rqt
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see rqt.
rqt: utilities for gene-level meta-analysis
Bioconductor version: 3.9
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("rqt")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | GenomeWideAssociation, PrincipalComponent, Regression, Sequencing, Software, StatisticalMethod, Survival |
| Version | 1.10.0 |
| 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 |
| 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_1.10.0.tar.gz |
| Windows Binary | rqt_1.10.0.zip |
| Mac OS X 10.11 (El Capitan) | rqt_1.10.0.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 3.9 | Source Archive |