EColiNetwork            Example TF-target graph from Regulon DB.
EColiOxygen             Example data set from E. Coli to sample TF
                        activities.
TFexpr                  Transcription factor expression values for the
                        aerobic-anaerobic growth experiment.
birteFitRidge           Fit ridge regression model given a defined set
                        of active regulators.
birtePredict            Prediction of gene expression via biRte.
birteRun                Main interface for Bayesian Inference of
                        Regulatory Influence on Expression (biRte).
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.
