rqt
This is the development version of rqt; for the stable release version, see rqt.
rqt: utilities for gene-level meta-analysis
DOI: 10.18129/B9.bioc.rqt
Bioconductor version: Development (3.24)
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("rqt")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("rqt")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | GenomeWideAssociation, PrincipalComponent, Regression, Sequencing, Software, StatisticalMethod, Survival |
| Version | 1.39.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 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 |
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 | |
| Windows Binary (x86_64) | rqt_1.39.0.zip |
| macOS Binary (big-sur-x86_64) | rqt_1.39.0.tgz |
| macOS Binary (sonoma-arm64) | rqt_1.39.0.tgz |
| 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 |