Systems biology tool to simulate gene regulatory circuits

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Documentation for package ‘sRACIPE’ version 2.0.0

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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