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GENIE3

GEne Network Inference with Ensemble of trees


Bioconductor version: Release (3.19)

This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.

Author: Van Anh Huynh-Thu, Sara Aibar, Pierre Geurts

Maintainer: Van Anh Huynh-Thu <vahuynh at uliege.be>

Citation (from within R, enter citation("GENIE3")):

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("GENIE3")

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("GENIE3")
GENIE3 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DecisionTree, GeneExpression, GraphAndNetwork, Network, NetworkInference, Regression, Software, SystemsBiology
Version 1.26.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL (>= 2)
Depends
Imports stats, reshape2, dplyr
System Requirements
URL
See More
Suggests knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me BioNERO, MetNet, bulkAnalyseR
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package GENIE3_1.26.0.tar.gz
Windows Binary GENIE3_1.26.0.zip
macOS Binary (x86_64) GENIE3_1.26.0.tgz
macOS Binary (arm64) GENIE3_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GENIE3
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GENIE3
Bioc Package Browser https://code.bioconductor.org/browse/GENIE3/
Package Short Url https://bioconductor.org/packages/GENIE3/
Package Downloads Report Download Stats