Last updated: 2024-06-11

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Knit directory: PPP/

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1 Pipeline

Pipeline

2 Virtual Inference of Protein-activity by Enriched Regulon Analysis

2.2 Context-specific Networks

Extract Context-Specific Networks

2.3 Build Regulon Object

Build Regulon Object

2.4 Run Virtual Inference of Protein-activity by Enriched Regulon Analysis

Run Viper

Export Viper Results

3 TieDIE: Tied Diffusion for Subnetwork Discovery.

3.1 Preparing Input and Run Analysis

Preparing Input and Run Analysis

3.2 Plot Network

Plot Network

4 Patient-specific and group-specific gene networks

msVIPER

5 Environment setup

Set up python2.7

To set up python2.7 on MacOs

Then run

conda create -n py27 --f py27.yml

To active it

source /opt/homebrew/Caskroom/mambaforge/base/etc/profile.d/conda.sh;  
conda activate py27;
Set up Viper 
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("viper")