birte: Bayesian Inference of Regulatory Influence on Expression (biRte)

Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. biRte uses regulatory networks of TFs, miRNAs and possibly other factors, together with mRNA, miRNA and other available expression data to predict the relative influence of a regulator on the expression of its target genes. Inference is done in a Bayesian modeling framework using Markov-Chain-Monte-Carlo. A special feature is the possibility for follow-up network reverse engineering between active regulators.

AuthorHolger Froehlich, contributions by Benedikt Zacher
Date of publicationNone
MaintainerHolger Froehlich <frohlich@bit.uni-bonn.de>
LicenseGPL (>= 2)
Version1.10.0

View on Bioconductor

Files in this package

birte/DESCRIPTION
birte/NAMESPACE
birte/R
birte/R/betaMixture.R birte/R/birtePredict.R birte/R/birteRun.R birte/R/birteStart.R birte/R/estimateNetwork.R birte/R/getPotentialSwaps.R birte/R/limmaAnalyis.R birte/R/plotConvergence.R birte/R/simplify.R birte/R/simulateData.R
birte/README
birte/build
birte/build/vignette.rds
birte/data
birte/data/EColiOxygen.rda
birte/data/datalist
birte/data/humanNetworkSimul.rda
birte/inst
birte/inst/CITATION
birte/inst/doc
birte/inst/doc/birte.R
birte/inst/doc/birte.Rnw
birte/inst/doc/birte.pdf
birte/man
birte/man/EColiNetwork.Rd birte/man/EColiOxygen.Rd birte/man/TFexpr.Rd birte/man/birteFitRidge.Rd birte/man/birtePredict.Rd birte/man/birteRun.Rd birte/man/estimateNetwork.Rd birte/man/getPotentialSwaps.Rd birte/man/humanNetwork.Rd birte/man/limmaAnalysis.Rd birte/man/plotConvergence.Rd birte/man/proposeInteractions.Rd birte/man/simplify.Rd birte/man/simulateData.Rd birte/man/suggestThreshold.Rd
birte/src
birte/src/BayesNetwork.cpp
birte/src/BayesNetwork.h
birte/src/Makevars
birte/src/Makevars.win
birte/src/getStates.cpp
birte/src/getStates.h
birte/vignettes
birte/vignettes/bibliography.bib
birte/vignettes/birte.Rnw

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