birta

This package is for version 3.6 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see birta.

Bayesian Inference of Regulation of Transcriptional Activity


Bioconductor version: 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. birta (Bayesian Inference of Regulation of Transcriptional Activity) uses the regulatory networks of TFs and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.

Author: Benedikt Zacher, Khalid Abnaof, Stephan Gade, Erfan Younesi, Achim Tresch, Holger Froehlich

Maintainer: Benedikt Zacher <zacher at lmb.uni-muenchen.de>, Holger Froehlich <frohlich at bit.uni-bonn.de>

Citation (from within R, enter citation("birta")):

Installation

To install this package, start R (version "3.4") and enter:


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

BiocManager::install("birta")

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("birta")
Bayesian Inference of Regulation of Transcriptional Activity PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, GraphAndNetwork, Microarray, Sequencing, Software, Transcription
Version 1.22.0
In Bioconductor since BioC 2.10 (R-2.15) (12 years)
License GPL (>= 2)
Depends limma, MASS, R (>= 2.10), Biobase, methods
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package birta_1.22.0.tar.gz
Windows Binary birta_1.22.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) birta_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/birta
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/birta
Package Short Url https://bioconductor.org/packages/birta/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.6 Source Archive