ClonalSim-package	ClonalSim-package
applyBiologicalNoise	applyBiologicalNoise
ClonalSim	ClonalSim-package
ClonalSimData	ClonalSimData
ClonalSimData-class	ClonalSimData-class
ClonalSimData-validity	ClonalSimData-class
getClonalStructure	getClonalStructure
getMetadata	getMetadata
getMutations	getMutations
getObservedVAF	getObservedVAF
getSimParams	getSimParams
getTrueVAF	getTrueVAF
plot,ClonalSimData,missing-method	plot-ClonalSimData-missing-method
print.summary.ClonalSimData	print.summary.ClonalSimData
show,ClonalSimData-method	show-ClonalSimData-method
simulateDepth	simulateDepth
simulateSequencingReads	simulateSequencingReads
simulateTumor	simulateTumor
summary,ClonalSimData-method	summary-ClonalSimData-method
toDataFrame	toDataFrame
toGRanges	toGRanges
toPyClone	toPyClone
toSciClone	toSciClone
toVCF	toVCF
