An R interface for computational modeling of tumor progression

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Documentation for package ‘CancerInSilico’ version 2.22.0

• 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