GNET2

DOI: 10.18129/B9.bioc.GNET2    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see GNET2.

Constructing gene regulatory networks from expression data through functional module inference

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

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

Details

biocViews	GeneExpression, Network, NetworkInference, Regression, Software
Version	1.12.0
In Bioconductor since	BioC 3.9 (R-3.6) (3.5 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
LinkingTo	Rcpp
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/chrischen1/GNET2
BugReports	https://github.com/chrischen1/GNET2/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	GNET2_1.12.0.tar.gz
Windows Binary	GNET2_1.12.0.zip
macOS Binary (x86_64)	GNET2_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GNET2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GNET2
Package Short Url	https://bioconductor.org/packages/GNET2/
Package Downloads Report	Download Stats