Man pages for sRACIPE
Systems biology tool to simulate gene regulatory circuits

annotation-RacipeSE-methodA method to get the annotation
annotation-set-RacipeSE-ANY-methodA method to set the circuit name or annotation
configDataConfiguration Data
CoupledToggleSwitchSAFive coupled toggle switches
demoCircuitA toggle switch circuit for demonstrations
densityPlotDensity Plot
dot-loadNetworkFileLoads the network/topology file.
dot-ModelPvalueReturns the variance array after permutations.
dot-NthMinFind nth minimum value from a vector
dot-PermutedVarFind variance of permutations
dot-SimulatedPValueAbsFinds the variance corresponding to a given value.
dot-SimulatedVarPValueFinds the variance corresponding to a given value.
EMT1A circuit for epithelial to mesenchymal transition
EMT2A circuit for epithelial to mesenchymal transition including...
RacipeSERacipeSE constructor
sRACIPEsRACIPE: A package for stochastic random circuit...
sracipeCircuitMethod to get the circuit
sracipeCircuit-setInitialize the circuit
sracipeConfigA method to access the simulation hyperparameters
sracipeConfig-setA method to access the simulation hyperparameters
sracipeGeneExRun GeneEx - webapp for sRACIPE
sracipeGenParamNamesGenerate parameter names for a circuit
sracipeGetTSA method to extract the time series
sracipeHeatmapSimilarityCalculates the similarity between two gene expression data.
sracipeICA method to get the initial conditions used for simulations
sracipeIC-setA method to set the initial conditions
sracipeKnockDownPerform in-silico knockdown analysis
sracipeNormalizeNormalize the simulated gene expression
sracipeOverExpPerform in-silico over expression analysis
sracipeParamsA method to access the simulation parameters
sracipeParams-setA method to set the simulation parameters
sracipePlotCircuitPlot Gene Regulatory Circuit
sracipePlotDataPlot sRACIPE data
sracipePlotParamBifurParameter bifurcation plots
sracipeSimulateSimulate a gene regulatory circuit
sRACIPE documentation built on Oct. 31, 2019, 4:08 a.m.