CancerInSilico-package	CancerInSilico
calibratePathway	calibratePathway
CancerInSilico	CancerInSilico
CellModel-class	CellModel-class
cellSummary	cellSummary-methods
cellSummary,CellModel-method	cellSummary-methods
CellType-class	CellType-class
checkDataSet	checkDataSet
combineGeneExpression	combineGeneExpression
DrasdoHohmeModel-class	DrasdoHohmeModel-class
Drug-class	Drug-class
GeneExpressionParams-class	GeneExpressionParams-class
getAxisAngle	getAxisAngle-methods
getAxisAngle,OffLatticeModel-method	getAxisAngle-methods
getAxisLength	getAxisLength-methods
getAxisLength,OffLatticeModel-method	getAxisLength-methods
getCellDistance	getCellDistance-methods
getCellDistance,OffLatticeModel-method	getCellDistance-methods
getCellPhase	getCellPhase-methods
getCellPhase,OffLatticeModel-method	getCellPhase-methods
getCellType	getCellType-methods
getCellType,OffLatticeModel-method	getCellType-methods
getCoordinates	getCoordinates-methods
getCoordinates,OffLatticeModel-method	getCoordinates-methods
getCycleLength	getCycleLength-methods
getCycleLength,OffLatticeModel-method	getCycleLength-methods
getDensity	getDensity-methods
getDensity,OffLatticeModel-method	getDensity-methods
getLocalDensity	getLocalDensity-methods
getLocalDensity,OffLatticeModel-method	getLocalDensity-methods
getMeanExp	getMeanExp
getNumberOfCells	getNumberOfCells-methods
getNumberOfCells,OffLatticeModel-method	getNumberOfCells-methods
getRadius	getRadius-methods
getRadius,OffLatticeModel-method	getRadius-methods
getTrialAcceptRate	getTrialAcceptRate-methods
getTrialAcceptRate,OffLatticeModel-method	getTrialAcceptRate-methods
initialize,CellModel-method	initialize-CellModel-method
initialize,DrasdoHohmeModel-method	initialize-DrasdoHohmeModel-method
initialize,OffLatticeModel-method	initialize-OffLatticeModel-method
initialize,Pathway-method	Pathway-class
inSilicoCellModel	inSilicoCellModel
inSilicoGeneExpression	inSilicoGeneExpression
inSilicoPathways	inSilicoPathways
interactivePlot	interactivePlot-methods
interactivePlot,CellModel-method	interactivePlot-methods
modCellTypes	modCellTypes
modDefault	modDefault
modDrugs	modDrugs
modHighDensity	modHighDensity
modLargeRun	modLargeRun
modLongRun	modLongRun
OffLatticeModel-class	OffLatticeModel-class
Pathway-class	Pathway-class
plotCells	plotCells-methods
plotCells,OffLatticeModel-method	plotCells-methods
pwyContactInhibition	pwyContactInhibition
pwyGrowth	pwyGrowth
pwyMitosis	pwyMitosis
pwySPhase	pwySPhase
referenceGeneExpression	referenceGeneExpression
run	run-methods
run,DrasdoHohmeModel-method	run-methods
simulateMicroArray	simulateMicroArray
simulatePathwayActivity	simulatePathwayActivity
simulateWithLimmaVoom	simulateWithLimmaVoom
simulateWithSplatter	simulateWithSplatter
voomErrorModel	voomErrorModel
