GeneNetworkBuilder
GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data
Bioconductor version: Release (3.17)
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 "4.3") 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 | ||
| NEWS | Text |
Details
| biocViews | GraphAndNetwork, Microarray, Sequencing, Software |
| Version | 1.42.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (11 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.15.1), Rcpp (>= 0.9.13) |
| Imports | plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods, grDevices, stats, graphics |
| Linking To | Rcpp |
| Suggests | RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db |
| System Requirements | |
| Enhances | |
| URL |
See More
| 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_1.42.0.tar.gz |
| Windows Binary | GeneNetworkBuilder_1.42.0.zip |
| macOS Binary (x86_64) | GeneNetworkBuilder_1.42.0.tgz |
| macOS Binary (arm64) | GeneNetworkBuilder_1.42.0.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 |