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 (3.24)
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 <jou at morgridge.org>
citation("GeneNetworkBuilder")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.55.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (14 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_1.55.0.tar.gz |
| Windows Binary (x86_64) | GeneNetworkBuilder_1.55.0.zip |
| macOS Binary (big-sur-x86_64) | GeneNetworkBuilder_1.55.0.tgz |
| macOS Binary (sonoma-arm64) | GeneNetworkBuilder_1.55.0.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 |