birte: Bayesian Inference of Regulatory Influence on Expression (biRte)
Version 1.12.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorHolger Froehlich, contributions by Benedikt Zacher
Bioconductor views Bayesian GeneExpression Microarray Network NetworkInference Regression Sequencing Transcription
Date of publicationNone
MaintainerHolger Froehlich <frohlich@bit.uni-bonn.de>
LicenseGPL (>= 2)
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("birte")

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...

Functions

EColiNetwork Man page
EColiOxygen Man page
SigGenes Source code
TFexpr Man page
affinities2 Man page
beta.EM Source code
birte.aux Source code
birte.limma.aux Source code
birteFitRidge Man page Source code
birteLimma Man page Source code
birtePredict Man page Source code
birteRun Man page Source code
birteStart Source code
bmixture.mle Source code
dmixture Source code
estimateNetwork Man page Source code
getComponent Source code
getPotentialSwaps Man page Source code
humanNetworkSimul Man page
limmaAnalysis Man page Source code
loglik Source code
plotConvergence Man page Source code
pmixture Source code
proposeInteractions Man page Source code
qmix Source code
rmix Source code
sample.mRNAData Source code
sample.miRNAData Source code
sampleExpressionData Source code
simplify Man page Source code
simulateData Man page Source code
suggestThreshold Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/betaMixture.R
R/birtePredict.R
R/birteRun.R
R/birteStart.R
R/estimateNetwork.R
R/getPotentialSwaps.R
R/limmaAnalyis.R
R/plotConvergence.R
R/simplify.R
R/simulateData.R
README
build
build/vignette.rds
data
data/EColiOxygen.rda
data/datalist
data/humanNetworkSimul.rda
inst
inst/CITATION
inst/doc
inst/doc/birte.R
inst/doc/birte.Rnw
inst/doc/birte.pdf
man
man/EColiNetwork.Rd
man/EColiOxygen.Rd
man/TFexpr.Rd
man/birteFitRidge.Rd
man/birtePredict.Rd
man/birteRun.Rd
man/estimateNetwork.Rd
man/getPotentialSwaps.Rd
man/humanNetwork.Rd
man/limmaAnalysis.Rd
man/plotConvergence.Rd
man/proposeInteractions.Rd
man/simplify.Rd
man/simulateData.Rd
man/suggestThreshold.Rd
src
src/BayesNetwork.cpp
src/BayesNetwork.h
src/Makevars
src/Makevars.win
src/getStates.cpp
src/getStates.h
vignettes
vignettes/bibliography.bib
vignettes/birte.Rnw
birte documentation built on May 20, 2017, 10:09 p.m.