To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("GeneNetworkBuilder")

In most cases, you don't need to download the package archive at all.

GeneNetworkBuilder

 

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

Bioconductor version: Release (3.1)

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 and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("GeneNetworkBuilder")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GeneNetworkBuilder")

 

PDF R Script GeneNetworkBuilder Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews GraphAndNetwork, Microarray, Sequencing, Software
Version 1.10.0
In Bioconductor since BioC 2.11 (R-2.15) (3 years)
License GPL (>= 2)
Depends R (>= 2.15.1), Rcpp (>= 0.9.13), graph
Imports plyr, graph
LinkingTo Rcpp
Suggests RUnit, BiocGenerics, Rgraphviz, XML, RCytoscape, RBGL
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source GeneNetworkBuilder_1.10.0.tar.gz
Windows Binary GeneNetworkBuilder_1.10.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GeneNetworkBuilder_1.10.0.tgz
Mac OS X 10.9 (Mavericks) GeneNetworkBuilder_1.10.0.tgz
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