rqt

DOI: 10.18129/B9.bioc.rqt    

This is the development version of rqt; for the stable release version, see rqt.

rqt: utilities for gene-level meta-analysis

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("rqt")

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

Documentation

PDF		Reference Manual

Details

biocViews	GenomeWideAssociation, PrincipalComponent, Regression, Sequencing, Software, StatisticalMethod, Survival
Version	1.25.0
In Bioconductor since	BioC 3.5 (R-3.4) (5.5 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
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/rqt
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rqt
Package Short Url	https://bioconductor.org/packages/rqt/
Package Downloads Report	Download Stats