[![License: All rights reserved]

GTEx_Pro

Visualizing gene expression in GTEx

Project Overview

This project contains data acquisition, preprocessing, normalization, batch correction, visualization, and organization code for GTEx dataset. It provides a comprehensive workflow for analyzing gene expression data from various tissues, facilitating downstream analysis and interpretation. This code implements a robust pipeline for analyzing gene expression data of GTEx effectively correcting for batch effects while retaining biological variations associated with sex (view the 3D interactive PCA plot below). The code isn't fully automated and requires manual inputs at specific points. Future updates will be focused on automating the code with less manual inputs

Table of Contents

• Project Overview
• Requirements
• Installation
• Usage
• License
• Contributing
• Acknowledgments

Requirements

To run this project, you will need:

• R version >= 4.0
• R packages:
  • dplyr
  • ggplot2
  • edgeR
  • limma
  • sva
  • officer
  • magrittr
  • Other dependencies as necessary

Installation

Install required R packages (if not already installed):

Usage

1. 

2. Follow the order of the scripts detailed steps on:

Data acquisition Data preprocessing Normalization Batch correction (sva-recommended)Visualization Organizing the data for further analysis

The final results and plots will be saved in the results.../ directory.

PCA

View the 3D PCA plot View 3D UMAP plot View 3D TNSE plot

License

This project is licensed under the All Rights Reserved license for the time being. If you'd like to request permission for use or modification, please contact dhana2403

Contributing

If you'd like to offer feedback on the workflow/code, please contact dhana2403

Acknowledgments

GTEx Project for providing the data. Partial preprocessing code was adapted from mdonertas.