VB2_network_analysis

This repository contains data, scripts and result for comparing gut microbial networks from a VB2 trial with four groups (Placebo, 1.4mg, 10mg, 75mg) across three time points (Week 0, 4, 12).

Repository Structure

VB2_network_analysis/
├── data/                    
│   ├── raw                         # raw counts and metadata
│   ├── intermediate                # preprocessed counts
├── notebooks/                  # Jupyter notebooks for proprocessing, analysis and visualization 
├── scripts/                # Bash scripts that run the R scripts
├── R                       # R scripts for network construction and comparison
├── output/                 # output from  network construction and comparison
├── report                  # report and used figures     
├── requirements.txt
└── README.md

Usage

This project primarily uses R for analysis. To set it up, you need to first install R version 4.3. Also install the required packages: NetCoMi, SPRING, limma.

To construct and compare the networks, run: Rscript ./R/netcomi_compare.R "$group1" "$group2" "$output_base_dir"