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.

AuthorBenedikt Zacher, Khalid Abnaof, Stephan Gade, Erfan Younesi, Achim Tresch, Holger Froehlich
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

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

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