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  "Type": "Package",
  "Title": "Statistical Transcriptome Analysis under a Dynamic Unified Model",
  "Version": "1.3.2",
  "Authors@R": "c(\nperson(\"Yixin\", \"Zhao\",\nemail = \"\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-7856-2818\")\n),\nperson(\"Lingjie\", \"Liu\",\nemail = \"\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-5765-1213\")\n),\nperson(\"Rebecca\", \"Hassett\",\nemail = \"hassett@cshl.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5133-9387\")\n),\nperson(\"Xin\", \"Zeng\",\nemail = \"zeng@cshl.edu\",\nrole = c(\"aut\", \"aut\")\n)\n)",
  "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.",
  "URL": "https://github.com/rhassett-cshl/STADyUM",
  "BugReports": "https://github.com/rhassett-cshl/STADyUM",
  "biocViews": "StatisticalMethod, Transcriptomics, Transcription,\nSequencing, Preprocessing",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-06-22 22:48:34 UTC",
  "RemoteUrl": "https://github.com/bioc/STADyUM",
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  "Packaged": {
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  "Author": "Yixin Zhao [aut] (ORCID: <https://orcid.org/0000-0002-7856-2818>),\nLingjie Liu [aut] (ORCID: <https://orcid.org/0000-0002-5765-1213>),\nRebecca Hassett [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5133-9387>),\nXin Zeng [aut, aut]",
  "Maintainer": "Rebecca Hassett <hassett@cshl.edu>",
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  "_type": "src",
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  "_expires": "2026-10-12T21:08:48.000Z",
  "_created": "2026-06-23T06:56:31.000Z",
  "_published": "2026-07-04T21:08:50.122Z",
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    "transcription",
    "sequencing",
    "preprocessing",
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  "_contributors": [
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_devurl": "https://github.com/rhassett-cshl/stadyum",
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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    "manual.pdf"
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  "_homeurl": "https://github.com/rhassett-cshl/stadyum",
  "_realowner": "bioc",
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  "_exports": [
    "betaTbl",
    "BetaViolinPlot",
    "chiTbl",
    "ChiViolinPlot",
    "combinedCellsData",
    "counts",
    "estimateTranscriptionRates",
    "finalPositionMatrix",
    "geneBodyRegions",
    "getAvailableTimePoints",
    "getCombinedCellsDataAtTime",
    "getPositionMatrixAtTime",
    "getSdGroupCutoff",
    "likelihoodRatioTest",
    "lrtTbl",
    "mergeBetaChiLRTStats",
    "omegaScale",
    "parameters",
    "pauseRegions",
    "pauseSites",
    "plotBetaQuantileHeatmap",
    "plotBetaScatter",
    "plotBetaVsChi",
    "plotChiDistrib",
    "plotCombinedCells",
    "plotDeltaBetaSigma",
    "plotExpectedVsActualPauseSiteCounts",
    "plotFksdDensity",
    "plotLfcMa",
    "plotMeanPauseDistrib",
    "plotPauseSiteContourMap",
    "plotPauseSiteContourMapTwoConditions",
    "plotPauseSites",
    "plotPolymerasePCA",
    "plotPositionHeatmap",
    "plotScatterDensity",
    "positionMatrices",
    "rates",
    "readCounts",
    "sampleReadCounts",
    "show",
    "simpol",
    "simulatePolymerase",
    "siteProbabilities",
    "spikeInFile",
    "stericHindrance",
    "transcriptionRates1",
    "transcriptionRates2"
  ],
  "_help": [
    {
      "page": "estimateTranscriptionRates",
      "title": "Generic function for estimating transcription rates",
      "topics": [
        "estimateTranscriptionRates"
      ]
    },
    {
      "page": "ExperimentTranscriptionRates-class",
      "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": [
        "getSdGroupCutoff"
      ]
    },
    {
      "page": "rates",
      "title": "Accessor for estimated rates",
      "topics": [
        "rates"
      ]
    },
    {
      "page": "show-ExperimentTranscriptionRates-method",
      "title": "Show method for ExperimentTranscriptionRates objects",
      "topics": [
        "show,ExperimentTranscriptionRates-method"
      ]
    },
    {
      "page": "SimulatePolymerase-class",
      "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"
      ]
    },
    {
      "page": "stericHindrance",
      "title": "Accessor for steric hindrance flag",
      "topics": [
        "stericHindrance"
      ]
    },
    {
      "page": "TranscriptionRates-class",
      "title": "Base class for TranscriptionRates objects",
      "topics": [
        "plotBetaVsChi",
        "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"
      ]
    },
    {
      "page": "TranscriptionRatesLRT-class",
      "title": "Constructor for TranscriptionRatesLRT object",
      "topics": [
        "betaTbl",
        "betaTbl,TranscriptionRatesLRT-method",
        "BetaViolinPlot",
        "BetaViolinPlot,TranscriptionRatesLRT-method",
        "chiTbl",
        "chiTbl,TranscriptionRatesLRT-method",
        "ChiViolinPlot",
        "ChiViolinPlot,TranscriptionRatesLRT-method",
        "likelihoodRatioTest",
        "lrtTbl",
        "lrtTbl,TranscriptionRatesLRT-method",
        "mergeBetaChiLRTStats",
        "mergeBetaChiLRTStats,TranscriptionRatesLRT-method",
        "plotBetaQuantileHeatmap",
        "plotBetaQuantileHeatmap,TranscriptionRatesLRT-method",
        "plotBetaScatter",
        "plotBetaScatter,TranscriptionRatesLRT-method",
        "plotDeltaBetaSigma",
        "plotDeltaBetaSigma,TranscriptionRatesLRT-method",
        "plotFksdDensity",
        "plotFksdDensity,TranscriptionRatesLRT-method",
        "plotLfcMa",
        "plotLfcMa,TranscriptionRatesLRT-method",
        "plotPauseSiteContourMapTwoConditions",
        "plotPauseSiteContourMapTwoConditions,TranscriptionRatesLRT-method",
        "spikeInFile",
        "spikeInFile,TranscriptionRatesLRT-method",
        "transcriptionRates1",
        "transcriptionRates1,TranscriptionRatesLRT-method",
        "transcriptionRates2",
        "transcriptionRates2,TranscriptionRatesLRT-method",
        "TranscriptionRatesLRT-class"
      ]
    }
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      "source": "STADyUM_LRT_Tutorial.Rmd",
      "filename": "STADyUM_LRT_Tutorial.html",
      "title": "Comparative Analysis of Promoter-Proximal Pausing using Likelihood Ratio Tests",
      "author": "Xin Zeng",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Setup",
        "Load Required Libraries and Data",
        "Running STADyUM",
        "Likelihood Ratio Test Calculations",
        "Visualization",
        "Pause-escape Rate Quantile Heatmap",
        "Pause-escape Rate Scatter Plot",
        "Pause-escape Rate and Pausing Dispersion Contour Plot",
        "Pausing Dispersion Contour Plot",
        "Summary",
        "Session Information"
      ],
      "created": "2026-06-10 21:46:40",
      "modified": "2026-06-22 22:48:34",
      "commits": 2
    },
    {
      "source": "STADyUM_Rate_Estimation_Tutorial.Rmd",
      "filename": "STADyUM_Rate_Estimation_Tutorial.html",
      "title": "Estimating Transcription Rates with STADyUM from PRO-seq Data",
      "author": "Xin Zeng",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Setup",
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