Man pages for CancerInSilico
An R interface for computational modeling of tumor progression

calibratePathwaycalibrate pathway with data
CancerInSilicoCancerInSilico
CellModel-classCellModel
cellSummary-methodssummary of cell model at a given time
CellType-classCellType
checkDataSetverify gene expression data set is valid for this package
combineGeneExpressionCombine Gene Expression Matrices
DrasdoHohmeModel-classDrasdoHohmeModel
Drug-classDrug
GeneExpressionParams-classGeneExpressionParams
getAxisAngle-methodsget cell axis angle at a given time
getAxisLength-methodsget cell axis length at a given time
getCellDistance-methodsget distance between two cells
getCellPhase-methodsget phase of a cell at a given time
getCellType-methodsget type of a cell at a given time
getCoordinates-methodsget coordinates of a cell at a given time
getCycleLength-methodsget cycle length of a cell at a given time
getDensity-methodsget density of the cell population at a given time
getLocalDensity-methodsget neighborhood density around a cell at a given time
getMeanExpCalculate Mean Expression Value
getNumberOfCells-methodsget number of cells in the model at a given time
getRadius-methodsget cell radius at a given time
getTrialAcceptRate-methodsget rate of growth acceptance of a given cell at a given time
initialize-CellModel-methodConstructor for CellModel
initialize-DrasdoHohmeModel-methodDrasdoHohmeModel Constructor
initialize-OffLatticeModel-methodOff-Lattice Model Constructor
inSilicoCellModelSimulates Cell Model
inSilicoGeneExpressionsimulate gene expression data
inSilicoPathwaysThis data contains the list of gene targets of modeled...
interactivePlot-methodsplot the cell population and interactively scroll through...
modCellTypessample cell model
modDefaultsample cell model
modDrugssample cell model
modHighDensitysample cell model
modLargeRunsample cell model
modLongRunsample cell model
OffLatticeModel-classOffLatticeModel
Pathway-classPathway Class
plotCells-methodsplot cell population at a given time
pwyContactInhibitionsample pathway
pwyGrowthsample pathway
pwyMitosissample pathway
pwySPhasesample pathway
referenceGeneExpressiongene expression data for genes in sample pathways
run-methodsrun a cell model
simulateMicroArrayBulk MicroArray Error Model
simulatePathwayActivitysimulate pathway activity based in model behavior
simulateWithLimmaVoomBulk RNA-seq Error Model
simulateWithSplatterSingle Cell RNA-seq Error Mpdel
voomErrorModelError Model found in Limma-Voom
CancerInSilico documentation built on May 2, 2018, 4:19 a.m.