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版本:版本(3.15)

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

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 appropriateBioconductor release.

Documentation

查看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	1.38.0
In Bioconductor since	BioC 2.11 (R-2.15) (9.5 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
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	GeneNetworkBuilder_1.38.0.tar.gz
Windows Binary	GeneNetworkBuilder_1.38.0.zip
macOS 10.13 (High Sierra)	GeneNetworkBuilder_1.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GeneNetworkBuilder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GeneNetworkBuilder
Package Short Url	//www.andersvercelli.com/packages/GeneNetworkBuilder/
Package Downloads Report	Download Stats