STAN-package	STAN-package
.bdHMM	bdHMM-class
.HMM	HMM-class
.HMMEmission	HMMEmission-class
bdHMM	bdHMM
bdHMM-class	bdHMM-class
binarizeData	binarizeData
c2optimize	c2optimize
call_dpoilog	call_dpoilog
data2Gviz	data2Gviz
DimNames	DimNames
DirScore	DirScore
Emission	Emission
EmissionParams	EmissionParams
example	example
fitBdClust	fitBdClust
fitHMM	fitHMM
flags	flags
getAvgSignal	getAvgSignal
getLogLik	getLogLik
getPosterior	getPosterior
getSizeFactors	getSizeFactors
getViterbi	getViterbi
HMM	HMM
HMM-class	HMM-class
HMMEmission	HMMEmission
HMMEmission-class	HMMEmission-class
initBdClust	initBdClust
initBdHMM	initBdHMM
initHMM	initHMM
InitProb	InitProb
LogLik	LogLik
observations	observations
pilot.hg19	pilot.hg19
runningMean	runningMean
StateNames	StateNames
trainRegions	trainRegions
Transitions	Transitions
ucscGenes	ucscGenes
viterbi2GRanges	viterbi2GRanges
viterbi2Gviz	viterbi2Gviz
yeastTF_databychrom_ex	yeastTF_databychrom_ex
yeastTF_SGDGenes	yeastTF_SGDGenes
[,bdHMM,ANY,ANY,ANY-method	sub-bdHMM-ANY-ANY-ANY-method
[,HMM,ANY,ANY,ANY-method	sub-HMM-ANY-ANY-ANY-method
