GPA

GPA (Genetic analysis incorporating Pleiotropy and Annotation)

Bioconductor version: Release (3.19)

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 (from within R, enter citation("GPA")):

Installation

To install this package, start R (version "4.4") 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	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, Clustering, DifferentialExpression, GeneExpression, Genetics, GenomeWideAssociation, MultipleComparison, Preprocessing, SNP, Software, StatisticalMethod
Version	1.16.0
In Bioconductor since	BioC 3.11 (R-4.0) (4.5 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

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_1.16.0.tar.gz
Windows Binary (x86_64)	GPA_1.16.0.zip
macOS Binary (x86_64)	GPA_1.16.0.tgz
macOS Binary (arm64)	GPA_1.16.0.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