Gastric_xQTL Project

Overview

This repository contains the codebase used in the study
"Transcriptome-wide association studies identify new gastric cancer susceptibility genes through genetic regulation of expression, alternative splicing and polyadenylation",
covering both main analyses and figures generation scripts.

The project aims to identify genetic variants contributing to gastric cancer risk by analyzing gastric-specific expression quantitative trait loci (eQTLs), splicing QTLs (sQTLs), and alternative polyadenylation QTLs (apaQTLs). The code is divided into two main sections:

1. Codes for Main Analyses: Scripts for quatifying events, mapping QTLs, and performing transcriptome-wide and regulome-wide association study (TWAS).
2. Codes for Figures: Scripts used to produce the main figures presented in the study.

---

Usage Instructions

Main Analyses

1. Clone the repository.
2. Install required environments (e.g., LeafCutter, DaPars2, FUSION).
3. Execute scripts under the "Codes for Main Analyses" section.

Figures Generation

1. Install R and required R packages.
2. Run the relevant R scripts to generate each figure.

---

Contact

For questions or issues regarding the code, please contact [[email protected]].

---