CellChat vs CellPhoneDB Comparison Project

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Table of Contents

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• Introduction
• Usage
• Contributors
• Project Description

Introduction

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This repository contains the analysis code used in the study "Comparing the Mathematical Basis of CellChat and CellPhoneDB for Immune Cell to Cell Communication in Diet-induced Liver Disease" (Qing, Qian, and Gupta, 2025). The code performs cell–cell communication inference using LIANA+, comparing CellChat and CellPhoneDB on single-cell RNA-seq data from liver non-parenchymal cells of diet-induced MASLD/MASH mice.

Usage

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To use this repository, please follow these steps:

1. Clone the repository using git clone https://github.com/xqing3/CellChat_vs_CellPhoneDB_Using_Experimental_Single-Cell_Data.git
2. Install the required libraries by running pip install -r requirements.txt
3. Run the analysis code using python RunCellChatCellPhoneDB/CellChatCellPhoneDBAllMice.py

Contributors

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• Crystal (Xin) Qing (qing3@wisc.edu) — Research Design, Data Curation, Analysis Support
• Siwei Qian (sqian32@wisc.edu) — Research Design, Data Curation, Analysis Support
• Aayush Gupta (gupta385@wisc.edu) - Research Design, Data Curation, Analysis Support
• Dr. Daifeng Wang (daifeng.wang@wisc.edu) — Project Advisor

Project Description

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This project compares the performance of CellChat and CellPhoneDB on single-cell RNA-seq data from liver non-parenchymal cells of diet-induced MASLD/MASH mice. The code includes scripts for data preprocessing, cell type annotation, and cell-cell communication inference using LIANA+. The results support methodological insights into CCC tool behavior under varying ligand–receptor expression patterns.