Statistical Transcriptome Analysis under a Dynamic Unified Model

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Documentation for package ‘STADyUM’ version 1.3.1

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

Help Pages

B C E F G L M O P R S T

-- B --

betaTbl	Constructor for TranscriptionRatesLRT object
betaTbl-method	Constructor for TranscriptionRatesLRT object
BetaViolinPlot	Constructor for TranscriptionRatesLRT object
BetaViolinPlot-method	Constructor for TranscriptionRatesLRT object

-- C --

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

-- E --

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

-- F --

finalPositionMatrix	Constructor for SimulatePolymerase object
finalPositionMatrix-method	Constructor for SimulatePolymerase object

-- G --

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
getSdGroupCutoff	Get SD Group Cutoff

-- L --

likelihoodRatioTest	Constructor for TranscriptionRatesLRT object
lrtTbl	Constructor for TranscriptionRatesLRT object
lrtTbl-method	Constructor for TranscriptionRatesLRT object

-- M --

mergeBetaChiLRTStats	Constructor for TranscriptionRatesLRT object
mergeBetaChiLRTStats-method	Constructor for TranscriptionRatesLRT object

-- O --

omegaScale	Constructor for ExperimentTranscriptionRates object
omegaScale-method	Constructor for ExperimentTranscriptionRates object

-- P --

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
plotBetaQuantileHeatmap	Constructor for TranscriptionRatesLRT object
plotBetaQuantileHeatmap-method	Constructor for TranscriptionRatesLRT object
plotBetaScatter	Constructor for TranscriptionRatesLRT object
plotBetaScatter-method	Constructor for TranscriptionRatesLRT 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
plotDeltaBetaSigma	Constructor for TranscriptionRatesLRT object
plotDeltaBetaSigma-method	Constructor for TranscriptionRatesLRT object
plotExpectedVsActualPauseSiteCounts	Base class for TranscriptionRates objects
plotExpectedVsActualPauseSiteCounts-method	Base class for TranscriptionRates objects
plotFksdDensity	Constructor for TranscriptionRatesLRT object
plotFksdDensity-method	Constructor for TranscriptionRatesLRT object
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
plotScatterDensity	Base class for TranscriptionRates objects
plotScatterDensity-method	Base class for TranscriptionRates objects
positionMatrices	Constructor for SimulatePolymerase object
positionMatrices-method	Constructor for SimulatePolymerase object

-- R --

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

-- S --

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

-- T --

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