birta

DOI: 10.18129/B9.bioc.birta    

This package is for version 3.11 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: 3.11

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	GeneExpression, GraphAndNetwork, Microarray, Sequencing, Software, Transcription
Version	1.31.0
In Bioconductor since	BioC 2.10 (R-2.15) (8.5 years)
License	GPL (>= 2)
Depends	limma, MASS, R (>= 2.10), Biobase, methods
Imports
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Build Report

Package Archives

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

Source Package	birta_1.31.0.tar.gz
Windows Binary	birta_1.31.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)
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