Cascade package is an integrated solution adding several new and original key features such as the ability to predict changes in gene expressions after a biological perturbation in the network and graphical outputs that allow monitoring the spread of a signal through the network.
Nicolas Jung, Frederic Bertrand, Myriam Maumy-Bertrand Laurent Vallat
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Bioinformatics. 2014 Feb 15;30(4):571-3. doi: 10.1093/bioinformatics/btt705. Epub 2013 Dec 3.
Cascade: a R package to study, predict and simulate the diffusion of a signal through a temporal gene network.
Jung N1, Bertrand F, Bahram S, Vallat L, Maumy-Bertrand M.