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>

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

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
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: