GENIE3

This is the development version of GENIE3; for the stable release version, see GENIE3.

GEne Network Inference with Ensemble of trees

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DOI: 10.18129/B9.bioc.GENIE3

Bioconductor version: Development (3.23)

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 "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DecisionTree, GeneExpression, GraphAndNetwork, Network, NetworkInference, Regression, Software, SystemsBiology

Version 1.33.0

In Bioconductor since BioC 3.6 (R-3.4) (8 years)

License GPL (>= 2)

Depends

Imports stats, reshape2, dplyr

System Requirements

URL

Suggests knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle

Linking To

Enhances

Depends On Me

Imports Me BioNERO, MetNet, scGraphVerse, 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_1.33.0.tar.gz

Windows Binary (x86_64) GENIE3_1.33.0.zip (64-bit only)

macOS Binary (x86_64) GENIE3_1.33.0.tgz

macOS Binary (arm64) GENIE3_1.33.0.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/

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