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  "Description": "STADyUM is a package with functionality for analyzing\nnascent RNA read counts to infer transcription rates. This\nincludes utilities for processing experimental nascent RNA read\ncounts as well as for simulating PRO-seq data. Rates such as\ninitiation, pause release and landing pad occupancy are\nestimated from either synthetic or experimental data. There are\nalso options for varying pause sites and including steric\nhindrance of initiation in the model.",
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    "parameters",
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    "plotBetaQuantileHeatmap",
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    "plotChiDistrib",
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    "plotPauseSiteContourMapTwoConditions",
    "plotPauseSites",
    "plotPolymerasePCA",
    "plotPositionHeatmap",
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    "positionMatrices",
    "rates",
    "readCounts",
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    "show",
    "simpol",
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    "siteProbabilities",
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    "stericHindrance",
    "transcriptionRates1",
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      "title": "Generic function for estimating transcription rates",
      "topics": [
        "estimateTranscriptionRates"
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    {
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      "title": "Constructor for ExperimentTranscriptionRates object",
      "topics": [
        "counts",
        "counts,ExperimentTranscriptionRates-method",
        "estimateTranscriptionRates,character-method",
        "ExperimentTranscriptionRates-class",
        "geneBodyRegions",
        "geneBodyRegions,ExperimentTranscriptionRates-method",
        "omegaScale",
        "omegaScale,ExperimentTranscriptionRates-method",
        "pauseRegions",
        "pauseRegions,ExperimentTranscriptionRates-method",
        "rates,ExperimentTranscriptionRates-method",
        "stericHindrance,ExperimentTranscriptionRates-method"
      ]
    },
    {
      "page": "getSdGroupCutoff",
      "title": "Get SD Group Cutoff",
      "topics": [
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    },
    {
      "page": "rates",
      "title": "Accessor for estimated rates",
      "topics": [
        "rates"
      ]
    },
    {
      "page": "show-ExperimentTranscriptionRates-method",
      "title": "Show method for ExperimentTranscriptionRates objects",
      "topics": [
        "show,ExperimentTranscriptionRates-method"
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    },
    {
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      "title": "Constructor for SimulatePolymerase object",
      "topics": [
        "combinedCellsData",
        "combinedCellsData,SimulatePolymerase-method",
        "finalPositionMatrix",
        "finalPositionMatrix,SimulatePolymerase-method",
        "getAvailableTimePoints",
        "getAvailableTimePoints,SimulatePolymerase-method",
        "getCombinedCellsDataAtTime",
        "getCombinedCellsDataAtTime,SimulatePolymerase-method",
        "getPositionMatrixAtTime",
        "getPositionMatrixAtTime,SimulatePolymerase-method",
        "parameters",
        "parameters,SimulatePolymerase-method",
        "pauseSites",
        "pauseSites,SimulatePolymerase-method",
        "plotCombinedCells",
        "plotCombinedCells,SimulatePolymerase-method",
        "plotPauseSites",
        "plotPauseSites,SimulatePolymerase-method",
        "plotPolymerasePCA",
        "plotPolymerasePCA,SimulatePolymerase-method",
        "plotPositionHeatmap",
        "plotPositionHeatmap,SimulatePolymerase-method",
        "positionMatrices",
        "positionMatrices,SimulatePolymerase-method",
        "readCounts",
        "readCounts,SimulatePolymerase-method",
        "sampleReadCounts",
        "sampleReadCounts,SimulatePolymerase-method",
        "show,SimulatePolymerase-method",
        "simulatePolymerase",
        "SimulatePolymerase-class",
        "siteProbabilities",
        "siteProbabilities,SimulatePolymerase-method"
      ]
    },
    {
      "page": "SimulationTranscriptionRates-class",
      "title": "Constructor for SimulationTranscriptionRates object",
      "topics": [
        "estimateTranscriptionRates,SimulatePolymerase-method",
        "rates,SimulationTranscriptionRates-method",
        "show,SimulationTranscriptionRates-method",
        "simpol",
        "simpol,SimulationTranscriptionRates-method",
        "SimulationTranscriptionRates-class",
        "stericHindrance,SimulationTranscriptionRates-method"
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    {
      "page": "stericHindrance",
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      "topics": [
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    {
      "page": "TranscriptionRates-class",
      "title": "Base class for TranscriptionRates objects",
      "topics": [
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        "plotBetaVsChi,TranscriptionRates-method",
        "plotChiDistrib",
        "plotChiDistrib,TranscriptionRates-method",
        "plotExpectedVsActualPauseSiteCounts",
        "plotExpectedVsActualPauseSiteCounts,TranscriptionRates-method",
        "plotMeanPauseDistrib",
        "plotMeanPauseDistrib,TranscriptionRates-method",
        "plotPauseSiteContourMap",
        "plotPauseSiteContourMap,TranscriptionRates-method",
        "plotScatterDensity",
        "plotScatterDensity,TranscriptionRates-method",
        "TranscriptionRates-class"
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    {
      "page": "TranscriptionRatesLRT-class",
      "title": "Constructor for TranscriptionRatesLRT object",
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        "betaTbl,TranscriptionRatesLRT-method",
        "BetaViolinPlot",
        "BetaViolinPlot,TranscriptionRatesLRT-method",
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        "plotPauseSiteContourMapTwoConditions",
        "plotPauseSiteContourMapTwoConditions,TranscriptionRatesLRT-method",
        "spikeInFile",
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        "transcriptionRates1",
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