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

Share:

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.

Author
Holger Froehlich, contributions by Benedikt Zacher
Date of publication
None
Maintainer
Holger Froehlich <frohlich@bit.uni-bonn.de>
License
GPL (>= 2)
Version
1.10.0

View on Bioconductor

Man pages

birteFitRidge
Fit ridge regression model given a defined set of active...
birtePredict
Prediction of gene expression via biRte.
birteRun
Main interface for Bayesian Inference of Regulatory Influence...
EColiNetwork
Example TF-target graph from Regulon DB.
EColiOxygen
Example data set from E. Coli to sample TF activities.
estimateNetwork
Estimate network between active regulators using Nested...
getPotentialSwaps
Calculate swap partner for TF-/miRNA-target graph. This...
humanNetwork
Subset of regulator-target gene network for human
limmaAnalysis
Simple limma analysis on expression data with one contrast.
plotConvergence
Plot the marginal log-likelihood of the model along MCMC...
proposeInteractions
Propose possible regulator-regulator interactions that could...
simplify
Simplify regulator-target gene network via clustering.
simulateData
Simulate expression data.
suggestThreshold
Automatically suggest suitable threshold for marginal...
TFexpr
Transcription factor expression values for the...

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