IMVGI - Integrative Multi-omics Variant-Gene Interaction Pipeline

IMVGI is a tool designed for Integrative Multi-omics Variant-Gene Interaction analysis, applicable to any trait research.

Project Structure

The project is organized into the following directory structure, which helps users understand the purpose of each file and folder:

IMVGI/
├── README.md # The main file that describes the project, installation instructions, and usage guidelines
├── data/ # Folder containing all the required data for the project
│ ├── WGS/ # Whole Genome Sequencing data
│ ├── epigenomic/ # Epigenomic data
│ ├── 3D_genomic/ # 3D Genomic data
│ └── transcriptomic/ # Transcriptomic data
├── scripts/ # Folder containing all the analysis scripts
│ ├── variant_calling.py # Script for variant calling
│ ├── selection_signature_analysis.py # Script for selection signature analysis
│ ├── epigenomic_annotation.py # Script for epigenomic annotation
│ ├── genomic_3d_interaction_analysis.py # Script for 3D genomic interaction analysis
│ └── wgcna_analysis.py # Script for Weighted Gene Co-expression Network Analysis (WGCNA)
├── output/ # Output folder, automatically generated, no need to upload
├── requirements.txt # File listing all the Python package dependencies
└── LICENSE # License file for the project

Installation

Follow these steps to install and run the project in your local environment:

1. Clone this repository

First, use git to clone the repository to your local machine. This command copies the entire project to your computer.

git clone https://github.com/your-username/IMVGI.git
cd IMVGI

2. Install dependencies

Use pip to install all the required Python packages. These packages are listed in the requirements.txt file. Run the following command to install them:

pip install -r requirements.txt

Usage

The following sections explain how to use each script to perform various analyses. Each script corresponds to a different step in the analysis process:

1. Call Variant

Run the following command to perform variant calling. This script identifies variants in the genome.

python scripts/variant_calling.py

2. Selection Signature Analysis

Use this script to perform selection signature analysis, which aims to identify regions of the genome that have been preserved during selection.

python scripts/selection_signature_analysis.py

3. Epigenomic Annotation

This script annotates epigenomic data onto the genome, helping to understand the impact of variants at the epigenomic level.

python scripts/epigenomic_annotation.py

4.3D Genomic Interaction Analysis

python scripts/genomic_3d_interaction_analysis.py

5. WGCNA Analysis

Run this script to perform Weighted Gene Co-expression Network Analysis (WGCNA) to study gene co-expression patterns.

python scripts/wgcna_analysis.py

Contributing

Contributions, issues, and feature requests are welcome! Feel free to submit issues or pull requests.

License

This project is licensed under the MIT License, which allows users to freely use, modify, and distribute the code.