Man pages for CancerInSilico
An R interface for computational modeling of tumor progression
| calibratePathway | calibrate pathway with data |
| CancerInSilico | CancerInSilico |
| CellModel-class | CellModel |
| cellSummary-methods | summary of cell model at a given time |
| CellType-class | CellType |
| checkDataSet | verify gene expression data set is valid for this package |
| combineGeneExpression | Combine Gene Expression Matrices |
| DrasdoHohmeModel-class | DrasdoHohmeModel |
| Drug-class | Drug |
| GeneExpressionParams-class | GeneExpressionParams |
| getAxisAngle-methods | get cell axis angle at a given time |
| getAxisLength-methods | get cell axis length at a given time |
| getCellDistance-methods | get distance between two cells |
| getCellPhase-methods | get phase of a cell at a given time |
| getCellType-methods | get type of a cell at a given time |
| getCoordinates-methods | get coordinates of a cell at a given time |
| getCycleLength-methods | get cycle length of a cell at a given time |
| getDensity-methods | get density of the cell population at a given time |
| getLocalDensity-methods | get neighborhood density around a cell at a given time |
| getMeanExp | Calculate Mean Expression Value |
| getNumberOfCells-methods | get number of cells in the model at a given time |
| getRadius-methods | get cell radius at a given time |
| getTrialAcceptRate-methods | get rate of growth acceptance of a given cell at a given time |
| initialize-CellModel-method | Constructor for CellModel |
| initialize-DrasdoHohmeModel-method | DrasdoHohmeModel Constructor |
| initialize-OffLatticeModel-method | Off-Lattice Model Constructor |
| inSilicoCellModel | Simulates Cell Model |
| inSilicoGeneExpression | simulate gene expression data |
| inSilicoPathways | This data contains the list of gene targets of modeled... |
| interactivePlot-methods | plot the cell population and interactively scroll through... |
| modCellTypes | sample cell model |
| modDefault | sample cell model |
| modDrugs | sample cell model |
| modHighDensity | sample cell model |
| modLargeRun | sample cell model |
| modLongRun | sample cell model |
| OffLatticeModel-class | OffLatticeModel |
| Pathway-class | Pathway Class |
| plotCells-methods | plot cell population at a given time |
| pwyContactInhibition | sample pathway |
| pwyGrowth | sample pathway |
| pwyMitosis | sample pathway |
| pwySPhase | sample pathway |
| referenceGeneExpression | gene expression data for genes in sample pathways |
| run-methods | run a cell model |
| simulateMicroArray | Bulk MicroArray Error Model |
| simulatePathwayActivity | simulate pathway activity based in model behavior |
| simulateWithLimmaVoom | Bulk RNA-seq Error Model |
| simulateWithSplatter | Single Cell RNA-seq Error Model |
| voomErrorModel | Error Model found in Limma-Voom |
