- Home
- Bioconductor 3.2
- Software Packages
- GeneNetworkBuilder
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GeneNetworkBuilder")
In most cases, you don't need to download the package archive at all.
GeneNetworkBuilder
|
This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see GeneNetworkBuilder.
Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
Bioconductor version: 3.2
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 umassmed.edu>
Citation (from within R,
enter citation("GeneNetworkBuilder")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GeneNetworkBuilder")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GeneNetworkBuilder")
| GeneNetworkBuilder Vignette | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GraphAndNetwork, Microarray, Sequencing, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (3.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.15.1), Rcpp (>= 0.9.13), graph |
| Imports | plyr, graph |
| LinkingTo | Rcpp |
| Suggests | RUnit, BiocGenerics, Rgraphviz, XML, RCytoscape, RBGL, knitr |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | GeneNetworkBuilder_1.12.0.tar.gz |
| Windows Binary | GeneNetworkBuilder_1.12.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | GeneNetworkBuilder_1.12.0.tgz |
| Mac OS X 10.9 (Mavericks) | GeneNetworkBuilder_1.12.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/GeneNetworkBuilder/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/GeneNetworkBuilder/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
