DOI: 10.18129/B9.bioc.GeneNetworkBuilder  

This package is for version 3.16 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

Bioconductor version: 3.16

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")):


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HTML R Script GeneNetworkBuilder Vignette
HTML R Script Generate Network from a list of gene
HTML R Script Working with BioGRID, STRING
PDF   Reference Manual
Text   NEWS


biocViews GraphAndNetwork, Microarray, Sequencing, Software
Version 1.40.0
In Bioconductor since BioC 2.11 (R-2.15) (10.5 years)
License GPL (>= 2)
Depends R (>= 2.15.1), Rcpp (>= 0.9.13)
Imports plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods, grDevices, stats, graphics
LinkingTo Rcpp
Suggests RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb, BiocStyle, magick, rmarkdown,
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