This repository contains the single-cell RNA sequencing analysis code used in the research paper "CD276-dependent efferocytosis by tumor-associated macrophages promotes immune evasion in bladder cancer". The code herein is intended to process, analyze, and visualize single-cell transcriptomics data to elucidate the role of CD276 in the efferocytosis process conducted by tumor-associated macrophages (TAMs) and its implications in immune evasion within the bladder cancer microenvironment.
cellchat.R: Code for performing cell-cell communication analysis using CellChat.cellphoneDB.R: Scripts for statistical analysis of cell-cell communication via CellPhoneDB.gsva.R: Gene set variation analysis (GSVA) for pathway enrichment analysis.harmony.R: Harmony algorithm for integrating multiple single-cell datasets.scenic.R: SCENIC pipeline for reconstructing gene regulatory networks.
Each script is named according to the analysis or tool used. To reproduce the results from the paper, run each script in the R environment. Ensure that all dependencies are installed before executing the scripts.
- R (version 3.6.0 or higher)
- CellChat
- CellPhoneDB
- GSVA
- Harmony
- SCENIC
- Additional R packages as required by the above
To run the analysis scripts, you will need to install the necessary R packages. Installation instructions for each package can be found at their respective websites or repositories.
The data used for this analysis is not included in this repository and must be obtained separately.
For questions or support, please open an issue in this repository or contact the corresponding author of the research paper.
If you use the code or methodologies in this repository in your research, please cite our paper:
[Author(s)], "CD276-dependent efferocytosis by tumor-associated macrophages promotes immune evasion in bladder cancer," [Journal], [Year].