Systems biology tool to simulate gene regulatory circuits

---

Documentation for package ‘sRACIPE’ version 1.20.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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