annotateTargets	annotateTargets
bootstrapResults	bootstrapResults
calculateBamCoverageByInterval	calculateBamCoverageByInterval
calculateGCContentByInterval	calculateGCContentByInterval
calculateIntervalWeights	calculateIntervalWeights
calculateLogRatio	calculateLogRatio
calculateMappingBiasVcf	calculateMappingBiasVcf
calculatePowerDetectSomatic	calculatePowerDetectSomatic
calculateTangentNormal	calculateTangentNormal
callAlterations	callAlterations
callAlterationsFromSegmentation	callAlterationsFromSegmentation
callLOH	callLOH
callMutationBurden	callMutationBurden
centromeres	centromeres
correctCoverageBias	correctCoverageBias
createCurationFile	createCurationFile
createNormalDatabase	createNormalDatabase
createTargetWeights	createTargetWeights
filterIntervals	filterIntervals
filterTargets	filterTargets
filterVcfBasic	filterVcfBasic
filterVcfMuTect	filterVcfMuTect
filterVcfMuTect2	filterVcfMuTect2
findFocal	findFocal
getSexFromCoverage	getSexFromCoverage
getSexFromVcf	getSexFromVcf
plotAbs	plotAbs
poolCoverage	poolCoverage
predictSomatic	predictSomatic
preprocessIntervals	preprocessIntervals
processMultipleSamples	processMultipleSamples
PureCN-defunct	PureCN-defunct
PureCN-deprecated	PureCN-deprecated
purecn.DNAcopy.bdry	purecn.DNAcopy.bdry
purecn.example.output	purecn.example.output
readCoverageFile	readCoverageFile
readCurationFile	readCurationFile
runAbsoluteCN	runAbsoluteCN
segmentationCBS	segmentationCBS
segmentationHclust	segmentationHclust
segmentationPSCBS	segmentationPSCBS
setMappingBiasVcf	setMappingBiasVcf
setPriorVcf	setPriorVcf
