Snakemake workflow for running differential expression and enrichment analyses for experimental setups with multiple groups or multiple conditions. Results are provided as a set of HTML files with plots and result description both for each comparison defined in the config file.

Workflow was derived from https://github.com/snakemake-workflows/rna-seq-star-deseq2, with alignment steps removed.

The quickest way to get up and running with this workflow is using

• conda
  • mamba
• snakemake
• pandas

git clone https://github.com/schlesnerlab/multicondition-deseq2-enrichment
cd multicondition-deseq-enrichment

You can install snakemake with the yaml provided in workflow/snakemake.yaml with

conda env create -n snakemake -f workflow/snakemake.yaml
conda activate snakemake

In case you use snakedeploy you could also deploy this workflow with

snakedeploy deploy-workflow https://github.com/schlesnerlab/multicondition-deseq2-enrichment multicondition-deseq2-enrichment --branch main 

If you wish to use analysis provided by Carnival you need to provide a solver supported by CARNIVAL. Right now the following solvers are supported:

• cplex

For academic users the cplex can be downloaded here. Then the path to the cplex executable needs to added to the config file.

To use this workflow you will need:

• RNAseq quantified data (f.e. counts) as a tsv or csv file
• a config yaml file for your project to control the workflow
• a tsv file with the sample information for the samples in the count file.

Further details on the configuration can be found in the config README

• gene count matrix