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.

Author
Benedikt Zacher, Khalid Abnaof, Stephan Gade, Erfan Younesi, Achim Tresch, Holger Froehlich
Date of publication
None
Maintainer
Benedikt Zacher <zacher@lmb.uni-muenchen.de>, Holger Froehlich <frohlich@bit.uni-bonn.de>
License
GPL (>= 2)
Version
1.18.0

View on Bioconductor

Man pages

birta-methods
Methods for Function 'birta' in Package 'birta'
birta-package
Joint Bayesian Inference of miRNA and Transcription Factor...
birta.run
Main interface for Bayesian Inference of Regulation of...
EColiNetwork
Example TF-target graph from Regulon DB.
EColiOxygen
Example data set from E. Coli to sample TF activities.
genesets
TF-target and miRNA-target networks for simulated example.
get_potential_swaps
Calculate swap partner for TF-/miRNA-target graph.
limmaAnalysis
Perform a limma analysis on expression data.
limmaAnalysis-methods
Methods for Function 'limmaAnalysis' in Package 'birta'
plotConvergence
Plotting the likelihood along MCMC sampling.
potential_swaps
Potential swap moves for TF-target and miRNA-target networks...
sim
Simulated expression data for mRNAs and miRNAs.
TFexpr
Transcription factor expression values for the...

Files in this package

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