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  "Title": "Secondary Structure Plotting for RNA",
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  "Date": "2024-04-24",
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  "Description": "Functions for creating and manipulating RNA secondary\nstructure plots.",
  "License": "GPL-3",
  "Repository": "https://jlp-bioinf.r-universe.dev",
  "Date/Publication": "2024-04-24 20:42:19 UTC",
  "RemoteUrl": "https://github.com/jlp-bioinf/rrna",
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    "User": "root"
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  "Author": "Jim Maher [ths],\nJP Bida [aut, cre],\nJonathan Price [ctb] (ORCID: <https://orcid.org/0000-0001-6554-5667>)",
  "Maintainer": "JP Bida <bida.john@gmail.com>",
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    "description": "Bioinformatician "
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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  "_realowner": "jlp-bioinf",
  "_cranurl": true,
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      "date": "2015-07-29"
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      "date": "2024-05-15"
    },
    {
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      "date": "2024-07-10"
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    "addBreaks",
    "alignCoord",
    "aptPlotCT",
    "backward",
    "bplfile",
    "circleCoord",
    "coord2comp",
    "ct2coord",
    "ct2knet",
    "ct2ss",
    "forward",
    "genCords",
    "genDB",
    "loadCoords",
    "loadCt",
    "loopLength",
    "makeCt",
    "pairScores",
    "pseudoKnot",
    "RNAPlot",
    "rotateS",
    "rotateV",
    "stemCords",
    "transformFold",
    "translate",
    "validCT"
  ],
  "_help": [
    {
      "page": "RRNA-package",
      "title": "RNA secondary structure ploting",
      "topics": [
        "RRNA-package",
        "RRNA"
      ]
    },
    {
      "page": "addBreaks",
      "title": "Internal Function - labels RNA structures taken from PDB with gaps in nucleotide sequences",
      "topics": [
        "addBreaks"
      ]
    },
    {
      "page": "alignCoord",
      "title": "Alignment of secondary structure folds to 2 nucleotides.",
      "topics": [
        "alignCoord"
      ]
    },
    {
      "page": "aptPlotCT",
      "title": "RNA secondary structure plotting from CT files",
      "topics": [
        "aptPlotCT"
      ]
    },
    {
      "page": "backward",
      "title": "Internal function for moving through secondary structures",
      "topics": [
        "backward"
      ]
    },
    {
      "page": "bplfile",
      "title": "Creates a bpl file from a coordinate file",
      "topics": [
        "bplfile"
      ]
    },
    {
      "page": "circleCoord",
      "title": "Internal function for finding the coordinates of NT's in a circle",
      "topics": [
        "circleCoord"
      ]
    },
    {
      "page": "coord2comp",
      "title": "Generates secondary structure components from a coordinate file",
      "topics": [
        "coord2comp"
      ]
    },
    {
      "page": "ct2coord",
      "title": "Generate coordinate file",
      "topics": [
        "ct2coord"
      ]
    },
    {
      "page": "ct2knet",
      "title": "creates a knet file from a CT file",
      "topics": [
        "ct2knet"
      ]
    },
    {
      "page": "ct2ss",
      "title": "Generates secondary structure components from a coordinate file",
      "topics": [
        "ct2ss"
      ]
    },
    {
      "page": "forward",
      "title": "Internal function for moving through secondary structures",
      "topics": [
        "forward"
      ]
    },
    {
      "page": "fuzzy2comp",
      "title": "Generate components from hydrogen bond data extracted from a PDB file using RSIM.",
      "topics": [
        "fuzzy2comp"
      ]
    },
    {
      "page": "fuzzy2ct",
      "title": "Convert hydrogen bond data from RSIM 3D RNA structure into 2D secondary structures",
      "topics": [
        "fuzzy2ct"
      ]
    },
    {
      "page": "genCords",
      "title": "Internal function that generates coordinates for a given loop starting and stopping at p1 and p2 respectfully",
      "topics": [
        "genCords"
      ]
    },
    {
      "page": "genDB",
      "title": "Internal Function for creating component database",
      "topics": [
        "genDB"
      ]
    },
    {
      "page": "loadCoords",
      "title": "Loads a coordinate file into a data frame",
      "topics": [
        "loadCoords"
      ]
    },
    {
      "page": "loadCt",
      "title": "Loads a CT file into an R data frame",
      "topics": [
        "loadCt"
      ]
    },
    {
      "page": "loopLength",
      "title": "internal function that determines the length of a loop",
      "topics": [
        "loopLength"
      ]
    },
    {
      "page": "makeCt",
      "title": "make a CT file from a structure and sequence",
      "topics": [
        "makeCt"
      ]
    },
    {
      "page": "pairScores",
      "title": "Identifies base-pairs from hydrogen bonding data",
      "topics": [
        "pairScores"
      ]
    },
    {
      "page": "pseudoKnot",
      "title": "removes pseudoknots from a ct file",
      "topics": [
        "pseudoKnot"
      ]
    },
    {
      "page": "RNAPlot",
      "title": "Generic RNA Secondary Structure Plotting Function",
      "topics": [
        "RNAPlot"
      ]
    },
    {
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      "title": "Internal function to rotate a single point",
      "topics": [
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      ]
    },
    {
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      "title": "internal function to rotate a vector of points",
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        "rotateV"
      ]
    },
    {
      "page": "stemCords",
      "title": "internal function that generates coordinates for a stem",
      "topics": [
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      ]
    },
    {
      "page": "transformFold",
      "title": "Internal function to translate and rotate a secondary structure plot",
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      ]
    },
    {
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      "topics": [
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      ]
    },
    {
      "page": "validCT",
      "title": "Validate a CT File",
      "topics": [
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      ]
    }
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