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epistasisGA

This is the development version of epistasisGA; for the stable release version, see epistasisGA.

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


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews GeneticVariability, Genetics, SNP, Software
Version 1.5.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 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
See More
Suggests BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0)
Linking To Rcpp, RcppArmadillo, BH, bigmemory
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 epistasisGA_1.5.0.tar.gz
Windows Binary
macOS Binary (x86_64) epistasisGA_1.5.0.tgz
macOS Binary (arm64)
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