{
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  "Package": "ncRNAtools",
  "Type": "Package",
  "Title": "An R toolkit for non-coding RNA",
  "Version": "1.23.2",
  "Date": "2021-06-27",
  "Authors@R": "c(\nperson(\"Lara\", \"Selles Vidal\", email = \"lara.selles@oist.jp\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0003-2537-6824\")),\nperson(\"Rafael\", \"Ayala\", email = \"rafael.ayala@oist.jp\", role = \"aut\", comment = c(ORCID = \"0000-0002-9332-4623\")),\nperson(\"Guy-Bart\", \"Stan\", email = \"g.stan@imperial.ac.uk\", role = \"aut\", comment = c(ORCID = \"0000-0002-5560-902X\")),\nperson(\"Rodrigo\", \"Ledesma-Amaro\", email = \"r.ledesma-amaro@imperial.ac.uk\", role = \"aut\", comment = c(ORCID = \"0000-0003-2631-5898\")))",
  "Description": "ncRNAtools provides a set of basic tools for handling and\nanalyzing non-coding RNAs. These include tools to access the\nRNAcentral database and to predict and visualize the secondary\nstructure of non-coding RNAs. The package also provides tools\nto read, write and interconvert the file formats most commonly\nused for representing such secondary structures.",
  "License": "GPL-3",
  "VignetteBuilder": "knitr",
  "biocViews": "FunctionalGenomics, DataImport, ThirdPartyClient,\nVisualization, StructuralPrediction",
  "NeedsCompilation": "no",
  "Encoding": "UTF-8",
  "BugReports": "https://github.com/LaraSellesVidal/ncRNAtools/issues",
  "Config/pak/sysreqs": "libxml2-dev libssl-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-30 02:16:32 UTC",
  "RemoteUrl": "https://github.com/bioc/ncRNAtools",
  "RemoteRef": "HEAD",
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  "Packaged": {
    "Date": "2026-06-20 06:18:11 UTC",
    "User": "root"
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  "_expires": "2026-10-13T00:00:00.000Z",
  "_created": "2026-06-20T06:18:11.000Z",
  "_published": "2026-07-05T00:00:05.168Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 4
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    "author": "LaraSellesVidal <lara.selles@oist.jp>",
    "committer": "LaraSellesVidal <lara.selles@oist.jp>",
    "message": "fix bugs\n",
    "time": 1777515392
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    "email": "lara.selles@oist.jp",
    "login": "larasellesvidal",
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    "thirdpartyclient",
    "visualization",
    "structuralprediction"
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  "_stars": 1,
  "_userbio": {
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    "type": "organization",
    "name": "Bioconductor",
    "followers": 440,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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  "_realowner": "bioc",
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  "_exports": [
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    "flattenDotBracket",
    "generatePairsProbabilityMatrix",
    "pairsToSecondaryStructure",
    "plotCompositePairsMatrix",
    "plotPairsProbabilityMatrix",
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    "rnaCentralRetrieveEntry",
    "rnaCentralTextSearch",
    "writeCT",
    "writeDotBracket"
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    {
      "page": "findPairedBases",
      "title": "Determines paired bases from secondary structure string",
      "topics": [
        "findPairedBases"
      ]
    },
    {
      "page": "flattenDotBracket",
      "title": "Converts an extended Dot-Bracket secondary structure to basic Dot-Bracket notation",
      "topics": [
        "flattenDotBracket"
      ]
    },
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      "title": "Generates a matrix of base pair probabilities",
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      ]
    },
    {
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      "title": "Generates a string with the secondary structure of an RNA sequence",
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        "pairsToSecondaryStructure"
      ]
    },
    {
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      "title": "Plots a composite matrix of base pair probabilities and paired bases",
      "topics": [
        "plotCompositePairsMatrix"
      ]
    },
    {
      "page": "plotPairsProbabilityMatrix",
      "title": "Plots a matrix of base pair probabilities",
      "topics": [
        "plotPairsProbabilityMatrix"
      ]
    },
    {
      "page": "predictAlternativeSecondaryStructures",
      "title": "Predicts alternative secondary structures of a given RNA sequence",
      "topics": [
        "predictAlternativeSecondaryStructures"
      ]
    },
    {
      "page": "predictSecondaryStructure",
      "title": "Predicts the secondary structure of a given RNA sequence",
      "topics": [
        "predictSecondaryStructure"
      ]
    },
    {
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      "title": "Reads a file with the secondary structure of an RNA in the CT format",
      "topics": [
        "readCT"
      ]
    },
    {
      "page": "readDotBracket",
      "title": "Reads a file with the sequence and secondary structure of an RNA in the Dot-Bracket format",
      "topics": [
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      ]
    },
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      "topics": [
        "rnaCentralGenomicCoordinatesSearch"
      ]
    },
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      "topics": [
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      ]
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      "title": "Searches the RNAcentral database with a text query",
      "topics": [
        "rnaCentralTextSearch"
      ]
    },
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      "title": "Writes a file with the secondary structure of an RNA in the CT format",
      "topics": [
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      ]
    },
    {
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      "title": "Writes a file with the sequence and secondary structure of an RNA in the Dot-Bracket format",
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      ]
    }
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