README.md

Deprecated Pipeline Notice

Important: The DGE pipeline is now deprecated and has been replaced by a DSL2 version, available at lconde-ucl/DGE2

DGE

Run DESeq2/GSEA on the featureCounts matrix or kallisto counts obtained from the nextflow_rnaseq pipeline

Introduction

The pipeline is built using Nextflow. It is a basic pipeline for differential gene expression analysis that is meant to be run after the data has been preprocessed with the rnaseq pipeline

Documentation

The nf-core/SGE pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation
2. Running the pipeline
3. Output and how to interpret the results
4. Troubleshooting