GeneNetworkBuilder

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see GeneNetworkBuilder.

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

DOI: 10.18129/B9.bioc.GeneNetworkBuilder

Bioconductor version: 3.10

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 "3.6") 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

Generate Network from a list of gene HTML R Script

Working with BioGRID, STRING HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GraphAndNetwork, Microarray, Sequencing, Software

Version 1.28.1

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

URL

Suggests RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb, BiocStyle, magick

Linking To Rcpp

Enhances

Depends On Me

Imports Me

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Links To Me

Build Report Build Report

Package Archives

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

Source Package GeneNetworkBuilder_1.28.1.tar.gz

Windows Binary GeneNetworkBuilder_1.28.1.zip

Mac OS X 10.11 (El Capitan) GeneNetworkBuilder_1.28.1.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

Old Source Packages for BioC 3.10 Source Archive