Bayesian Inference of Regulatory Influence on Expression (biRte)

Documentation for package ‘birte’ version 1.18.0

affinities2	Subset of regulator-target gene network for human
birteFitRidge	Fit ridge regression model given a defined set of active regulators.
birteLimma	Main interface for Bayesian Inference of Regulatory Influence on Expression (biRte).
birtePredict	Prediction of gene expression via biRte.
birteRun	Main interface for Bayesian Inference of Regulatory Influence on Expression (biRte).
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 Effects Models (NEMs).
getPotentialSwaps	Calculate swap partner for TF-/miRNA-target graph. This function is usually only called internally, but may be used to speed up repetitive calls to 'birteRun'.
humanNetworkSimul	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 samples (after thinning).
proposeInteractions	Propose possible regulator-regulator interactions that could be worthwhile to be tested into the biRte model.
simplify	Simplify regulator-target gene network via clustering.
simulateData	Simulate expression data.
suggestThreshold	Automatically suggest suitable threshold for marginal regulator activities.
TFexpr	Transcription factor expression values for the aerobic-anaerobic growth experiment.