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
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
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	bdHMM-class
[,bdHMM,ANY,ANY-method	sub-bdHMM-ANY-ANY-method
[,HMM,ANY,ANY,ANY-method	HMM-class
[,HMM,ANY,ANY-method	sub-HMM-ANY-ANY-method
