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