Project description

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. Scripts include scRNA-seq preprocessing (Scanpy), cell type annotation (CellTypist), CCC inference using LIANA+, and downstream comparative analyses focused on scoring functions, expression averages, and significant interaction overlap. Results support methodological insights into CCC tool behavior under varying ligand–receptor expression patterns.

This folder contains all our Code

• All the folders have sepreate READE.md files explaining what code in spresent in the folder.
• CellChatvsCellPhoneDBMeanScore.ipynb helps us understand selectiveness of CellChat and CellPhoneBD.
• CombinedCellPhoneDBCellChatBoxPlot.ipynb helps us understand shared output of CellChat and CellPhoneBD.
• ExploreCellChat.ipynb is when we were exploring different tools in CellChat.
• test_gold_standard.py is making a dot plot for a perticular interaction.
• The full paper describing this project can be found in the BMI_776_Final_Paper.pdf

Contributors

• 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