.ModelPvalue            Returns the variance array after permutations.
.NthMin                 Find nth minimum value from a vector
.PermutedVar            Find variance of permutations
.SimulatedPValueAbs     Finds the variance corresponding to a given
                        value.
.SimulatedVarPValue     Finds the variance corresponding to a given
                        value.
.loadNetworkFile        Loads the network/topology file.
CoupledToggleSwitchSA   Five coupled toggle switches
EMT1                    A circuit for epithelial to mesenchymal
                        transition
EMT2                    A circuit for epithelial to mesenchymal
                        transition including microRNAs
RacipeSE                RacipeSE constructor
RacipeSE-class          RacipeSE
annotation,RacipeSE-method
                        A method to get the annotation
annotation<-,RacipeSE,ANY-method
                        A method to set the circuit name or annotation
configData              Configuration Data
demoCircuit             A toggle switch circuit for demonstrations
densityPlot             Density Plot
sRACIPE                 sRACIPE: A package for stochastic random
                        circuit perturbation.
sracipeCircuit          Method to get the circuit
sracipeCircuit<-        Initialize the circuit
sracipeConfig           A method to access the simulation
                        hyperparameters
sracipeConfig<-         A method to access the simulation
                        hyperparameters
sracipeGenParamNames    Generate parameter names for a circuit
sracipeGetTS            A method to extract the time series
sracipeHeatmapSimilarity
                        Calculates the similarity between two gene
                        expression data.
sracipeIC               A method to get the initial conditions used for
                        simulations
sracipeIC<-             A method to set the initial conditions
sracipeKnockDown        Perform in-silico knockdown analysis
sracipeNormalize        Normalize the simulated gene expression
sracipeOverExp          Perform in-silico over expression analysis
sracipeParams           A method to access the simulation parameters
sracipeParams<-         A method to set the simulation parameters
sracipePlotCircuit      Plot Gene Regulatory Circuit
sracipePlotData         Plot sRACIPE data
sracipePlotParamBifur   Parameter bifurcation plots
sracipeSimulate         Simulate a gene regulatory circuit
