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GNET2

This is the development version of GNET2; for the stable release version, see GNET2.

Constructing gene regulatory networks from expression data through functional module inference


Bioconductor version: Development (3.19)

Cluster genes to functional groups with E-M process. Iteratively perform TF assigning and Gene assigning, until the assignment of genes did not change, or max number of iterations is reached.

Author: Chen Chen, Jie Hou and Jianlin Cheng

Maintainer: Chen Chen <ccm3x at mail.missouri.edu>

Citation (from within R, enter citation("GNET2")):

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("GNET2")

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("GNET2")
Build functional gene modules with GNET2 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, Network, NetworkInference, Regression, Software
Version 1.19.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License Apache License 2.0
Depends R (>= 3.6)
Imports ggplot2, xgboost, Rcpp, reshape2, grid, DiagrammeR, methods, stats, matrixStats, graphics, SummarizedExperiment, dplyr, igraph, grDevices, utils
System Requirements
URL https://github.com/chrischen1/GNET2
Bug Reports https://github.com/chrischen1/GNET2/issues
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Suggests knitr, rmarkdown
Linking To Rcpp
Enhances
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Package Archives

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

Source Package GNET2_1.19.0.tar.gz
Windows Binary GNET2_1.19.0.zip
macOS Binary (x86_64) GNET2_1.19.0.tgz
macOS Binary (arm64) GNET2_1.19.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GNET2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GNET2
Bioc Package Browser https://code.bioconductor.org/browse/GNET2/
Package Short Url https://bioconductor.org/packages/GNET2/
Package Downloads Report Download Stats