modulediscovery pipeline demonstration

This repository contains Jupyter notebooks that were used to prepare the input data for and analyse the results of the demonstrations run of the nf-core/diseasemodulediscovery pipeline.

Setup

Clone repository:

git clone https://github.com/REPO4EU/modulediscovery_demonstration.git

Install dependencies with conda:

cd modulediscovery_demonstration
conda env create -f environment.yml
conda activate mdp_demonstration

Download the pipeline run results and place the unzipped results folder in pipeline_runs/main. Alternatively, you can reproduce the pipeline run using the command.sh script from within the pipeline_runs/main folder.

Notebooks

• src/01_seed_selection.ipynb: Prepares the input seed files for the demonstration run.
• src/02_visualize_network_topology.ipynb: Visualizes topological features of the input PPI networs.
• src/03_visualize_seed_genes.ipynb: Visualizes properties of the input seed sets.
• src/04_visualize_module_topology.ipynb: Visualizes topological features of the inferred disease modules.
• src/05_module_overlap.ipynb: Vsualizes overlaps between different disease modules.
• src/06_visualize_seed_perturbation.ipynb: Visualizes the results of the seed perturbation analysis (robustness and rediscovery).
• src/07_visualize_network_perturbation.ipynb: Visualizes the results of the degree-preserving network rewiring analysis.
• src/08_visualize_digest.ipynb: Visualizes the functional coherence analysis results.
• src/09_visualize_ora.ipynb: Visualizes the over-representation analysis results.