AIC,INSPEcT-method	AIC-INSPEcT-method
AIC,INSPEcT_model-method	AIC-INSPEcT-method
AIC-INSPEcT-method	AIC-INSPEcT-method
allcounts	allcounts
calculateDelta	processingDelay
calculateDelta,INSPEcT-method	processingDelay
calculateRatePvals	calculateRatePvals
calculateRatePvals,INSPEcT-method	calculateRatePvals
calculateTau	processingDelay
calculateTau,INSPEcT-method	processingDelay
chisqmodel	chisqmodel
chisqmodel,INSPEcT-method	chisqmodel
chisqtest	chisqtest
chisqtest,INSPEcT-method	chisqtest
chisqtest,INSPEcT_model-method	chisqtest
combine	combine
combine,INSPEcT,INSPEcT-method	combine
compareSteady	compareSteady
compareSteady,INSPEcT-method	compareSteady
compareSteadyNoNascent	compareSteadyNoNascent
compareSteadyNoNascent,INSPEcT_steadyNoNascent-method	compareSteadyNoNascent
computeConfidenceIntervals	computeConfidenceIntervals
computeConfidenceIntervals,INSPEcT-method	computeConfidenceIntervals
convergence	convergence
convergence,INSPEcT-method	convergence
correlationPlot	correlationPlot
correlationPlot,INSPEcT_model,INSPEcT-method	correlationPlot
degradation	INSPEcT_diffsteady-class
degradation,INSPEcT_diffsteady-method	INSPEcT_diffsteady-class
dim,INSPEcT-method	dim-INSPEcT-method
Extract	Extract
featureNames,INSPEcT-method	featureNames-INSPEcT-method
featureNames,INSPEcT_diffsteady-method	INSPEcT_diffsteady-class
featureNames<-,INSPEcT-method	featureNames-INSPEcT-method
featureWidths	featureWidths
geneClass	geneClass
geneClass,INSPEcT-method	geneClass
geneClass,INSPEcT_diffsteady-method	geneClass
geneClass,INSPEcT_model-method	geneClass
inHeatmap	inHeatmap
inHeatmap,INSPEcT-method	inHeatmap
INSPEcT	INSPEcT
INSPEcT-class	INSPEcT-class
INSPEcT-shinyApps	INSPEcT-shinyApps
inspectFromBAM	inspectFromBAM
inspectFromPCR	inspectFromPCR
INSPEcT_diffsteady-class	INSPEcT_diffsteady-class
INSPEcT_model-class	INSPEcT_model-class
INSPEcT_steadyNoNascent-class	INSPEcT_steadyNoNascent-class
labeledSF	labeledSF
labeledSF,INSPEcT-method	labeledSF
libsizes	libsizes
logLik	logLik
logLik,INSPEcT-method	logLik
logLik,INSPEcT_model-method	logLik
makeModelRates	makeModelRates
makeModelRates,INSPEcT-method	makeModelRates
makeModelRates,INSPEcT_model-method	makeModelRates
makeOscillatorySimModel	makeOscillatorySimModel
makeOscillatorySimModel,INSPEcT-method	makeOscillatorySimModel
makeSimDataset	makeSimDataset
makeSimDataset,INSPEcT_model-method	makeSimDataset
makeSimModel	makeSimModel
makeSimModel,INSPEcT-method	makeSimModel
mature	mature
mature,INSPEcT_steadyNoNascent-method	mature
matureVar	matureVar
matureVar,INSPEcT_steadyNoNascent-method	matureVar
modelingParams	modelingParams
modelingParams,INSPEcT-method	modelingParams
modelRates	modelRates
modelRates,INSPEcT-method	modelRates
modelRatesNF	modelRatesNF
modelRatesNF,INSPEcT-method	modelRatesNF
modelSelection	modelSelection
modelSelection,INSPEcT-method	modelSelection
modelSelection,INSPEcT_model-method	modelSelection
newINSPEcT	newINSPEcT
nGenes	nGenes
nGenes,INSPEcT-method	nGenes
nTpts	nTpts
nTpts,INSPEcT-method	nTpts
plotGene	plotGene
plotGene,INSPEcT-method	plotGene
plotMA	plotMA
plotMA,INSPEcT_diffsteady-method	plotMA
plotPMgene	plotPMgene
plotPMgene,INSPEcT_steadyNoNascent-method	plotPMgene
plotPMtrend	plotPMtrend
plotPMtrend,INSPEcT_steadyNoNascent-method	plotPMtrend
premature	premature
premature,INSPEcT_steadyNoNascent-method	premature
prematureVar	prematureVar
prematureVar,INSPEcT_steadyNoNascent-method	prematureVar
processing	INSPEcT_diffsteady-class
processing,INSPEcT_diffsteady-method	INSPEcT_diffsteady-class
processingDelay	processingDelay
processingDelay,INSPEcT-method	processingDelay
PTratio	PTratio
PTratio,INSPEcT_steadyNoNascent-method	PTratio
PTreg	PTreg
PTreg,INSPEcT_steadyNoNascent-method	PTreg
quantifyExpressionsFromBAMs	quantifyExpressionsFromBAMs
quantifyExpressionsFromBWs	quantifyExpressionsFromBWs
quantifyExpressionsFromTrAbundance	quantifyExpressionsFromTrAbundance
quantifyExpressionsFromTrCounts	quantifyExpressionsFromTrCounts
ratePvals	ratePvals
ratePvals,INSPEcT-method	ratePvals
ratesFirstGuess	ratesFirstGuess
ratesFirstGuess,INSPEcT-method	ratesFirstGuess
ratesFirstGuessVar	ratesFirstGuessVar
ratesFirstGuessVar,INSPEcT-method	ratesFirstGuessVar
removeModel	removeModel
removeModel,INSPEcT-method	removeModel
rocCurve	rocCurve
rocCurve,INSPEcT_model,INSPEcT-method	rocCurve
rocThresholds	rocThresholds
rocThresholds,INSPEcT_model,INSPEcT-method	rocThresholds
runINSPEcTGUI	INSPEcT-shinyApps
runProcessingRateDelay	INSPEcT-shinyApps
setConfidenceIntervals	setConfidenceIntervals
setConfidenceIntervals,INSPEcT-method	setConfidenceIntervals
show,INSPEcT-method	INSPEcT-class
show,INSPEcT_diffsteady-method	INSPEcT_diffsteady-class
show,INSPEcT_model-method	INSPEcT_model-class
show,INSPEcT_steadyNoNascent-method	INSPEcT_steadyNoNascent-class
simData3rep_Nascent	simData3rep_Nascent
simData3rep_NoNascent	simData3rep_NoNascent
simData4rep_Nascent	simData4rep_Nascent
simData4rep_NoNascent	simData4rep_NoNascent
split	split
split,INSPEcT,ANY-method	split
synthesis	INSPEcT_diffsteady-class
synthesis,INSPEcT_diffsteady-method	INSPEcT_diffsteady-class
tpts	tpts
tpts,INSPEcT-method	tpts
viewConfidenceIntervals	viewConfidenceIntervals
viewConfidenceIntervals,INSPEcT-method	viewConfidenceIntervals
viewModelRates	viewModelRates
viewModelRates,INSPEcT-method	viewModelRates
[,INSPEcT,ANY,ANY,ANY-method	Extract
[,INSPEcT_diffsteady,ANY,ANY,ANY-method	Extract
[,INSPEcT_model,ANY,ANY,ANY-method	Extract
[,INSPEcT_steadyNoNascent,ANY,ANY,ANY-method	INSPEcT_steadyNoNascent-class
