evanfloden / nf-toxomix

OpenRiskNet pipeline for TGX case study: toxicology predictions based on transcriptomic profiles

NF-toxomix

Pipeline for toxicology predictions based on transcriptomic profiles.

It acts a pilot workflow as part of the OpenRiskNet project with the goal to incorperate genomic data into the OpenRiskNet infrastructure.

Introduction

NF-toxomix: Pipeline for toxicology predictions based on transcriptomic profiles

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.

The pipeline from Juma Bayjan at Maastricht University which in turn aimed to reproduce the article "A transcriptomics-based in vitro assay for predicting chemical genotoxicity in vivo", by C.Magkoufopoulou et. al.

This pipeline focuses on training the genotoxicity model.

Documentation

The NF-toxomix pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation
2. Pipeline configuration
   • Local installation
   • Adding your own system
3. Running the pipeline
4. Output and how to interpret the results
5. Troubleshooting

Credits

This pipeline was written by Evan Floden (evanfloden) at Center for Genomic Regulation (CRG).