epistasisGA

DOI: 10.18129/B9.bioc.epistasisGA  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see epistasisGA.

An R package to identify multi-snp effects in nuclear family studies using the GADGETS method

Bioconductor version: 3.17

This package runs the GADGETS method to identify epistatic effects in nuclear family studies. It also provides functions for permutation-based inference and graphical visualization of the results.

Author: Michael Nodzenski [aut, cre], Juno Krahn [ctb]

Maintainer: Michael Nodzenski <michael.nodzenski at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("epistasisGA")

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("epistasisGA")

 

HTML	R Script	Detecting Maternal-SNP Interactions
HTML	R Script	E-GADGETS
HTML	R Script	GADGETS
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneticVariability, Genetics, SNP, Software
Version	1.2.1
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
License	GPL-3
Depends	R (>= 4.2)
Imports	BiocParallel, data.table, matrixStats, stats, survival, igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid, bigmemory, graphics, utils
LinkingTo	Rcpp, RcppArmadillo, BH, bigmemory
Suggests	BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/mnodzenski/epistasisGA
BugReports	https://github.com/mnodzenski/epistasisGA/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	epistasisGA_1.2.1.tar.gz
Windows Binary	epistasisGA_1.2.1.zip
macOS Binary (x86_64)	epistasisGA_1.2.1.tgz
macOS Binary (arm64)	epistasisGA_1.2.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/epistasisGA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/epistasisGA
Bioc Package Browser	https://code.bioconductor.org/browse/epistasisGA/
Package Short Url	https://bioconductor.org/packages/epistasisGA/
Package Downloads Report	Download Stats