GeneNetworkBuilder
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 duke.edu>
citation("GeneNetworkBuilder")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Reference Manual | ||
NEWS | Text |
Details
biocViews | GraphAndNetwork, Microarray, Sequencing, Software |
Version | 1.47.4 |
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, RCy3, rjson, XML, methods, grDevices, stats, graphics |
System Requirements | |
URL |
See More
Suggests | RUnit, BiocGenerics, RBGL, knitr, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db |
Linking To | Rcpp |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | GeneNetworkBuilder_1.47.4.tar.gz |
Windows Binary | GeneNetworkBuilder_1.47.4.zip (64-bit only) |
macOS Binary (x86_64) | GeneNetworkBuilder_1.47.4.tgz |
macOS Binary (arm64) | GeneNetworkBuilder_1.47.4.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 |