GTN Bot

The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.

These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!

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 ...

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

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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, ...

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 ...

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

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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): ...

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 ...

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 ...

This workflow allows you to annotate a genome with Helixer and evaluate the quality of the annotation using BUSCO and Genome Annotation statistics. GFFRead is also used to predict protein sequences derived from this annotation, and BUSCO and OMArk are used to assess proteome quality.

Associated Tutorial

This workflows is part of the tutorial Genome annotation with Helixer, available ...

Refining Genome Annotations with Apollo

Associated Tutorial

This workflows is part of the tutorial Refining Genome Annotations with Apollo (prokaryotes), available in the GTN

Thanks to...

Tutorial Author(s): Anthony Bretaudeau, [Helena ...