birta: Bayesian Inference of Regulation of Transcriptional Activity

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("birta")
AuthorBenedikt Zacher, Khalid Abnaof, Stephan Gade, Erfan Younesi, Achim Tresch, Holger Froehlich
Bioconductor views GeneExpression GraphAndNetwork Microarray Sequencing Transcription
Date of publicationNone
MaintainerBenedikt Zacher <zacher@lmb.uni-muenchen.de>, Holger Froehlich <frohlich@bit.uni-bonn.de>
LicenseGPL (>= 2)
Version1.18.0

View on Bioconductor

Functions

birta Man page
birta,ExpressionSet,ExpressionSet,ExpressionSet-method Man page
birta,ExpressionSet,ExpressionSet,missing-method Man page
birta,ExpressionSet,missing,ExpressionSet-method Man page
birta,ExpressionSet,missing,missing-method Man page
birta,matrix,matrix,matrix-method Man page
birta,matrix,matrix,missing-method Man page
birta,matrix,missing,matrix-method Man page
birta,matrix,missing,missing-method Man page
birta-methods Man page
birta-package Man page
EColiNetwork Man page
EColiOxygen Man page
genesets Man page
get_potential_swaps Man page
limmaAnalysis Man page
limmaAnalysis,ExpressionSet,matrix,character-method Man page
limmaAnalysis,matrix,matrix,character-method Man page
limmaAnalysis-methods Man page
plotConvergence Man page
potential_swaps Man page
sim Man page
TFexpr Man page

Files

DESCRIPTION
NAMESPACE
R
R/Fisher.pretest.R R/birta.run.R R/birta.start.R R/get_potential_swaps.R R/limmaAnalyis.R R/plot.convergence.R
build
build/vignette.rds
data
data/EColiOxygen.rda
data/datalist
data/humanSim.rda
inst
inst/NEWS
inst/doc
inst/doc/birta.R
inst/doc/birta.Rnw
inst/doc/birta.pdf
man
man/EColiNetwork.Rd man/EColiOxygen.Rd man/TFexpr.Rd man/birta-methods.Rd man/birta-package.Rd man/birta.run.Rd man/genesets.Rd man/get_potential_swaps.Rd man/limmaAnalysis-methods.Rd man/limmaAnalysis.Rd man/plotConvergence.Rd man/potential_swaps.Rd man/sim.Rd
src
src/BayesNetwork.cpp
src/BayesNetwork.h
src/BayesNetworkNC.cpp
src/BayesNetworkNC.h
src/getStates.cpp
src/getStates.h
vignettes
vignettes/bibliography.bib
vignettes/birta.Rnw

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