{
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  "Package": "R4RNA",
  "Type": "Package",
  "Title": "An R package for RNA visualization and analysis",
  "Version": "1.40.0",
  "Date": "2015-11-02",
  "Author": "Daniel Lai, Irmtraud Meyer <irmtraud.meyer@cantab.net>",
  "Maintainer": "Daniel Lai <jujubix@cs.ubc.ca>",
  "Description": "A package for RNA basepair analysis, including the\nvisualization of basepairs as arc diagrams for easy comparison\nand annotation of sequence and structure.  Arc diagrams can\nadditionally be projected onto multiple sequence alignments to\nassess basepair conservation and covariation, with numerical\nmethods for computing statistics for each.",
  "License": "GPL-3",
  "biocViews": "Alignment, MultipleSequenceAlignment, Preprocessing,\nVisualization, DataImport, DataRepresentation,\nMultipleComparison",
  "URL": "http://www.e-rna.org/r-chie/",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:09 UTC",
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    "helixConservation",
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    "helixToVienna",
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    "isConflictingHelix",
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    "isOverlappingHelix",
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    "logseq",
    "maxHeight",
    "plotArc",
    "plotArcs",
    "plotCovariance",
    "plotDoubleCovariance",
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    "plotOverlapCovariance",
    "plotOverlapHelix",
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    "readVienna",
    "structureMismatchScore",
    "unknottedGroups",
    "viennaToHelix",
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      "title": "Helices predicted by TRANSAT with p-values",
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      "title": "Helices predicted by TRANSAT with p-values",
      "object": "helix",
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        "length",
        "value"
      ],
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      "table": true,
      "tojson": true
    },
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      "title": "Helices predicted by TRANSAT with p-values",
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    {
      "page": "R4RNA-package",
      "title": "An R package for RNA visualization and analysis",
      "topics": [
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        "R4RNA"
      ]
    },
    {
      "page": "alignmentStatistics",
      "title": "Compute statistics for a multiple sequence alignments",
      "topics": [
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        "alignmentConservation",
        "alignmentCovariation",
        "alignmentPercentGaps",
        "baseConservation",
        "basepairCanonical",
        "basepairConservation",
        "basepairCovariation",
        "helixCanonical",
        "helixConservation",
        "helixCovariation"
      ]
    },
    {
      "page": "basepairFrequency",
      "title": "Calculates the frequency of each basepair",
      "topics": [
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      ]
    },
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        "expandHelix"
      ]
    },
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      "page": "as.helix",
      "title": "Coerce to a Helix Data Frame",
      "topics": [
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        "is.helix",
        "parseBracket"
      ]
    },
    {
      "page": "colourHelices",
      "title": "Assign colours to helices",
      "topics": [
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        "colourByCanonical",
        "colourByConservation",
        "colourByCount",
        "colourByCovariation",
        "colourByUnknottedGroups",
        "colourByValue",
        "defaultPalette"
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    },
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      "title": "Convert helix structures to and from other formats",
      "topics": [
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        "helixToConnect",
        "helixToVienna",
        "viennaToHelix"
      ]
    },
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      "topics": [
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        "plotDoubleCovariance",
        "plotOverlapCovariance"
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        "maxHeight"
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    },
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      "title": "Helices predicted by TRANSAT with p-values",
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        "helix",
        "known"
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      "topics": [
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      ]
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        "isDuplicatingHelix",
        "isOverlappingHelix"
      ]
    },
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        "logseq"
      ]
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        "plotArcs",
        "plotDoubleHelix",
        "plotHelix",
        "plotOverlapHelix"
      ]
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        "readConnect",
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        "readVienna"
      ]
    },
    {
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      ]
    },
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      ]
    }
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