{
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  "Package": "RgnTX",
  "Title": "Colocalization analysis of transcriptome elements in the\npresence of isoform heterogeneity and ambiguity",
  "Version": "1.14.0",
  "Authors@R": "c(\nperson(\"Yue\", \"Wang\", , \"yue.wang19@student.xjtlu.edu.cn\", role = c(\"aut\", \"cre\")),\nperson(\"Jia\", \"Meng\", , \"jia.meng@xjtlu.edu.cn\", role = c(\"aut\")))",
  "Description": "RgnTX allows the integration of transcriptome annotations\nso as to model the complex alternative splicing patterns. It\nsupports the testing of transcriptome elements without clear\nisoform association, which is often the real scenario due to\ntechnical limitations. It involves functions that do permutaion\ntest for evaluating association between features and\ntranscriptome regions.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.2.0",
  "biocViews": "AlternativeSplicing, Sequencing, RNASeq, MethylSeq,\nTranscription, SplicedAlignment",
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  "PackageStatus": "Deprecated",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:58:30 UTC",
  "RemoteUrl": "https://github.com/bioc/RgnTX",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "299af2aa504b356ad15e4d3761f721ee4389bdfe",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-10 10:45:16 UTC",
    "User": "root"
  },
  "Author": "Yue Wang [aut, cre],\nJia Meng [aut]",
  "Maintainer": "Yue Wang <yue.wang19@student.xjtlu.edu.cn>",
  "MD5sum": "25408657d0c960a3d72f8c2e954d9e01",
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  "_created": "2026-06-10T10:45:16.000Z",
  "_published": "2026-06-10T10:55:33.529Z",
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  "_tags": [],
  "_topics": [
    "alternativesplicing",
    "sequencing",
    "rnaseq",
    "methylseq",
    "transcription",
    "splicedalignment"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
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    "source": "https://www.bioconductor.org/packages/stats/bioc/RgnTX"
  },
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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    "extra/contents.json",
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    "extra/NEWS.txt",
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    "extra/readme.md",
    "extra/RgnTX.html",
    "manual.pdf"
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  "_cranurl": false,
  "_exports": [
    "calculateShift",
    "distanceTx",
    "extractRegions",
    "getPermSpaceByFeatures",
    "getPermSpaceByTxID",
    "getPermSpaceByType",
    "getStopCodon",
    "getTransInfo",
    "GRanges2GRangesList",
    "GRangesList2GRanges",
    "overlapCountsTx",
    "overlapCountsTxIA",
    "overlapWidthTx",
    "permTestTx",
    "permTestTx_customAll",
    "permTestTx_customPick",
    "permTestTxIA",
    "permTestTxIA_customPick",
    "plotPermResults",
    "plotShiftedZScoreTx",
    "randomizeFeaturesTx",
    "randomizeFeaturesTxIA",
    "randomizeTransByOrder",
    "randomizeTx",
    "shiftedZScoreTx",
    "shiftTx"
  ],
  "_help": [
    {
      "page": "calculateShift",
      "title": "Calculate positional shifting over transcriptome",
      "topics": [
        "calculateShift"
      ]
    },
    {
      "page": "distanceTx",
      "title": "Evaluation function",
      "topics": [
        "distanceTx"
      ]
    },
    {
      "page": "extractRegions",
      "title": "Extract regions",
      "topics": [
        "extractRegions"
      ]
    },
    {
      "page": "getFormatCorrect",
      "title": "getFormatCorrect",
      "topics": [
        "getFormatCorrect"
      ]
    },
    {
      "page": "getPermSpaceByFeatures",
      "title": "Get permutation space for features",
      "topics": [
        "getPermSpaceByFeatures"
      ]
    },
    {
      "page": "getPermSpaceByTxID",
      "title": "Get permutation space by specifying transcript ids",
      "topics": [
        "getPermSpaceByTxID"
      ]
    },
    {
      "page": "getPermSpaceByType",
      "title": "Get permutation space by specifying type",
      "topics": [
        "getPermSpaceByType"
      ]
    },
    {
      "page": "getPvalZscore",
      "title": "getPvalZscore",
      "topics": [
        "getPvalZscore"
      ]
    },
    {
      "page": "getStopCodon",
      "title": "getStopCodon",
      "topics": [
        "getStopCodon"
      ]
    },
    {
      "page": "getTransInfo",
      "title": "Get transcript information",
      "topics": [
        "getTransInfo"
      ]
    },
    {
      "page": "GRanges2GRangesList",
      "title": "Convert a GRanges object to a GRangesList object",
      "topics": [
        "GRanges2GRangesList"
      ]
    },
    {
      "page": "GRangesList2GRanges",
      "title": "Convert a GRangesList object to a GRanges object",
      "topics": [
        "GRangesList2GRanges"
      ]
    },
    {
      "page": "overlapCountsTx",
      "title": "Evaluation function",
      "topics": [
        "overlapCountsTx"
      ]
    },
    {
      "page": "overlapCountsTxIA",
      "title": "Evaluation function",
      "topics": [
        "overlapCountsTxIA"
      ]
    },
    {
      "page": "overlapWidthTx",
      "title": "Evaluation function",
      "topics": [
        "overlapWidthTx"
      ]
    },
    {
      "page": "permTestTx",
      "title": "Perform permutation test",
      "topics": [
        "permTestTx"
      ]
    },
    {
      "page": "permTestTx_customAll",
      "title": "Perform permutation test",
      "topics": [
        "permTestTx_customAll"
      ]
    },
    {
      "page": "permTestTx_customPick",
      "title": "Perform permutation test",
      "topics": [
        "permTestTx_customPick"
      ]
    },
    {
      "page": "permTestTxIA",
      "title": "Perform permutation test",
      "topics": [
        "permTestTxIA"
      ]
    },
    {
      "page": "permTestTxIA_customPick",
      "title": "Perform permutation test",
      "topics": [
        "permTestTxIA_customPick"
      ]
    },
    {
      "page": "plotPermResults",
      "title": "Plot permutation test results",
      "topics": [
        "plotPermResults"
      ]
    },
    {
      "page": "plotShiftedZScoreTx",
      "title": "Plot shifted z scores",
      "topics": [
        "plotShiftedZScoreTx"
      ]
    },
    {
      "page": "randomizeFeaturesTx",
      "title": "Randomize features into transcriptome",
      "topics": [
        "randomizeFeaturesTx"
      ]
    },
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      "title": "Randomize features into transcriptome",
      "topics": [
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      ]
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      "title": "Randomize features into transcriptome",
      "topics": [
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      ]
    },
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      "page": "randomizeTx",
      "title": "Get randmized regions over transcriptome",
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      "topics": [
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      ]
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      "page": "shiftTx",
      "title": "Shift over transcripts",
      "topics": [
        "shiftTx"
      ]
    },
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      "page": "vector2GRangesList",
      "title": "vector2GRangesList",
      "topics": [
        "vector2GRangesList"
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