rqt

DOI: 10.18129/B9.bioc.rqt  

rqt: utilities for gene-level meta-analysis

Bioconductor version: Release (3.17)

Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: "Gene-set association tests for next-generation sequencing data" by Lee et al (2016), Bioinformatics, 32(17), i611-i619, .

Author: I. Y. Zhbannikov, K. G. Arbeev, A. I. Yashin.

Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov at duke.edu>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rqt")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("rqt")

 

HTML	R Script	Tutorial for rqt package
PDF		Reference Manual
Text		NEWS

Details

biocViews	GenomeWideAssociation, PrincipalComponent, Regression, Sequencing, Software, StatisticalMethod, Survival
Version	1.26.0
In Bioconductor since	BioC 3.5 (R-3.4) (6.5 years)
License	GPL
Depends	R (>= 3.4), SummarizedExperiment
Imports	stats, Matrix, ropls, methods, car, RUnit, metap, CompQuadForm, glmnet, utils, pls
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/izhbannikov/rqt
BugReports	https://github.com/izhbannikov/rqt/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	rqt_1.26.0.tar.gz
Windows Binary	rqt_1.26.0.zip (64-bit only)
macOS Binary (x86_64)	rqt_1.26.0.tgz
macOS Binary (arm64)	rqt_1.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rqt
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rqt
Bioc Package Browser	https://code.bioconductor.org/browse/rqt/
Package Short Url	https://bioconductor.org/packages/rqt/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive