part of the tutorial Workflow 3: Functional Information, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
...
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 tutorial, available in the GTN
Features
- Includes [Galaxy Workflow ...
Protein target prediction of a bioactive ligand with Align-it and ePharmaLib
Associated Tutorial
This workflows is part of the tutorial Zauberkugel, available in the GTN
Thanks to...
Tutorial Author(s): Aurélien F. A. Moumbock, [Simon ...
Microbiome - Variant calling and Consensus Building
Associated Tutorial
This workflows is part of the tutorial Allele-based Pathogen Identification, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes ...
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Associated Tutorial
This workflows is part of the tutorial Workflow 3: Functional Information (quick), available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks
...
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 rDock and pose scoring, available in the GTN
Thanks to...
Tutorial Author(s): Simon Bray ...
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-tiled-amplicon-ref-masking, 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 PathoGFAIR Samples Aggregation and Visualisation, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Associated Tutorial
This workflows is part of the tutorial Main Metatranscriptomics Analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Uses subworkflows ...
CTB Unittest workflow
Associated Tutorial
This workflows is part of the tutorial CTB Workflow, available in the GTN
Thanks to...
Tutorial Author(s): Simon Bray
[![gtn star logo followed by the word ...
Analysis of variation within individual COVID-19 samples (Paired End Illumina). Does not use paured
Associated Tutorial
This workflows is part of the tutorial Simple COVID-19 - PE Variation, available in the GTN
Thanks to...
Tutorial Author(s): Marius van den Beek, ...
Microbiome - Taxonomy Profiling
Associated Tutorial
This workflows is part of the tutorial Taxonomy Profiling and Visualization with Krona, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy ...
Running molecular dynamics simulations using NAMD
Associated Tutorial
This workflows is part of the tutorial NAMD MD From CHARMM GUI, available in the GTN
Thanks to...
Tutorial Author(s): Christopher Barnett, [Tharindu ...
Running molecular dynamics simulations using NAMD
Associated Tutorial
This workflows is part of the tutorial MD NAMD, available in the GTN
Thanks to...
Tutorial Author(s): Christopher Barnett, [Tharindu ...
Analyses of metagenomics data - The global picture
Associated Tutorial
This workflows is part of the tutorial Amplicon Tutorial, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Saskia ...
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 workflow, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Predict variants and drug resistance from M. tuberculosis sequence samples (Illumina)
Associated Tutorial
This workflows is part of the tutorial TB Variant Analysis v1.0, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes ...
Analyses of metagenomics data - The global picture
Associated Tutorial
This workflows is part of the tutorial WGS Part In "Analyses Of Metagenomics Data - The Global Picture", available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, [Bérénice ...
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 workflow, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
16S rRNA analysis with Nanopore reads
Associated Tutorial
This workflows is part of the tutorial Training: 16S rRNA Analysis with Nanopore Sequencing Reads, available in the GTN
Thanks to...
Tutorial Author(s): Cristóbal Gallardo
[![gtn star logo ...
Mass spectrometry: LC-MS analysis
Associated Tutorial
This workflows is part of the tutorial Workflow Constructed From History 'imported: testpourGCC', available in the GTN
Thanks to...
Tutorial Author(s): Mélanie Petera, [Gildas Le ...
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 ...
High Throughput Molecular Dynamics and Analysis
Associated Tutorial
This workflows is part of the tutorial Workflow constructed from history 'Hsp90-MDAnalysis', available in the GTN
Thanks to...
Tutorial Author(s): Simon Bray, [Tharindu ...
Mass spectrometry imaging: Examining the spatial distribution of analytes
Associated Tutorial
This workflows is part of the tutorial MSI Workflow: spatial distribution, available in the GTN
Thanks to...
Tutorial Author(s): Melanie Föll, [Maren ...
16S Microbial Analysis with mothur (short)
Associated Tutorial
This workflows is part of the tutorial Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur], available in the GTN
Thanks to...
Tutorial Author(s): Saskia Hiltemann, ...