Causal Sparse Low Rank Microbiome Tutorial

This repository contains a tutorial for using a randomization-based causal inference framework with sparse+low-rank graphical models in microbiome data analysis.

Table of Contents

• Introduction
• Installation
• Pair-matching
• Differential abundance
• Network analysis
• Usage
• License

Introduction

Microbiome data analysis often involves high-dimensional and sparse datasets. This tutorial demonstrates how to apply causal inference techniques to such data using sparse and low-rank methods.

Installation

To get started, clone the repository and install the required dependencies:

git clone https://github.com/yourusername/Causal_Sparse_Low_Rank_Microbiome_Tutorial.git
cd Causal_Sparse_Low_Rank_Microbiome_Tutorial
pip install -r requirements.txt

Pair-matching

Differential abundance

Network analysis

Usage

Follow the steps in the tutorial notebooks to learn how to apply causal inference methods to microbiome data. The notebooks are located in the notebooks directory.

Contributing

Contributions are welcome! Please open an issue or submit a pull request if you have any improvements or bug fixes.

License

This project is licensed under the MIT License. See the LICENSE file for details.