# Systems biology tool to simulate gene regulatory circuits

## Documentation for package ‘sRACIPE’ version 2.4.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

sRACIPE-package | sRACIPE: A package for stochastic random circuit perturbation.
.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.
allTypesDemoCircuit | A circuit with every interaction type for simulations
annotation-method | A method to get the annotation
annotation<--method | A method to set the circuit name or annotation
cellCycle | A circuit for modeling the yeast cell cycle
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
repressilator | A loop motif for demonstrating limit cycles in gene expression
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
sracipeCombineRacipeSE | A method to combine RacipeSE objects with the same config
sracipeCombineRacipeSE-method | A method to combine RacipeSE objects with the same config
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
sracipeConverge | A method to get the convergence results for deterministic simulations
sracipeConverge-method | A method to get the convergence results for deterministic simulations
sracipeConvergeDist | A method to visualize convergence distributions
sracipeConvergeDist-method | A method to visualize convergence distributions
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
sracipeUniqueStates | A method for grabbing unique states
sracipeUniqueStates-method | A method for grabbing unique states