DysRegNet analysis workflow

This repository contains the analysis workflow for the DysRegNet manuscript: DysRegNet: Patient-specific and confounder-aware dysregulated network inference. The workflow is implemented using the Snakemake workflow management system. The workflow will perform the following steps:

• Data preprocessing
• Reference network inference
• Patient-specific network inference with DysRegNet and SSN
• Evaluation and plot generation
• Build the database for the DysRegNet web application

The main workflow is orchestrated in the workflow/Snakefile. The profiles directory contains configuration files for different execution environments (e.g., slurm, local). The workflow\scripts directory contains all analysis scripts used by the workflow.

Usage

After cloning the repository, install the required packages using conda and the environment.yaml file:

conda env create -f environment.yaml

Activate the environment:

conda activate drn

If necessary, adjust data (expected to contain all input files) and result directories specified by the DATA_DIR and RESULT_DIR variables in workflow/Snakefile.

Run the workflow via slurm:

snakemake --profile profiles/slurm

The slurm profile contains cluster-specific configuration. For development and pipeline testing, a local executor and/or the dry-run feature can be used:

snakemake --profile profiles/local -n