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GeneGeneInteR

Tools for Testing Gene-Gene Interaction at the Gene Level


Bioconductor version: Release (3.18)

The aim of this package is to propose several methods for testing gene-gene interaction in case-control association studies. Such a test can be done by aggregating SNP-SNP interaction tests performed at the SNP level (SSI) or by using gene-gene multidimensionnal methods (GGI) methods. The package also proposes tools for a graphic display of the results. .

Author: Mathieu Emily [aut, cre], Nicolas Sounac [ctb], Florian Kroell [ctb], Magalie Houee-Bigot [aut]

Maintainer: Mathieu Emily <mathieu.emily at agrocampus-ouest.fr>

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

Installation

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


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

BiocManager::install("GeneGeneInteR")

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("GeneGeneInteR")
GeneGeneInteR Introduction PDF R Script
Pairwise interaction tests PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneticVariability, Genetics, GenomeWideAssociation, SNP, Software
Version 1.28.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL (>= 2)
Depends R (>= 4.0)
Imports snpStats, mvtnorm, Rsamtools, igraph, kernlab, FactoMineR, IRanges, GenomicRanges, data.table, grDevices, graphics, stats, utils, methods
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Package Archives

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

Source Package GeneGeneInteR_1.28.0.tar.gz
Windows Binary GeneGeneInteR_1.28.0.zip
macOS Binary (x86_64) GeneGeneInteR_1.28.0.tgz
macOS Binary (arm64) GeneGeneInteR_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GeneGeneInteR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GeneGeneInteR
Bioc Package Browser https://code.bioconductor.org/browse/GeneGeneInteR/
Package Short Url https://bioconductor.org/packages/GeneGeneInteR/
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