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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
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Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
Bioconductor version: Release (3.5)
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
| HTML | R Script | GeneNetworkBuilder Vignette |
| HTML | R Script | Working with BioGRID, STRING |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GraphAndNetwork, Microarray, Sequencing, Software |
| Version | 1.18.1 |
| In Bioconductor since | BioC 2.11 (R-2.15) (5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.15.1), Rcpp (>= 0.9.13) |
| Imports | plyr, graph, htmlwidgets, Rgraphviz, rjson, XML |
| LinkingTo | Rcpp |
| Suggests | RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb |
| 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.
| Source Package | GeneNetworkBuilder_1.18.1.tar.gz |
| Windows Binary | GeneNetworkBuilder_1.18.1.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | GeneNetworkBuilder_1.18.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GeneNetworkBuilder |
| Package Short Url | http://bioconductor.org/packages/GeneNetworkBuilder/ |
| Package Downloads Report | Download Stats |
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