Galaxy Training Network

Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.

• Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
• Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
• Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
• Scalable: Galaxy can run ...

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 ...

Pathogens of all samples report generation and visualization

Associated Tutorial

This workflows is part of the tutorial Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition, available in the GTN

Features

• Includes a [Galaxy Workflow ...

Microbiome - QC and Contamination Filtering

Associated Tutorial

This workflows is part of the tutorial Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

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 ...

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 ...

Metatranscriptomics analysis using microbiome RNA-seq data

Associated Tutorial

This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes ...

Metatranscriptomics analysis using microbiome RNA-seq data (short)

Associated Tutorial

This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Metatranscriptomics analysis using microbiome RNA-seq data (short)

Associated Tutorial

This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Metatranscriptomics analysis using microbiome RNA-seq data (short)

Associated Tutorial

This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Assembly of metagenomic sequencing data

Associated Tutorial

This workflows is part of the tutorial Assembly of metagenomic sequencing data, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a [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 ...