birte

This package is for version 3.7 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see birte.

Bayesian Inference of Regulatory Influence on Expression (biRte)


Bioconductor version: 3.7

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 (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("birte")

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("birte")
Bayesian Inference of Regulation of Transcriptional Activity PDF R Script
Reference Manual PDF
README Text

Details

biocViews Bayesian, GeneExpression, Microarray, Network, NetworkInference, Regression, Sequencing, Software, Transcription
Version 1.16.0
In Bioconductor since BioC 3.1 (R-3.2) (9 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
System Requirements BLAS, LAPACK
URL
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Suggests knitr
Linking To RcppArmadillo, Rcpp
Enhances Rgraphviz
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 birte_1.16.0.tar.gz
Windows Binary birte_1.16.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) birte_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/birte
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/birte
Package Short Url https://bioconductor.org/packages/birte/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive