as.data.frame,MutabilityModel-method	MutabilityModel-class
Baseline	Baseline-class
Baseline-class	Baseline-class
Baseline-method	Baseline-class
calcBaseline	calcBaseline
calcExpectedMutations	calcExpectedMutations
calcObservedMutations	calcObservedMutations
calcTargetingDistance	calcTargetingDistance
calculateMutability	calculateMutability
CHARGE_MUTATIONS	MUTATION_SCHEMES
collapseClones	collapseClones
consensusSequence	consensusSequence
createBaseline	createBaseline
createMutabilityMatrix	createMutabilityMatrix
createMutationDefinition	createMutationDefinition
createRegionDefinition	createRegionDefinition
createSubstitutionMatrix	createSubstitutionMatrix
createTargetingMatrix	createTargetingMatrix
createTargetingModel	createTargetingModel
DensityThreshold	DensityThreshold-class
DensityThreshold-class	DensityThreshold-class
DensityThreshold-method	DensityThreshold-class
distToNearest	distToNearest
editBaseline	editBaseline
expectedMutations	expectedMutations
extendMutabilityMatrix	extendMutabilityMatrix
extendSubstitutionMatrix	extendSubstitutionMatrix
findThreshold	findThreshold
GmmThreshold	GmmThreshold-class
GmmThreshold-class	GmmThreshold-class
GmmThreshold-method	GmmThreshold-class
groupBaseline	groupBaseline
HH_S1F	HH_S1F
HH_S5F	HH_S5F
HKL_S1F	HKL_S1F
HKL_S5F	HKL_S5F
HYDROPATHY_MUTATIONS	MUTATION_SCHEMES
IMGT_SCHEMES	IMGT_SCHEMES
IMGT_V	IMGT_SCHEMES
IMGT_V_BY_CODONS	IMGT_SCHEMES
IMGT_V_BY_REGIONS	IMGT_SCHEMES
IMGT_V_BY_SEGMENTS	IMGT_SCHEMES
makeAverage1merMut	makeAverage1merMut
makeAverage1merSub	makeAverage1merSub
makeDegenerate5merMut	makeDegenerate5merMut
makeDegenerate5merSub	makeDegenerate5merSub
minNumMutationsTune	minNumMutationsTune
minNumSeqMutationsTune	minNumSeqMutationsTune
MK_RS1NF	MK_RS1NF
MK_RS5NF	MK_RS5NF
MutabilityModel	MutabilityModel-class
MutabilityModel-class	MutabilityModel-class
MutabilityModel-method	MutabilityModel-class
MutationDefinition	MutationDefinition-class
MutationDefinition-class	MutationDefinition-class
MUTATION_SCHEMES	MUTATION_SCHEMES
observedMutations	observedMutations
plot,Baseline,character-method	Baseline-class
plot,DensityThreshold,missing-method	DensityThreshold-class
plot,GmmThreshold,missing-method	GmmThreshold-class
plot,TargetingModel,missing-method	TargetingModel-class
plotBaselineDensity	plotBaselineDensity
plotBaselineSummary	plotBaselineSummary
plotDensityThreshold	plotDensityThreshold
plotGmmThreshold	plotGmmThreshold
plotMutability	plotMutability
plotTune	plotTune
POLARITY_MUTATIONS	MUTATION_SCHEMES
print,DensityThreshold-method	DensityThreshold-class
print,GmmThreshold-method	GmmThreshold-class
print,MutabilityModel-method	MutabilityModel-class
RegionDefinition	RegionDefinition-class
RegionDefinition-class	RegionDefinition-class
shazam	shazam
shmulateSeq	shmulateSeq
shmulateTree	shmulateTree
slideWindowDb	slideWindowDb
slideWindowSeq	slideWindowSeq
slideWindowTune	slideWindowTune
slideWindowTunePlot	slideWindowTunePlot
summarizeBaseline	summarizeBaseline
summary,Baseline-method	Baseline-class
TargetingMatrix	TargetingMatrix-class
TargetingMatrix-class	TargetingMatrix-class
TargetingModel	TargetingModel-class
TargetingModel-class	TargetingModel-class
TargetingModel-method	TargetingModel-class
testBaseline	testBaseline
U5N	U5N
VOLUME_MUTATIONS	MUTATION_SCHEMES
writeTargetingDistance	writeTargetingDistance
