GeneNetworkBuilder

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

Bioconductor version: Development (3.0)

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 and Lihua Julie Zhu

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

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("GeneNetworkBuilder")

Documentation

PDF R Script GeneNetworkBuilder Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews GraphAndNetwork, Microarray, Sequencing, Software
Version 1.7.0
In Bioconductor since BioC 2.11 (R-2.15)
License GPL (>= 2)
Depends R (>= 2.15.1), Rcpp (>= 0.9.13), graph
Imports plyr, graph
Suggests RUnit, BiocGenerics, Rgraphviz, XML, RCytoscape
System Requirements
URL
Depends On Me
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Package Downloads

Package Source GeneNetworkBuilder_1.7.0.tar.gz
Windows Binary GeneNetworkBuilder_1.7.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GeneNetworkBuilder_1.7.0.tgz
Mac OS X 10.9 (Mavericks)
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