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RIPE (Regulatory network Inference from joint Perturbation and Expression data) is a novel three-step method that integrates both perturbation data and steady state gene expression data in order to estimate a regulatory network. The ripe package is written in R, with additional functionality provided by a MATLAB executable file. The executable file uses a runtime engine called the MATLAB Compiler Runtime (MCR).
The Automated Parameter Estimation and Model Selection Toolkit is a fast, parallelized MCMC engine written in C for Bayesian inference (parameter estimation and model selection).