GNET2

This package is for version 3.17 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: 3.17

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 "4.3") 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")
Build functional gene modules with GNET2 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, Network, NetworkInference, Regression, Software
Version 1.16.0
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
See More
Suggests knitr, rmarkdown
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package GNET2_1.16.0.tar.gz
Windows Binary GNET2_1.16.0.zip
macOS Binary (x86_64) GNET2_1.16.0.tgz
macOS Binary (arm64) GNET2_1.16.0.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
Old Source Packages for BioC 3.17 Source Archive