srnadiff-package	srnadiff
buildDataHmm	buildDataHmm
computePvalues	computePvalues
plotRegion	plotRegion
rcpp_buildHmm	rcpp_buildHmm
rcpp_naive	rcpp_naive
rcpp_normalization	rcpp_normalization
rcpp_slice	rcpp_slice
rcpp_viterbi	rcpp_viterbi
readAnnotation	readAnnotation
readMiRBaseMatureAnnotation	readMiRBaseMatureAnnotation
readMiRBasePreAnnotation	readMiRBasePreAnnotation
readWholeGenomeAnnotation	readWholeGenomeAnnotation
regions	regions-method
regions,sRNADiff,ANY-method	regions-method
regions,sRNADiff,numeric-method	regions-method
runAll	runAll
runAllAnnotation	runAllAnnotation
runAllHmm	runAllHmm
runAllNaive	runAllNaive
runAllSlice	runAllSlice
runHmm	runHmm
runSlice	runSlice
setEmissionProbabilities	setEmissionProbabilities-method
setEmissionProbabilities,sRNADiff,numeric-method	setEmissionProbabilities-method
setEmissionThreshold	setEmissionThreshold-method
setEmissionThreshold,sRNADiff,numeric-method	setEmissionThreshold-method
setMergeDistance	setMergeDistance-method
setMergeDistance,sRNADiff,numeric-method	setMergeDistance-method
setMinDepth	setMinDepth-method
setMinDepth,sRNADiff,numeric-method	setMinDepth-method
setMinDifferences	setMinDifferences-method
setMinDifferences,sRNADiff,numeric-method	setMinDifferences-method
setMinOverlap	setMinOverlap-method
setMinOverlap,sRNADiff,numeric-method	setMinOverlap-method
setNThreads	setNThreads-method
setNThreads,sRNADiff,numeric-method	setNThreads-method
setSizes	setSizes-method
setSizes,sRNADiff,numeric,numeric-method	setSizes-method
setStrategies	setStrategies-method
setStrategies,sRNADiff,logical,logical,logical,logical-method	setStrategies-method
setTransitionProbabilities	setTransitionProbabilities-method
setTransitionProbabilities,sRNADiff,numeric,numeric-method	setTransitionProbabilities-method
show,sRNADiff-method	show-sRNADiff-method
srnadiff	srnadiff
sRNADiff-class	sRNADiff-class
sRNADiffExample	sRNADiffExample
sRNADiffExp	sRNADiffExp
