# An R interface for computational modeling of tumor progression

## Documentation for package ‘CancerInSilico’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

CancerInSilico-package | CancerInSilico
calibratePathway | calibrate pathway with data
CancerInSilico | CancerInSilico
CellModel-class | CellModel
cellSummary | summary of cell model at a given time
cellSummary-method | summary of cell model at a given time
CellType-class | CellType
checkDataSet | verify gene expression data set is valid for this package
DrasdoHohmeModel-class | DrasdoHohmeModel
Drug-class | Drug
GeneExpressionParams-class | GeneExpressionParams
getAxisAngle | get cell axis angle at a given time
getAxisAngle-method | get cell axis angle at a given time
getAxisLength | get cell axis length at a given time
getAxisLength-method | get cell axis length at a given time
getCellDistance | get distance between two cells
getCellDistance-method | get distance between two cells
getCellPhase | get phase of a cell at a given time
getCellPhase-method | get phase of a cell at a given time
getCellType | get type of a cell at a given time
getCellType-method | get type of a cell at a given time
getCoordinates | get coordinates of a cell at a given time
getCoordinates-method | get coordinates of a cell at a given time
getCycleLength | get cycle length of a cell at a given time
getCycleLength-method | get cycle length of a cell at a given time
getDensity | get density of the cell population at a given time
getDensity-method | get density of the cell population at a given time
getLocalDensity | get neighborhood density around a cell at a given time
getLocalDensity-method | get neighborhood density around a cell at a given time
getNumberOfCells | get number of cells in the model at a given time
getNumberOfCells-method | get number of cells in the model at a given time
getRadius | get cell radius at a given time
getRadius-method | get cell radius at a given time
getTrialAcceptRate | get rate of growth acceptance of a given cell at a given time
getTrialAcceptRate-method | get rate of growth acceptance of a given cell at a given time
initialize-method | Pathway Class
initialize-method | Constructor for CellModel
initialize-method | DrasdoHohmeModel Constructor
initialize-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 signaling pathways
interactivePlot | plot the cell population and interactively scroll through time points
interactivePlot-method | plot the cell population and interactively scroll through time points
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 | plot cell population at a given time
plotCells-method | 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 | run a cell model
run-method | run a cell model