GPA

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see GPA.

GPA (Genetic analysis incorporating Pleiotropy and Annotation)

Bioconductor version: 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/

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