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 (3.19)

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>

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")

# 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GenomeWideAssociation, PrincipalComponent, Regression, Sequencing, Software, StatisticalMethod, Survival
Version	1.29.0
In Bioconductor since	BioC 3.5 (R-3.4) (7 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
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Build Report	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