xQTLbiolinks: An R package aims to query, download, visualize and perform colocalization analyses between xQTL data and GWAS signals

xQTLbiolinks is a well-developed R package that enables users-customized query, extraction, and visualization of molecular QTLs (eQTLs and sQTLs) and gene expression data from public resources (e.g., GTEx) through the application programming interface (API) of GTEx and eQTL Catalogue.

xQTLbiolinks consists of tailored functions that can be grouped into four modules: Query, Download, Analyze and Visualization.

Instructions, documentation, and tutorials can be found at here.

Quick Start

1. xQTLbiolinks has been successfully installed on Mac OS X, Linux, and Windows, using the install.package function to install directly from CRAN with command install.package("xQTLbiolinks"). Check more details in section “Installation” below.
2. Find the Full document for a quick application of colocalization analysis with xQTLbiolinks.
3. Go through a whole Case study of detection of casual vairants and genes in prostate cancer using xQTLbiolinks.
4. Then walk through these vignettes to learn more about xQTLbiolinks: Function Instruction and Visualization of expression and xQTL.

Citation

If you find the xQTLbiolinks package or any of the source code in this repository useful for your work, please cite:

Ruofan Ding, Xudong Zou, Yangmei Qin, Gao Wang, Lei Li. xQTLbiolinks: an R package for integrative analysis of xQTL data. (submitted)

Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China

Installation

1. We strongly recommend to install in the environment of R, instead of Rstudio.

2. Package SummarizedExperiment is required but reposited in Biocouductor. If you haven’t installed it, please install SummarizedExperiment from Biocouductor with following command.

# install required bioconductor package SummarizedExperiment:
if (!require("BiocManager")){install.packages("BiocManager")}
BiocManager::install("SummarizedExperiment")

3. Install xQTLbiolinks from CRAN or github.

# This command should automatically install any missing dependencies that are available from CRAN
install.packages("xQTLbiolinks")

# Or install from github.
if(!require("remotes")){install.packages("remotes")}
remotes::install_github("dingruofan/xQTLbiolinks")