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GeneNetworkBuilder

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

GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data

Bioconductor version: Development (3.18)

Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF.

Author: Jianhong Ou, Haibo Liu, Heidi A Tissenbaum and Lihua Julie Zhu

Maintainer: Jianhong Ou <jianhong.ou at duke.edu>

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

Installation

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

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

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

BiocManager::install("GeneNetworkBuilder")

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("GeneNetworkBuilder")
GeneNetworkBuilder Vignette HTML R Script
Generate Network from a list of gene HTML R Script
Working with BioGRID, STRING HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GraphAndNetwork, Microarray, Sequencing, Software
Version 1.43.0
In Bioconductor since BioC 2.11 (R-2.15) (11 years)
License GPL (>= 2)
Depends R (>= 2.15.1), Rcpp (>= 0.9.13)
Imports plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods, grDevices, stats, graphics
Linking To Rcpp
Suggests RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db
System Requirements
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Package Archives

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

Source Package GeneNetworkBuilder_1.43.0.tar.gz
Windows Binary GeneNetworkBuilder_1.43.0.zip
macOS Binary (x86_64) GeneNetworkBuilder_1.43.0.tgz
macOS Binary (arm64) GeneNetworkBuilder_1.43.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GeneNetworkBuilder
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GeneNetworkBuilder
Bioc Package Browser https://code.bioconductor.org/browse/GeneNetworkBuilder/
Package Short Url https://bioconductor.org/packages/GeneNetworkBuilder/
Package Downloads Report Download Stats