xQTLbiolinks
is a end-to-end bioinformatic tool for efficient mining and analyzing public and user-customized xQTLs data for the discovery of disease susceptibility genes. xQTLbiolinks consists of tailored functions that can be grouped into four modules: Data retrieval, Pre-processing, Analysis and Visualization.
Instructions, documentation, and tutorials can be found at here.
xQTLbiolinks
can be installed and used on any operator systems supporting R. Once the R (version 4.0 or later) is available, using install.packages("xQTLbiolinks")
to install the steady version (v1.6.2) of xQTLbiolinks
. The latest version (v1.6.3) is also available at GitHub repository and it can be installed through devtools::install_github("dingruofan/xQTLbiolinks”)
. For more details, please refer to the instructions at Installation section below.xQTLbiolinks
.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, Hui Chen, Xuelian Ma, Gao Wang, Lei Li. xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs. (submitted)
Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
R packages: BiocGenerics, cowplot (>= 1.1.1), curl (>= 4.3.2), data.table (>= 1.14.2), DBI, SummarizedExperiment, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2 (>= 3.3.6), ggrepel, IRanges, jsonlite (>= 1.7.2), viridis, RMySQL, stringr (>= 1.4.0), utils (>= 4.0.3),VariantAnnotation, TxDb.Hsapiens.UCSC.hg38.knownGene, PupillometryR, coloc, hyprcoloc, knitr, rtracklayer, usethis, ggridges, CMplot, R.utils, ggforestplot.
To install this R package, you will need to have required package SummarizedExperiment
installed from Bioconductor with following command:
if (!require("BiocManager", quietly = TRUE)){install.packages("BiocManager")}
BiocManager::install("SummarizedExperiment") # For windows or linux
BiocManager::install("SummarizedExperiment",type="source") # For MAC
Once you have installed the required package, you can then install xQTLbiolinks
from CRAN or github(recommended) using following command:
# Install from github to get the latest version.
if(!require("devtools")){install.packages("devtools")}
devtools::install_github("dingruofan/xQTLbiolinks")
# This command should automatically install any missing dependencies that are available from CRAN
install.packages("xQTLbiolinks")