The PANDA approach is to model the regulatory network as a bipartite network and estimate edge weights based on the evidence that information from a particular transcription factor i is successfully being passed to a particular gene j. This package provides a straightforward tool for applying this established method.
Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing Messages Between Biological Networks to Refine Predicted Interactions, PLoS One, 2013 May 31;8(5):e64832
To get the latest development version:
install.packages("devtools")
devtools::install_github("QuackenbushLab/pandaR")