# Statistical Transcriptome Analysis under a Dynamic Unified Model

## Documentation for package ‘STADyUM’ version 1.2.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

betaTbl | Constructor for TranscriptionRatesLRT object
betaTbl-method | Constructor for TranscriptionRatesLRT object
BetaViolinPlot | Constructor for TranscriptionRatesLRT object
BetaViolinPlot-method | Constructor for TranscriptionRatesLRT object
chiTbl | Constructor for TranscriptionRatesLRT object
chiTbl-method | Constructor for TranscriptionRatesLRT object
ChiViolinPlot | Constructor for TranscriptionRatesLRT object
ChiViolinPlot-method | Constructor for TranscriptionRatesLRT object
combinedCellsData | Constructor for SimulatePolymerase object
combinedCellsData-method | Constructor for SimulatePolymerase object
counts | Constructor for ExperimentTranscriptionRates object
counts-method | Constructor for ExperimentTranscriptionRates object
estimateTranscriptionRates | Generic function for estimating transcription rates
estimateTranscriptionRates-method | Constructor for ExperimentTranscriptionRates object
estimateTranscriptionRates-method | Constructor for SimulationTranscriptionRates object
ExperimentTranscriptionRates-class | Constructor for ExperimentTranscriptionRates object
finalPositionMatrix | Constructor for SimulatePolymerase object
finalPositionMatrix-method | Constructor for SimulatePolymerase object
geneBodyRegions | Constructor for ExperimentTranscriptionRates object
geneBodyRegions-method | Constructor for ExperimentTranscriptionRates object
getAvailableTimePoints | Constructor for SimulatePolymerase object
getAvailableTimePoints-method | Constructor for SimulatePolymerase object
getCombinedCellsDataAtTime | Constructor for SimulatePolymerase object
getCombinedCellsDataAtTime-method | Constructor for SimulatePolymerase object
getPositionMatrixAtTime | Constructor for SimulatePolymerase object
getPositionMatrixAtTime-method | Constructor for SimulatePolymerase object
likelihoodRatioTest | Constructor for TranscriptionRatesLRT object
omegaScale | Constructor for ExperimentTranscriptionRates object
omegaScale-method | Constructor for ExperimentTranscriptionRates object
parameters | Constructor for SimulatePolymerase object
parameters-method | Constructor for SimulatePolymerase object
pauseRegions | Constructor for ExperimentTranscriptionRates object
pauseRegions-method | Constructor for ExperimentTranscriptionRates object
pauseSites | Constructor for SimulatePolymerase object
pauseSites-method | Constructor for SimulatePolymerase object
plotBetaVsChi | Base class for TranscriptionRates objects
plotBetaVsChi-method | Base class for TranscriptionRates objects
plotChiDistrib | Base class for TranscriptionRates objects
plotChiDistrib-method | Base class for TranscriptionRates objects
plotCombinedCells | Constructor for SimulatePolymerase object
plotCombinedCells-method | Constructor for SimulatePolymerase object
plotExpectedVsActualPauseSiteCounts | Base class for TranscriptionRates objects
plotExpectedVsActualPauseSiteCounts-method | Base class for TranscriptionRates objects
plotLfcMa | Constructor for TranscriptionRatesLRT object
plotLfcMa-method | Constructor for TranscriptionRatesLRT object
plotMeanPauseDistrib | Base class for TranscriptionRates objects
plotMeanPauseDistrib-method | Base class for TranscriptionRates objects
plotPauseSiteContourMap | Base class for TranscriptionRates objects
plotPauseSiteContourMap-method | Base class for TranscriptionRates objects
plotPauseSiteContourMapTwoConditions | Constructor for TranscriptionRatesLRT object
plotPauseSiteContourMapTwoConditions-method | Constructor for TranscriptionRatesLRT object
plotPauseSites | Constructor for SimulatePolymerase object
plotPauseSites-method | Constructor for SimulatePolymerase object
plotPolymerasePCA | Constructor for SimulatePolymerase object
plotPolymerasePCA-method | Constructor for SimulatePolymerase object
plotPositionHeatmap | Constructor for SimulatePolymerase object
plotPositionHeatmap-method | Constructor for SimulatePolymerase object
positionMatrices | Constructor for SimulatePolymerase object
positionMatrices-method | Constructor for SimulatePolymerase object
rates | Accessor for estimated rates
rates-method | Constructor for ExperimentTranscriptionRates object
rates-method | Constructor for SimulationTranscriptionRates object
readCounts | Constructor for SimulatePolymerase object
readCounts-method | Constructor for SimulatePolymerase object
sampleReadCounts | Constructor for SimulatePolymerase object
sampleReadCounts-method | Constructor for SimulatePolymerase object
show-method | Constructor for SimulatePolymerase object
show-method | Constructor for SimulationTranscriptionRates object
show-method | Show method for ExperimentTranscriptionRates objects
simpol | Constructor for SimulationTranscriptionRates object
simpol-method | Constructor for SimulationTranscriptionRates object
simulatePolymerase | Constructor for SimulatePolymerase object
SimulatePolymerase-class | Constructor for SimulatePolymerase object
SimulationTranscriptionRates-class | Constructor for SimulationTranscriptionRates object
siteProbabilities | Constructor for SimulatePolymerase object
siteProbabilities-method | Constructor for SimulatePolymerase object
spikeInFile | Constructor for TranscriptionRatesLRT object
spikeInFile-method | Constructor for TranscriptionRatesLRT object
stericHindrance | Accessor for steric hindrance flag
stericHindrance-method | Constructor for ExperimentTranscriptionRates object
stericHindrance-method | Constructor for SimulationTranscriptionRates object
TranscriptionRates-class | Base class for TranscriptionRates objects
transcriptionRates1 | Constructor for TranscriptionRatesLRT object
transcriptionRates1-method | Constructor for TranscriptionRatesLRT object
transcriptionRates2 | Constructor for TranscriptionRatesLRT object
transcriptionRates2-method | Constructor for TranscriptionRatesLRT object
TranscriptionRatesLRT-class | Constructor for TranscriptionRatesLRT object