This repository contains the analysis scripts and data processing workflows for the manuscript:
TBD
The repository includes scripts and notebooks to:
- Pre-process metagenomic and metabolomic data from public IBD, IBS, and ESRD cohorts.
- Apply the MAAMOUL framework to identify data-driven metabolic modules.
- Reproduce the comparative pathway-level and feature-level analyses presented in the study.
- Generate the manuscript figures and supplementary visualizations.
The core MAAMOUL method is available as an R package at: https://github.com/borenstein-lab/MAAMOUL.