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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

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

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
See More
Suggests BiocStyle, knitr, rmarkdown
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Build Report Build Report

Package Archives

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

Source Package rqt_1.29.0.tar.gz
Windows Binary rqt_1.29.0.zip
macOS Binary (x86_64) rqt_1.29.0.tgz
macOS Binary (arm64) rqt_1.29.0.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