An R interface for computational modeling of tumor progression

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Documentation for package ‘CancerInSilico’ version 2.8.0

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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