{
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  "Package": "InPAS",
  "Title": "Identify Novel Alternative PolyAdenylation Sites (PAS) from\nRNA-seq data",
  "Version": "2.21.1",
  "Authors@R": "c(person(\"Jianhong\", \"Ou\", role = c(\"aut\", \"cre\"), \nemail = \"jou@morgridge.org\"),\nperson(\"Haibo\", \"Liu\", role = c(\"aut\"),\nemail = \"haibo.liu@umassmed.edu\"),\nperson(\"Lihua Julie\", \"Zhu\", role = c(\"aut\"),\nemail = \"Julie.Zhu@umassmed.edu\"),\nperson(\"Sungmi M.\", \"Park\", role = \"aut\"),\nperson(\"Michael R.\", \"Green\", role = \"aut\"))",
  "Maintainer": "Jianhong Ou <jou@morgridge.org>",
  "Description": "Alternative polyadenylation (APA) is one of the important\npost- transcriptional regulation mechanisms which occurs in\nmost human genes. InPAS facilitates the discovery of novel APA\nsites and the differential usage of APA sites from RNA-Seq\ndata. It leverages cleanUpdTSeq to fine tune identified APA\nsites by removing false sites.",
  "biocViews": "Alternative Polyadenylation, Differential Polyadenylation\nSite Usage, RNA-seq, Gene Regulation, Transcription",
  "License": "GPL (>= 2)",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-09-25 14:55:53 UTC",
  "RemoteUrl": "https://github.com/bioc/InPAS",
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  "Author": "Jianhong Ou [aut, cre],\nHaibo Liu [aut],\nLihua Julie Zhu [aut],\nSungmi M. Park [aut],\nMichael R. Green [aut]",
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  "_created": "2026-10-25T12:06:00.000Z",
  "_published": "2026-10-25T12:22:11.028Z",
  "_upstream": "https://github.com/bioc/InPAS",
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  "_exports": [
    "addChr2Exclude",
    "addInPASEnsDb",
    "addInPASGenome",
    "addInPASOutputDirectory",
    "addInPASTxDb",
    "addLockName",
    "assemble_allCov",
    "extract_UTR3Anno",
    "filter_testOut",
    "find_minMSEDistr",
    "get_chromosomes",
    "get_lastCDSUTR3",
    "get_regionCov",
    "get_ssRleCov",
    "get_usage4plot",
    "get_UTR3eSet",
    "getChr2Exclude",
    "getInPASEnsDb",
    "getInPASGenome",
    "getInPASOutputDirectory",
    "getInPASSQLiteDb",
    "getInPASTxDb",
    "getLockName",
    "parse_TxDb",
    "plot_utr3Usage",
    "run_coverageQC",
    "run_limmaAnalysis",
    "search_CPs",
    "set_globals",
    "setup_CPsSearch",
    "setup_GSEA",
    "setup_parCPsSearch",
    "setup_sqlitedb",
    "test_dPDUI"
  ],
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      "name": "utr3.mm10",
      "title": "Annotation of 3' UTRs for mouse (mm10)",
      "object": "utr3.mm10",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
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  "_help": [
    {
      "page": "addChr2Exclude",
      "title": "Add a globally-applied requirement for filtering out scaffolds from all analysis",
      "topics": [
        "addChr2Exclude"
      ]
    },
    {
      "page": "addInPASEnsDb",
      "title": "Add a globally defined EnsDb to some InPAS functions.",
      "topics": [
        "addInPASEnsDb"
      ]
    },
    {
      "page": "addInPASGenome",
      "title": "Add a globally defined genome to all InPAS functions.",
      "topics": [
        "addInPASGenome"
      ]
    },
    {
      "page": "addInPASOutputDirectory",
      "title": "Add a globally defined output directory to some InPAS functions.",
      "topics": [
        "addInPASOutputDirectory"
      ]
    },
    {
      "page": "addInPASTxDb",
      "title": "Add a globally defined TxDb for InPAS functions.",
      "topics": [
        "addInPASTxDb"
      ]
    },
    {
      "page": "addLockName",
      "title": "Add a filename for locking a SQLite database",
      "topics": [
        "addLockName"
      ]
    },
    {
      "page": "assemble_allCov",
      "title": "Assemble coverage files for a given chromosome for all samples",
      "topics": [
        "assemble_allCov"
      ]
    },
    {
      "page": "extract_UTR3Anno",
      "title": "extract 3' UTR information from a GenomicFeatures::TxDb object",
      "topics": [
        "extract_UTR3Anno"
      ]
    },
    {
      "page": "filter_testOut",
      "title": "filter 3' UTR usage test results",
      "topics": [
        "filter_testOut"
      ]
    },
    {
      "page": "find_minMSEDistr",
      "title": "Visualization of MSE profiles, 3' UTR coverage and minimal MSE distribution",
      "topics": [
        "find_minMSEDistr"
      ]
    },
    {
      "page": "get_chromosomes",
      "title": "Identify chromosomes/scaffolds for CP site discovery",
      "topics": [
        "get_chromosomes"
      ]
    },
    {
      "page": "get_lastCDSUTR3",
      "title": "Extract the last unspliced region of each transcript",
      "topics": [
        "get_lastCDSUTR3"
      ]
    },
    {
      "page": "get_regionCov",
      "title": "Get coverage for 3' UTR and last CDS regions on a single chromosome",
      "topics": [
        "get_regionCov"
      ]
    },
    {
      "page": "get_ssRleCov",
      "title": "Get Rle coverage from a bedgraph file for a sample",
      "topics": [
        "get_ssRleCov"
      ]
    },
    {
      "page": "get_usage4plot",
      "title": "prepare coverage data and fitting data for plot",
      "topics": [
        "get_usage4plot"
      ]
    },
    {
      "page": "get_UTR3eSet",
      "title": "prepare 3' UTR coverage data for usage test",
      "topics": [
        "get_UTR3eSet"
      ]
    },
    {
      "page": "getChr2Exclude",
      "title": "Get a globally-applied requirement for filtering scaffolds.",
      "topics": [
        "getChr2Exclude"
      ]
    },
    {
      "page": "getInPASEnsDb",
      "title": "Get the globally defined EnsDb.",
      "topics": [
        "getInPASEnsDb"
      ]
    },
    {
      "page": "getInPASGenome",
      "title": "Get the globally defined genome",
      "topics": [
        "getInPASGenome"
      ]
    },
    {
      "page": "getInPASOutputDirectory",
      "title": "Get the path to a output directory for InPAS analysis",
      "topics": [
        "getInPASOutputDirectory"
      ]
    },
    {
      "page": "getInPASSQLiteDb",
      "title": "Get the path to an SQLite database",
      "topics": [
        "getInPASSQLiteDb"
      ]
    },
    {
      "page": "getInPASTxDb",
      "title": "Get the globally defined TxDb.",
      "topics": [
        "getInPASTxDb"
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    },
    {
      "page": "getLockName",
      "title": "Get the path to a file for locking the SQLite database",
      "topics": [
        "getLockName"
      ]
    },
    {
      "page": "InPAS",
      "title": "A package for identifying novel Alternative PolyAdenylation Sites (PAS) based on RNA-seq data",
      "topics": [
        "-package",
        "InPAS"
      ]
    },
    {
      "page": "parse_TxDb",
      "title": "Extract gene models from a TxDb object",
      "topics": [
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    {
      "page": "plot_utr3Usage",
      "title": "Visualize the dPDUI events using ggplot2",
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    {
      "page": "run_coverageQC",
      "title": "Quality control on read coverage over gene bodies and 3UTRs",
      "topics": [
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    {
      "page": "search_CPs",
      "title": "Estimate the CP sites for UTRs on a given chromosome",
      "topics": [
        "search_CPs"
      ]
    },
    {
      "page": "set_globals",
      "title": "Set up global variables for an InPAS analysis",
      "topics": [
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    },
    {
      "page": "setup_CPsSearch",
      "title": "prepare data for predicting cleavage and polyadenylation (CP) sites",
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      "topics": [
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    {
      "page": "test_dPDUI",
      "title": "do test for dPDUI",
      "topics": [
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    },
    {
      "page": "utr3.mm10",
      "title": "Annotation of 3' UTRs for mouse (mm10)",
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    },
    {
      "page": "UTR3eSet-class",
      "title": "UTR3eSet-class and its methods",
      "topics": [
        "$,UTR3eSet-method",
        "$<-,UTR3eSet-method",
        "coerce,UTR3eSet,ExpressionSet-method",
        "coerce,UTR3eSet,GRanges-method",
        "show,UTR3eSet-method",
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  "_vignettes": [
    {
      "source": "InPAS.Rmd",
      "filename": "InPAS.html",
      "title": "InPAS Vignette",
      "author": "Jianhong Ou, Haibo Liu, Sungmi Park, Michael Green, Lihua Julie Zhu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "How to run InPAS",
        "Step 1: set up a SQLite database",
        "Step 2: Extracting 3' UTR annotation",
        "Step 3: reformatting coverage data",
        "Step 4: Identifying potential CP sites",
        "Step 5: Estimate usage of proximal and distal CP sites",
        "Step 6. identifying differential PDUI events",
        "Step 7. Visualizing dPDUI events and preparing files for GSEA",
        "Session Info"
      ],
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