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  "Title": "Insertion/Deletion Dynamics for Transposable Elements",
  "License": "MIT + file LICENSE",
  "Description": "Provides functions to estimate the insertion and deletion\nrates of transposable element (TE) families. The estimation of\ninsertion rate consists of an improved estimate of the age\ndistribution that takes into account random mutations, and an\nadjustment by the deletion rate. A hypothesis test for a\nuniform insertion rate is also implemented. This package\nimplements the methods proposed in Dai et al (2018).",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-05 08:51:47 UTC",
    "User": "root"
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  "Author": "Xiongtao Dai [aut, cre, cph], Hao Wang [aut], Jan Dvorak [ctb],\nJeffrey Bennetzen [ctb], Hans-Georg Mueller [ctb]",
  "Maintainer": "Xiongtao Dai <xdai@iastate.edu>",
  "Repository": "https://xdaiisu.r-universe.dev",
  "Date/Publication": "2018-08-22 18:40:06 UTC",
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    "MasterGene",
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    "nbLackOfFitKL",
    "PlotFamilies",
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  ],
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      ],
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        "Chr",
        "Start",
        "Stop",
        "GroupID",
        "sup",
        "recRt5",
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        "data.frame"
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      "page": "AetLTR",
      "title": "LTR retrotransposons in _Aegilops tauschii_",
      "topics": [
        "AetLTR"
      ]
    },
    {
      "page": "AlyLTR",
      "title": "LTR retrotransposons in _Arabidopsis lyrata_",
      "topics": [
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      ]
    },
    {
      "page": "EstDynamics",
      "title": "Estimate TE dynamics using mismatch data",
      "topics": [
        "EstDynamics",
        "EstDynamics2"
      ]
    },
    {
      "page": "MasterGene",
      "title": "Implements the master gene model in Marchani et al (2009)",
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        "MasterGene"
      ]
    },
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        "MatrixModel"
      ]
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      "topics": [
        "nbLackOfFitKL"
      ]
    },
    {
      "page": "PlotFamilies",
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      "topics": [
        "PlotFamilies"
      ]
    },
    {
      "page": "print.TEfit",
      "title": "Print a TEfit or TEfit2 object",
      "topics": [
        "print.TEfit",
        "print.TEfit2"
      ]
    },
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      "title": "Generate sensitivity plots",
      "topics": [
        "SensitivityPlot"
      ]
    },
    {
      "page": "TE",
      "title": "TE: Insertion/Deletion Dynamics for Transposable Elements",
      "topics": [
        "TE-package",
        "TE"
      ]
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