.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 |