# Bayesian Inference of Regulatory Influence on Expression (biRte)

## Documentation for package ‘birte’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.