epistasisGA

This is the released version of epistasisGA; for the devel version, see epistasisGA.

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

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DOI: 10.18129/B9.bioc.epistasisGA

Bioconductor version: Release (3.22)

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>

Citation (from within R, enter citation("epistasisGA")):

Installation

To install this package, start R (version "4.5") 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")

Detecting Maternal-SNP Interactions HTML R Script

E-GADGETS HTML R Script

GADGETS HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneticVariability, Genetics, SNP, Software

Version 1.12.0

In Bioconductor since BioC 3.16 (R-4.2) (3 years)

License GPL-3

Depends R (>= 4.2)

Imports BiocParallel, data.table, matrixStats, stats, survival, igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid, bigmemory, graphics, utils

System Requirements

URL https://github.com/mnodzenski/epistasisGA

Bug Reports https://github.com/mnodzenski/epistasisGA/issues

Suggests BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0)

Linking To Rcpp, RcppArmadillo, BH, bigmemory

Enhances

Depends On Me

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Package Archives

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

Source Package epistasisGA_1.12.0.tar.gz

Windows Binary (x86_64) epistasisGA_1.12.0.zip

macOS Binary (x86_64) epistasisGA_1.12.0.tgz

macOS Binary (arm64) epistasisGA_1.12.0.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/

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