Function reference • sRACIPE

# Reference

## All functions
`CoupledToggleSwitchSA` | Five coupled toggle switches
`EMT1` | A circuit for epithelial to mesenchymal transition
`EMT2` | A circuit for epithelial to mesenchymal transition including microRNAs
`RacipeSE-class` | RacipeSE
`RacipeSE()` | RacipeSE constructor
`annotation(<RacipeSE>)` | A method to get the annotation
``annotation<-`(<RacipeSE>,<ANY>)` | A method to set the circuit name or annotation
`configData` | Configuration Data
`demoCircuit` | A toggle switch circuit for demonstrations
`densityPlot()` | Density Plot
`.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.
`sRACIPE` | sRACIPE: A package for stochastic random circuit perturbation.
``sracipeCircuit<-`()` | Initialize the circuit
`sracipeCircuit()` | Method to get 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 set the initial conditions
`sracipeIC()` | A method to get the initial conditions used for simulations
`sracipeKnockDown()` | Perform in-silico knockdown analysis
`sracipeNormalize()` | Normalize the simulated gene expression
`sracipeOverExp()` | Perform in-silico over expression analysis
``sracipeParams<-`()` | A method to set the simulation parameters
`sracipeParams()` | A method to access the simulation parameters
`sracipePlotCircuit()` | Plot Gene Regulatory Circuit
`sracipePlotData()` | Plot sRACIPE data
`sracipePlotParamBifur()` | Parameter bifurcation plots
`sracipeSimulate()` | Simulate a gene regulatory circuit