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. |