betaTbl	TranscriptionRatesLRT-class
betaTbl,TranscriptionRatesLRT-method	TranscriptionRatesLRT-class
BetaViolinPlot	TranscriptionRatesLRT-class
BetaViolinPlot,TranscriptionRatesLRT-method	TranscriptionRatesLRT-class
chiTbl	TranscriptionRatesLRT-class
chiTbl,TranscriptionRatesLRT-method	TranscriptionRatesLRT-class
ChiViolinPlot	TranscriptionRatesLRT-class
ChiViolinPlot,TranscriptionRatesLRT-method	TranscriptionRatesLRT-class
combinedCellsData	SimulatePolymerase-class
combinedCellsData,SimulatePolymerase-method	SimulatePolymerase-class
counts	ExperimentTranscriptionRates-class
counts,ExperimentTranscriptionRates-method	ExperimentTranscriptionRates-class
estimateTranscriptionRates	estimateTranscriptionRates
estimateTranscriptionRates,character-method	ExperimentTranscriptionRates-class
estimateTranscriptionRates,SimulatePolymerase-method	SimulationTranscriptionRates-class
ExperimentTranscriptionRates-class	ExperimentTranscriptionRates-class
finalPositionMatrix	SimulatePolymerase-class
finalPositionMatrix,SimulatePolymerase-method	SimulatePolymerase-class
geneBodyRegions	ExperimentTranscriptionRates-class
geneBodyRegions,ExperimentTranscriptionRates-method	ExperimentTranscriptionRates-class
getAvailableTimePoints	SimulatePolymerase-class
getAvailableTimePoints,SimulatePolymerase-method	SimulatePolymerase-class
getCombinedCellsDataAtTime	SimulatePolymerase-class
getCombinedCellsDataAtTime,SimulatePolymerase-method	SimulatePolymerase-class
getPositionMatrixAtTime	SimulatePolymerase-class
getPositionMatrixAtTime,SimulatePolymerase-method	SimulatePolymerase-class
likelihoodRatioTest	TranscriptionRatesLRT-class
omegaScale	ExperimentTranscriptionRates-class
omegaScale,ExperimentTranscriptionRates-method	ExperimentTranscriptionRates-class
parameters	SimulatePolymerase-class
parameters,SimulatePolymerase-method	SimulatePolymerase-class
pauseRegions	ExperimentTranscriptionRates-class
pauseRegions,ExperimentTranscriptionRates-method	ExperimentTranscriptionRates-class
pauseSites	SimulatePolymerase-class
pauseSites,SimulatePolymerase-method	SimulatePolymerase-class
plotBetaVsChi	TranscriptionRates-class
plotBetaVsChi,TranscriptionRates-method	TranscriptionRates-class
plotChiDistrib	TranscriptionRates-class
plotChiDistrib,TranscriptionRates-method	TranscriptionRates-class
plotCombinedCells	SimulatePolymerase-class
plotCombinedCells,SimulatePolymerase-method	SimulatePolymerase-class
plotExpectedVsActualPauseSiteCounts	TranscriptionRates-class
plotExpectedVsActualPauseSiteCounts,TranscriptionRates-method	TranscriptionRates-class
plotLfcMa	TranscriptionRatesLRT-class
plotLfcMa,TranscriptionRatesLRT-method	TranscriptionRatesLRT-class
plotMeanPauseDistrib	TranscriptionRates-class
plotMeanPauseDistrib,TranscriptionRates-method	TranscriptionRates-class
plotPauseSiteContourMap	TranscriptionRates-class
plotPauseSiteContourMap,TranscriptionRates-method	TranscriptionRates-class
plotPauseSiteContourMapTwoConditions	TranscriptionRatesLRT-class
plotPauseSiteContourMapTwoConditions,TranscriptionRatesLRT-method	TranscriptionRatesLRT-class
plotPauseSites	SimulatePolymerase-class
plotPauseSites,SimulatePolymerase-method	SimulatePolymerase-class
plotPolymerasePCA	SimulatePolymerase-class
plotPolymerasePCA,SimulatePolymerase-method	SimulatePolymerase-class
plotPositionHeatmap	SimulatePolymerase-class
plotPositionHeatmap,SimulatePolymerase-method	SimulatePolymerase-class
positionMatrices	SimulatePolymerase-class
positionMatrices,SimulatePolymerase-method	SimulatePolymerase-class
rates	rates
rates,ExperimentTranscriptionRates-method	ExperimentTranscriptionRates-class
rates,SimulationTranscriptionRates-method	SimulationTranscriptionRates-class
readCounts	SimulatePolymerase-class
readCounts,SimulatePolymerase-method	SimulatePolymerase-class
sampleReadCounts	SimulatePolymerase-class
sampleReadCounts,SimulatePolymerase-method	SimulatePolymerase-class
show,ExperimentTranscriptionRates-method	show-ExperimentTranscriptionRates-method
show,SimulatePolymerase-method	SimulatePolymerase-class
show,SimulationTranscriptionRates-method	SimulationTranscriptionRates-class
simpol	SimulationTranscriptionRates-class
simpol,SimulationTranscriptionRates-method	SimulationTranscriptionRates-class
simulatePolymerase	SimulatePolymerase-class
SimulatePolymerase-class	SimulatePolymerase-class
SimulationTranscriptionRates-class	SimulationTranscriptionRates-class
siteProbabilities	SimulatePolymerase-class
siteProbabilities,SimulatePolymerase-method	SimulatePolymerase-class
spikeInFile	TranscriptionRatesLRT-class
spikeInFile,TranscriptionRatesLRT-method	TranscriptionRatesLRT-class
stericHindrance	stericHindrance
stericHindrance,ExperimentTranscriptionRates-method	ExperimentTranscriptionRates-class
stericHindrance,SimulationTranscriptionRates-method	SimulationTranscriptionRates-class
TranscriptionRates-class	TranscriptionRates-class
transcriptionRates1	TranscriptionRatesLRT-class
transcriptionRates1,TranscriptionRatesLRT-method	TranscriptionRatesLRT-class
transcriptionRates2	TranscriptionRatesLRT-class
transcriptionRates2,TranscriptionRatesLRT-method	TranscriptionRatesLRT-class
TranscriptionRatesLRT-class	TranscriptionRatesLRT-class
