diffeRenTES (from French various, different, separate) is a package written in R for computing, starting from a Boolean network, the ATM (Attractor Transition Matrix) structure and tree-like structures based on the TES (Threshold Ergodic Sets) concept that describe the process of differentiation.
TESs are the mathematical abstractions with which a powerful model of differentiation represents the different cell types arising during ontogenesis. The aforementioned model of differentiation based on Boolean networks is firstly described in "A Dynamical Model of Genetic Networks for Cell Differentiation" Villani M, Barbieri A, Serra R (2011) A Dynamical Model of Genetic Networks for Cell Differentiation. PLOS ONE 6(3): e17703. https://doi.org/10.1371/journal.pone.0017703
This package requires the folowing R libraries:
install.packages("diffeRenTES_RELEASE_VERSION.tar.gz", repos = NULL, type="source")
net <- BoolNet::generateRandomNKNetwork(10, 2) attractors <- BoolNet::getAttractors(net) ATM <- computeATM(net, attractors) # attractors transition matrix computation TESs <- computeTESs(ATM) #TESs computation saveDotFileDifferentiationTree(TESs, "exampleTree") #saving the TES-based differentiation tree
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