rqt

rqt: utilities for gene-level meta-analysis

Bioconductor version: Release (3.20)

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: Ilya Zhbannikov [aut, cre], Konstantin Arbeev [aut], Anatoliy Yashin [aut]

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

Citation (from within R, enter citation("rqt")):

Installation

To install this package, start R (version "4.4") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GenomeWideAssociation, PrincipalComponent, Regression, Sequencing, Software, StatisticalMethod, Survival
Version	1.32.0
In Bioconductor since	BioC 3.5 (R-3.4) (7.5 years)
License	GPL
Depends	R (>= 3.4), SummarizedExperiment
Imports	stats, Matrix, ropls, methods, car, RUnit, metap, CompQuadForm, glmnet, utils, pls
System Requirements
URL	https://github.com/izhbannikov/rqt
Bug Reports	https://github.com/izhbannikov/rqt/issues

Suggests	BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	rqt_1.32.0.tar.gz
Windows Binary (x86_64)	rqt_1.32.0.zip (64-bit only)
macOS Binary (x86_64)	rqt_1.32.0.tgz
macOS Binary (arm64)	rqt_1.31.1.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