GeneNetworkBuilder

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see GeneNetworkBuilder.

Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data


Bioconductor version: 3.7

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 umassmed.edu>

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

Installation

To install this package, start R (version "3.5") and enter:


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

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
Working with BioGRID, STRING HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GraphAndNetwork, Microarray, Sequencing, Software
Version 1.22.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License GPL (>= 2)
Depends R (>= 2.15.1), Rcpp (>= 0.9.13)
Imports plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods, grDevices, stats, graphics
System Requirements
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Suggests RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb
Linking To Rcpp
Enhances
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Package Archives

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

Source Package GeneNetworkBuilder_1.22.0.tar.gz
Windows Binary GeneNetworkBuilder_1.22.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) GeneNetworkBuilder_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GeneNetworkBuilder
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GeneNetworkBuilder
Package Short Url https://bioconductor.org/packages/GeneNetworkBuilder/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive