GeneGeneInteR
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see GeneGeneInteR.
Tools for Testing Gene-Gene Interaction at the Gene Level
Bioconductor version: 3.11
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, Nicolas Sounac, Florian Kroell, Magalie Houee-Bigot
Maintainer: Mathieu Emily <mathieu.emily at agrocampus-ouest.fr>, Magalie Houee-Bigot <magalie.houee at agrocampus-ouest.fr>
citation("GeneGeneInteR")):
Installation
To install this package, start R (version "4.0") 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 | R Script | |
| Pairwise interaction tests | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneticVariability, Genetics, GenomeWideAssociation, SNP, Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 4.0) |
| Imports | snpStats, mvtnorm, GGtools, Rsamtools, igraph, kernlab, FactoMineR, plspm, IRanges, GenomicRanges, data.table, grDevices, graphics, stats, utils, methods |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GeneGeneInteR_1.14.0.tar.gz |
| Windows Binary | GeneGeneInteR_1.14.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | GeneGeneInteR_1.14.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |