To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("birte")

In most cases, you don't need to download the package archive at all.

birte

DOI: 10.18129/B9.bioc.birte    

Bayesian Inference of Regulatory Influence on Expression (biRte)

Bioconductor version: Release (3.6)

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:// URLs are not supported
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")

 

PDF R Script Bayesian Inference of Regulation of Transcriptional Activity
PDF   Reference Manual
Text   README

Details

biocViews Bayesian, GeneExpression, Microarray, Network, NetworkInference, Regression, Sequencing, Software, Transcription
Version 1.14.0
In Bioconductor since BioC 3.1 (R-3.2) (2.5 years)
License GPL (>= 2)
Depends R (>= 3.0.0), RcppArmadillo (>= 0.3.6.1), Rcpp
Imports MASS, limma(>= 3.22.0), glmnet, Biobase, nem, graphics, stats, utils
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.

Source Package birte_1.14.0.tar.gz
Windows Binary birte_1.14.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) birte_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/birte
Package Short Url http://bioconductor.org/packages/birte/
Package Downloads Report Download Stats

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