Man pages for lusystemsbio/sRACIPE
Systems biology tool to simulate gene regulatory circuits
| allTypesDemoCircuit | A circuit with every interaction type for simulations |
| annotation-RacipeSE-method | A method to get the annotation |
| annotation-set-RacipeSE-ANY-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 |
| dot-loadNetworkFile | Loads the network/topology file. |
| dot-ModelPvalue | Returns the variance array after permutations. |
| dot-NthMin | Find nth minimum value from a vector |
| dot-PermutedVar | Find variance of permutations |
| dot-SimulatedPValueAbs | Finds the variance corresponding to a given value. |
| dot-SimulatedVarPValue | Finds the variance corresponding to a given value. |
| EMT1 | A circuit for epithelial to mesenchymal transition |
| EMT2 | A circuit for epithelial to mesenchymal transition including... |
| RacipeSE | RacipeSE constructor |
| RacipeSE-class | RacipeSE |
| repressilator | A loop motif for demonstrating limit cycles in gene... |
| sRACIPE | sRACIPE: A package for stochastic random circuit... |
| sracipeCircuit | Method to get the circuit |
| sracipeCircuit-set | Initialize the circuit |
| sracipeCombineRacipeSE | A method to combine RacipeSE objects with the same config |
| sracipeConfig | A method to access the simulation hyperparameters |
| sracipeConfig-set | A method to access the simulation hyperparameters |
| sracipeConverge | A method to get the convergence results for deterministic... |
| sracipeConvergeDist | A method to visualize convergence distributions |
| sracipeGenParamNames | Generate parameter names for a circuit |
| sracipeGetTS | 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-set | A method to set the initial conditions |
| sracipeKnockDown | Perform in-silico knockdown analysis |
| sracipeNormalize | Normalize the simulated gene expression |
| sracipeOverExp | Perform in-silico over expression analysis |
| sracipeParams | A method to access the simulation parameters |
| sracipeParams-set | A method to set the simulation parameters |
| sracipePlotCircuit | Plot Gene Regulatory Circuit |
| sracipePlotData | Plot sRACIPE data |
| sracipePlotParamBifur | Parameter bifurcation plots |
| sracipeSimulate | Simulate a gene regulatory circuit |
| sracipeUniqueStates | A method for grabbing unique states |
