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

GeneNetworkBuilder

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

Bioconductor version: 2.13

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>

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	GraphsAndNetworks, HighThroughputSequencing, Microarray, Software
Version	1.4.1
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
Imports Me
Suggests Me

Package Archives

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

Package Source	GeneNetworkBuilder_1.4.1.tar.gz
Windows Binary	GeneNetworkBuilder_1.4.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	GeneNetworkBuilder_1.4.1.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats