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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 (3.18)

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 "4.3") 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 1.3.0
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
Linking To Rcpp, RcppArmadillo, BH, bigmemory
Suggests BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0)
System Requirements
Enhances
URL https://github.com/mnodzenski/epistasisGA
Bug Reports https://github.com/mnodzenski/epistasisGA/issues
See More
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_1.3.0.tar.gz
Windows Binary epistasisGA_1.3.0.zip (64-bit only)
macOS Binary (x86_64) epistasisGA_1.3.0.tgz
macOS Binary (arm64) epistasisGA_1.3.0.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/
Package Downloads Report Download Stats