To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("birte")
In most cases, you don't need to download the package archive at all.
birte
Bayesian Inference of Regulatory Influence on Expression (biRte)
Bioconductor version: 3.1
Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. biRte uses regulatory networks of TFs, miRNAs and possibly other factors, together with mRNA, miRNA and other available expression data to predict the relative influence of a regulator on the expression of its target genes. Inference is done in a Bayesian modeling framework using Markov-Chain-Monte-Carlo. A special feature is the possibility for follow-up network reverse engineering between active regulators.
Author: Holger Froehlich, contributions by Benedikt Zacher
Maintainer: Holger Froehlich <frohlich at bit.uni-bonn.de>
Citation (from within R,
enter citation("birte")):
Installation
To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("birte")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("birte")
| R Script | Bayesian Inference of Regulation of Transcriptional Activity | |
| Reference Manual | ||
| Text | README |
Details
| biocViews | Bayesian, GeneExpression, Microarray, Network, NetworkInference, Regression, Sequencing, Software, Transcription |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (< 6 months) |
| License | GPL (>= 2) |
| Depends | R (>= 3.0.0), RcppArmadillo (>= 0.3.6.1), Rcpp |
| Imports | MASS, limma(>= 3.22.0), ridge, Biobase, nem |
| LinkingTo | RcppArmadillo, Rcpp |
| Suggests | knitr |
| SystemRequirements | BLAS, LAPACK |
| Enhances | Rgraphviz |
| 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 | birte_1.2.0.tar.gz |
| Windows Binary | birte_1.2.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | birte_1.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | birte_1.2.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/birte/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/birte/ |
| Package Downloads Report | Download Stats |
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