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This is the development version of GeneNetworkBuilder; for the stable release version, see GeneNetworkBuilder.

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

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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

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


biocViews GraphAndNetwork, Microarray, Sequencing, Software
Version 1.47.0
In Bioconductor since BioC 2.11 (R-2.15) (12 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, BiocStyle, magick, rmarkdown,
Linking To Rcpp
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Follow Installation instructions to use this package in your R session.

Source Package GeneNetworkBuilder_1.47.0.tar.gz
Windows Binary
macOS Binary (x86_64) GeneNetworkBuilder_1.47.0.tgz
macOS Binary (arm64) GeneNetworkBuilder_1.47.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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