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GRENITS

Gene Regulatory Network Inference Using Time Series


Bioconductor version: Release (3.18)

The package offers four network inference statistical models using Dynamic Bayesian Networks and Gibbs Variable Selection: a linear interaction model, two linear interaction models with added experimental noise (Gaussian and Student distributed) for the case where replicates are available and a non-linear interaction model.

Author: Edward Morrissey

Maintainer: Edward Morrissey <edward.morrissey at gmail.com>

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

Installation

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


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

BiocManager::install("GRENITS")

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("GRENITS")
GRENITS PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, GeneExpression, GeneRegulation, GraphAndNetwork, Network, NetworkInference, Software, TimeCourse
Version 1.54.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License GPL (>= 2)
Depends R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0)
Imports graphics, grDevices, reshape2, stats, utils
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Linking To Rcpp, RcppArmadillo
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Package Archives

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

Source Package GRENITS_1.54.0.tar.gz
Windows Binary GRENITS_1.54.0.zip
macOS Binary (x86_64) GRENITS_1.54.0.tgz
macOS Binary (arm64) GRENITS_1.54.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GRENITS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GRENITS
Bioc Package Browser https://code.bioconductor.org/browse/GRENITS/
Package Short Url https://bioconductor.org/packages/GRENITS/
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