diffeRenTES (from French various, different) is a package written in R that, starting from the Boolean networks of the BoolNet package, computes the ATM (Attractor Transition Matrix) structure and the tree-like structure, based on the TES concept, describing the cell differentiation process.
TESs (Threshold Ergodic Sets) are the mathematical abstractions that represent the different cell types arising during ontogenesis.
TESs and the powerful model of biological differentiation based on Boolean networks to which it belongs have been 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 following R libraries:
install.packages("diffeRenTES_RELEASE_VERSION.tar.gz", repos = NULL, type="source")
Or, alternatively, directly from GitHub:
library(devtools)
devtools::install_github("mbraccini/diffeRenTES")
#Boolean network generation by means of 'BoolNet' package
net <- BoolNet::generateRandomNKNetwork(10, 2)
#Attractors computation
attractors <- BoolNet::getAttractors(net)
#Attractors Transition Matrix computation
ATM <- getATM(net, attractors)
#TESs computation
TESs <- getTESs(ATM)
#Saving the image of the TES-based differentiation tree
saveDifferentiationTreeToFile(TESs, "example.svg")
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.