NOD2: Code Companion for "Distinct Colitis-Associated Macrophages Drive NOD2-Dependent Bacterial Sensing and Gut Homeostasis"

Overview

This repository provides the computational framework and analysis scripts used in the study:
“Distinct Colitis-Associated Macrophages Drive NOD2-Dependent Bacterial Sensing and Gut Homeostasis”
by Katkar et al. (2024).

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Repository Contents

• NOD2(1).ipynb – Primary analysis notebook for evaluating ColAM signatures, composite score calculations, and plotting.
• bone(1).py – Module for Boolean Network Explorer (BoNE) composite score calculations.
• icolam.txt – gene list for iCoLAM signature.
• nicolam.txt – gene list for niCoLAM signature.

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Setup Instructions

Prerequisites

• Python ≥ 3.8
• Jupyter Notebook

Required Python Packages

Install dependencies using pip:

pip install numpy pandas matplotlib seaborn scipy scikit-learn