{
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  "Package": "R4RNA",
  "Type": "Package",
  "Title": "An R package for RNA visualization and analysis",
  "Version": "1.41.0",
  "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/",
  "NeedsCompilation": "no",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:09 UTC",
  "RemoteUrl": "https://github.com/bioc/R4RNA",
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    "dataimport",
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "alignmentPercentGaps",
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    "basepairCanonical",
    "basepairConservation",
    "basepairCovariation",
    "basepairFrequency",
    "blankPlot",
    "collapseHelix",
    "colourByBasepairFrequency",
    "colourByCanonical",
    "colourByConservation",
    "colourByCount",
    "colourByCovariation",
    "colourByUnknottedGroups",
    "colourByValue",
    "defaultPalette",
    "expandHelix",
    "helixCanonical",
    "helixConservation",
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    "helixToBpseq",
    "helixToConnect",
    "helixToVienna",
    "is.helix",
    "isConflictingHelix",
    "isDuplicatingHelix",
    "isOverlappingHelix",
    "logceiling",
    "logfloor",
    "logseq",
    "maxHeight",
    "plotArc",
    "plotArcs",
    "plotCovariance",
    "plotDoubleCovariance",
    "plotDoubleHelix",
    "plotHelix",
    "plotOverlapCovariance",
    "plotOverlapHelix",
    "readBpseq",
    "readConnect",
    "readHelix",
    "readVienna",
    "structureMismatchScore",
    "unknottedGroups",
    "viennaToHelix",
    "writeHelix"
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      "title": "Helices predicted by TRANSAT with p-values",
      "object": "helix",
      "file": "helix.RData",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
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      "name": "helix",
      "title": "Helices predicted by TRANSAT with p-values",
      "object": "helix",
      "file": "helix.RData",
      "class": [
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      ],
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        "j",
        "length",
        "value"
      ],
      "rows": 56,
      "table": true,
      "tojson": true
    },
    {
      "name": "known",
      "title": "Helices predicted by TRANSAT with p-values",
      "object": "helix",
      "file": "helix.RData",
      "class": [
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      ],
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      "rows": 60,
      "table": true,
      "tojson": true
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  "_help": [
    {
      "page": "R4RNA-package",
      "title": "An R package for RNA visualization and analysis",
      "topics": [
        "R4RNA-package",
        "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": [
        "basepairFrequency"
      ]
    },
    {
      "page": "expandCollapseHelix",
      "title": "Expand or collapse helices to and from basepairs",
      "topics": [
        "collapseHelix",
        "expandHelix"
      ]
    },
    {
      "page": "as.helix",
      "title": "Coerce to a Helix Data Frame",
      "topics": [
        "as.helix",
        "is.helix",
        "parseBracket"
      ]
    },
    {
      "page": "colourHelices",
      "title": "Assign colours to helices",
      "topics": [
        "colourByBasepairFrequency",
        "colourByCanonical",
        "colourByConservation",
        "colourByCount",
        "colourByCovariation",
        "colourByUnknottedGroups",
        "colourByValue",
        "defaultPalette"
      ]
    },
    {
      "page": "viennaToHelix",
      "title": "Convert helix structures to and from other formats",
      "topics": [
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        "helixToConnect",
        "helixToVienna",
        "viennaToHelix"
      ]
    },
    {
      "page": "plotCovariance",
      "title": "Plot nucleotide sequence coloured by covariance",
      "topics": [
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        "plotDoubleCovariance",
        "plotOverlapCovariance"
      ]
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    {
      "page": "blankPlot",
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      "topics": [
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        "maxHeight"
      ]
    },
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      "title": "Helices predicted by TRANSAT with p-values",
      "topics": [
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        "helix",
        "known"
      ]
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      "title": "Partition basepairs into unknotted groups",
      "topics": [
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      ]
    },
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      "title": "Logical filters of helix by type",
      "topics": [
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        "isDuplicatingHelix",
        "isOverlappingHelix"
      ]
    },
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      "title": "Log base 10 sequence, floor and ceiling",
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        "logfloor",
        "logseq"
      ]
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      "topics": [
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        "plotArcs",
        "plotDoubleHelix",
        "plotHelix",
        "plotOverlapHelix"
      ]
    },
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      "title": "Read secondary structure file",
      "topics": [
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        "readConnect",
        "readHelix",
        "readVienna"
      ]
    },
    {
      "page": "structureMismatchScore",
      "title": "Scores how a basepair structure fits a sequence",
      "topics": [
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      ]
    },
    {
      "page": "writeHelix",
      "title": "Write out a helix data frame into a text file",
      "topics": [
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      ]
    }
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