GeneNetworkBuilder

DOI: 10.18129/B9.bioc.GeneNetworkBuilder  

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

Bioconductor version: Release (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 duke.edu>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

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, org.Hs.eg.db
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	GeneNetworkBuilder_1.40.0.tar.gz
Windows Binary	GeneNetworkBuilder_1.40.0.zip
macOS Binary (x86_64)	GeneNetworkBuilder_1.40.0.tgz
macOS Binary (arm64)	GeneNetworkBuilder_1.40.0.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