Workflow for the Galaxy Training Network tutorial "Hybrid genome assembly - Nanopore and Illumina"

Associated Tutorial

This workflows is part of the tutorial Hybrid genome assembly - Nanopore and Illumina, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Text mining a museum collection in tabular format to extract from which year most objects derive and what they are.

Associated Tutorial

This workflows is part of the tutorial OpenRefine Tutorial for researching cultural data, available in the GTN

Features

• Includes [Galaxy Workflow ...

To perform Qualification, Nitrate Calibration, Validation of One Argo float or One Glider by using Neural Network and Climatology. Copy past before running and change calibration parametrization if necessary

Associated Tutorial

This workflows is part of the tutorial Nitrate DMQC for autonomous platforms such as Argo floats, available in the GTN ...

The workflow serves as a short introduction to Galaxy for users from the Humanities who mostly work with texts. The workflow compares two texts, visualises the differences with 'diff' and a wordcloud and extracts selected passaged for further analysis.

Associated Tutorial

This workflows is part of the tutorial Introduction to Digital Humanities in Galaxy, available in ...

This workflow shows Flexynesis usage for predicting survival markers from a multi-omics dataset

Associated Tutorial

This workflows is part of the tutorial Identifing Survival Markers of Brain tumor with Flexynesis, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

This WF applies Flexynesis on BRCA data from Metabric for a classification task

Associated Tutorial

This workflows is part of the tutorial Modeling Breast Cancer Subtypes with Flexynesis, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Workflow for long read quality control, contamination filtering, assembly, variant calling and annotation.

Steps:

• Preprocessing of reference file : https://workflowhub.eu/workflows/1818
• LongReadSum before and after filtering (read quality control)
• Filtlong filter on quality and length
• Flye assembly
• Minimap2 mapping of reads and assembly
• Clair3 variant calling of reads
• Freebayes variant calling of assembly
• Optional Bakta annotation of genomes with no reference
• SnpEff building ...

Classification and visualization of ITS regions.

Associated Tutorial

This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN

Features

• Includes a Galaxy Workflow Report
• Uses ...

The MAPseq to Ampvis workflow processes MAPseq OTU tables and associated metadata for analysis in Ampvis2. This workflow involves reformatting MAPseq output datasets to produce structured output files suitable for Ampvis2.

Associated Tutorial

This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN

Features

...

Quality control subworkflow for paired-end reads.

Associated Tutorial

This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN

Features

• Includes a Galaxy Workflow Report

Thanks to...

Workflow Author(s): ...

MGnify's amplicon pipeline v5.0. Including the Quality control for single-end and paired-end reads, rRNA-prediction, and ITS sub-WFs.

Associated Tutorial

This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN

Features

• Includes a Galaxy Workflow Report ...

Unsupervised Classification of Bone marrow cells

Associated Tutorial

This workflows is part of the tutorial Unsupervised Analysis of Bone Marrow Cells with Flexynesis, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a ...

This workflow creates taxonomic summary tables out of the amplicon pipeline results.

Associated Tutorial

This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN

Features

• Includes a Galaxy Workflow Report
• Uses ...

Quality control subworkflow for single-end reads.

Associated Tutorial

This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN

Features

• Includes a Galaxy Workflow Report

Thanks to...

Workflow Author(s): ...

Download data from cBioPortal and prepare it for Flexynesis

Associated Tutorial

This workflows is part of the tutorial Prepare data from CbioPortal for Flexynesis integration, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes ...

This workflow performs step-by-step quantification of electrophoresis gel bands by processing QuPath-generated ROI files in Galaxy, automatically measuring band intensity and producing tabular results for visualization.

Associated Tutorial

This workflows is part of the tutorial Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools, ...

Workflow for the GTN tutorial: "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

Features

• Includes Galaxy Workflow Tests ...

Classification and visualization of SSU, LSU sequences.

Associated Tutorial

This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN

Features

• Includes a Galaxy Workflow Report
• Uses ...

YOLO based tail analysis workflow for image segmentation and detection. The workflow is based on https://git.embl.org/grp-cba/tail-analysis/-/blob/main/analysis_workflow.md

Associated Tutorial

This workflows is part of the tutorial Training Custom YOLO Models for Object Detection and Segmentation in Bioimages, available in the GTN

...

Prediction of HLA binding for verified candidates

Associated Tutorial

This workflows is part of the tutorial Neoantigen 5a: Predicting HLA Binding, available in the GTN

Features

• Includes a Galaxy Workflow Report

Thanks to...

...

Merging Fusion and non-normal databases + Discovery peptidomics using FragPipe

Associated Tutorial

This workflows is part of the tutorial Neoantigen 2: Database merge and FragPipe discovery, available in the GTN

Features

• Includes a Galaxy Workflow Report ...

Create a protein Fusion database through the Arriba workflow

Associated Tutorial

This workflows is part of the tutorial Neoantigen 1a: Fusion-Database-Generation, available in the GTN

Features

• Includes a Galaxy Workflow Report ...

Validate the NeoAntigen Candidates from FragPipe discovery through the PepQuery Novel search

Associated Tutorial

This workflows is part of the tutorial Neoantigen 3: PepQuery2 Verification, available in the GTN

Features

• Includes a Galaxy Workflow Report ...

Annotating the novel peptides

Associated Tutorial

This workflows is part of the tutorial Neoantigen 4: Variant Annotation, available in the GTN

Features

• Includes a Galaxy Workflow Report

Thanks to...

Workflow Author(s): GalaxyP ...

Predict binding using IEDB and check novelty peptides with PepQuery

Associated Tutorial

This workflows is part of the tutorial Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides, available in the GTN

Features

• Includes a Galaxy Workflow Report ...

Generating non-reference protein database for FragPipe discovery

Associated Tutorial

This workflows is part of the tutorial Neoantigen 1b: Non-Reference-Database-Generation, available in the GTN

Features

• Includes a Galaxy Workflow Report ...

The idea of this workflow is to compare annotation with two annotation tools that differ in their approach and operation.

Associated Tutorial

This workflows is part of the tutorial Comparison of two annotation tools - Helixer and Braker3, available in the GTN

Features

• Includes [Galaxy Workflow ...

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 ...

This workflow is generated from the GTN tutorial Whole transcriptome analysis of Arabidopsis thaliana (https://gxy.io/GTN:T00292).

Associated Tutorial

This workflows is part of the tutorial Whole transcriptome analysis of Arabidopsis thaliana, available in the GTN

Features

• Includes [Galaxy Workflow ...

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 ...