cTOP: Combinatorial Transcription Factor Oriented Program

Introduction

This repository contains the implementation of the cTOP (Combinatorial Transcription Factor Oriented Program) model used in the research paper "High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration." The cTOP model integrates single-cell RNA-seq data with bulk regulatory networks to uncover the regulation of key cellular programs during antler regeneration.

Installation

To use the cTOP model, please follow the steps below to set up your environment.

Prerequisites

• MATLAB R2014b or higher
• Python 3.8 or higher
• Required Python packages (listed in requirements.txt)

Steps

1. Clone the repository:

   git clone https://github.com/AMSSwanglab/cTOP_new.git
   cd cTOP

2. Create and activate a virtual environment (optional but recommended):

   python3 -m venv venv
   source venv/bin/activate

3. Install the required packages:

   pip install -r requirements.txt

Usage

To reproduce the results from the research paper and conduct similar analyses, follow these steps. The cTOP model requires three types of input data: paired bulk RNA-seq & ATAC-seq and scRNA-seq data, all of which can be found in the supplementary data of the publication. For ease of use, the Input folder already includes the regulatory network generated from the paired bulk RNA-seq & ATAC-seq data via the PECA model, detailed at the PECA repository. This setup allows you to focus solely on downloading the scRNA-seq data to replicate the study's findings.

To run the cTOP model, execute the following command in your terminal:

bash run_cTOP.sh $sample

$sample is the name of the sample you are analyzing. For this example, use POPP_B as the sample name.

Results from the cTOP model can be saved in the Results folder for easy reference (this folder might need to be created before running the model to store the results).

File Structure

• src/: Contains the source code for the cTOP model.
• tools/: Contains the tools for the cTOP model.
• main/: Contains main code for the cTOP model.
• example/: Contains example input data for testing.
• requirements.txt: Lists the Python packages required to run the cTOP model.

Reference

This work is based on the following paper: Li, Z., Xu, Z., Zhu, L., Qin, T., Ma, J., Feng, Z., Yue, H., Guan, Q., Zhou, B., Han, G., Zhang, G., Li, C., Jia, S., Qiu, Q., Hao, D., Wang, Y., & Wang, W. (2024). High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration. in review.

Contact

For any questions or issues, please contact:

• Ziyu Xu: xuziyu231@mails.ucas.ac.cn