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GeneNetworkBuilder

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


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews GraphAndNetwork, Microarray, Sequencing, Software
Version 1.44.0
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
See More
Suggests RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db
Linking To Rcpp
Enhances
Depends On Me
Imports Me
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Links To Me
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Package Archives

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

Source Package GeneNetworkBuilder_1.44.0.tar.gz
Windows Binary GeneNetworkBuilder_1.44.0.zip
macOS Binary (x86_64) GeneNetworkBuilder_1.44.0.tgz
macOS Binary (arm64) GeneNetworkBuilder_1.44.0.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