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.
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.
The NF-toxomix pipeline comes with documentation about the pipeline, found in the docs/ directory:
- Installation
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
- Troubleshooting
This pipeline was written by Evan Floden (evanfloden) at Center for Genomic Regulation (CRG).