groHMM-package	groHMM-package
averagePlot	averagePlot
breakTranscriptsOnGenes	breakTranscriptsOnGenes
combineTranscripts	combineTranscripts
countMappableReadsInInterval	countMappableReadsInInterval
detectTranscripts	detectTranscripts
evaluateHMMInAnnotations	evaluateHMMInAnnotations
expressedGenes	expressedGenes
getCores	getCores
getTxDensity	getTxDensity
groHMM	groHMM-package
limitToXkb	limitToXkb
makeConsensusAnnotations	makeConsensusAnnotations
metaGene	metaGene
metaGeneMatrix	metaGeneMatrix
metaGene_nL	metaGene_nL
pausingIndex	pausingIndex
polymeraseWave	polymeraseWave
readBed	readBed
RgammaMLE	RgammaMLE
Rnorm	Rnorm
Rnorm.exp	Rnorm.exp
runMetaGene	runMetaGene
tlsDeming	tlsDeming
tlsLoess	tlsLoess
tlsSvd	tlsSvd
windowAnalysis	windowAnalysis
writeWiggle	writeWiggle
