GPA
This is the released version of GPA; for the devel version, see GPA.
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
DOI: 10.18129/B9.bioc.GPA
Bioconductor version: Release (3.23)
This package provides functions for fitting GPA, a statistical framework to prioritize GWAS results by integrating pleiotropy information and annotation data. In addition, it also includes ShinyGPA, an interactive visualization toolkit to investigate pleiotropic architecture.
Author: Dongjun Chung, Emma Kortemeier, Carter Allen
Maintainer: Dongjun Chung <dongjun.chung at gmail.com>
citation("GPA")):
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")
BiocManager::install("GPA")
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("GPA")| GPA | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Clustering, DifferentialExpression, GeneExpression, Genetics, GenomeWideAssociation, MultipleComparison, Preprocessing, SNP, Software, StatisticalMethod |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 4.0.0), methods, graphics, Rcpp |
| Imports | parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS, stats, utils, grDevices |
| System Requirements | GNU make |
| URL | http://dongjunchung.github.io/GPA/ |
| Bug Reports | https://github.com/dongjunchung/GPA/issues |
See More
| Suggests | gpaExample |
| Linking To | Rcpp |
| 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 | GPA_1.24.0.tar.gz |
| Windows Binary (x86_64) | GPA_1.24.0.zip |
| macOS Binary (big-sur-x86_64) | GPA_1.24.0.tgz |
| macOS Binary (sonoma-arm64) | GPA_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GPA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GPA |
| Bioc Package Browser | https://code.bioconductor.org/browse/GPA/ |
| Package Short Url | https://bioconductor.org/packages/GPA/ |
| Package Downloads Report | Download Stats |