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        "key": "XVector::_set_XVectorList_names()",
        "hash": "55c0d367bcabfa54"
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  },
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/CNEr.html",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/ge11232002/cner",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "Axt",
    "axtChain",
    "axtInfo",
    "binFromCoordRange",
    "binRangesFromCoordRange",
    "binRestrictionString",
    "blatCNE",
    "ceScan",
    "chainMergeSort",
    "chainNetSyntenic",
    "chainPreNet",
    "CNE",
    "CNE12",
    "CNE21",
    "CNEDensity",
    "CNEFinal",
    "cneMerge",
    "CNEMerged",
    "fetchChromSizes",
    "first",
    "fixCoordinates",
    "GRangePairs",
    "grglist",
    "last",
    "lastal",
    "lastz",
    "lavToPsl",
    "makeAncoraFiles",
    "makeAxtTracks",
    "makeCNEDensity",
    "makeGRBs",
    "matchDistribution",
    "N50",
    "N90",
    "netToAxt",
    "plotCNEDistribution",
    "plotCNEWidth",
    "psubAxt",
    "queryRanges",
    "querySeqs",
    "read.rmMask.GRanges",
    "read.rmskFasta",
    "readAncora",
    "readAncoraIntoSQLite",
    "readAxt",
    "readBed",
    "readCNERangesFromSQLite",
    "reverseCigar",
    "saveCNEToSQLite",
    "score",
    "scoringMatrix",
    "second",
    "seqinfo",
    "seqnames",
    "strand",
    "subAxt",
    "summary",
    "swap",
    "symCount",
    "syntenicDotplot",
    "targetRanges",
    "targetSeqs",
    "thresholds",
    "unique",
    "writeAxt"
  ],
  "_datasets": [
    {
      "name": "axisTrack",
      "title": "Example data for plotting annotation.",
      "object": "axisTrack",
      "file": "axisTrack.rda",
      "class": [
        "GenomeAxisTrack"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "CNEDanRer10Hg38",
      "title": "CNEHg38DanRer10 and CNEDanRer10Hg38 dataset",
      "object": "CNEDanRer10Hg38",
      "file": "CNEDanRer10Hg38.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "cneFinalListDanRer10Hg38",
      "title": "cneFinalListDanRer10Hg38 dataset",
      "object": "cneFinalListDanRer10Hg38",
      "file": "cneFinalListDanRer10Hg38.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "CNEHg38DanRer10",
      "title": "CNEHg38DanRer10 and CNEDanRer10Hg38 dataset",
      "object": "CNEHg38DanRer10",
      "file": "CNEHg38DanRer10.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "cpgIslands",
      "title": "Example data for plotting annotation.",
      "object": "cpgIslands",
      "file": "cpgIslands.rda",
      "class": [
        "AnnotationTrack"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "grangesPairsForDotplot",
      "title": "grangesPairsForDotplot",
      "object": "grangesPairsForDotplot",
      "file": "grangesPairsForDotplot.rda",
      "class": [
        "GRangePairs"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "refGenes",
      "title": "Example data for plotting annotation.",
      "object": "refGenes",
      "file": "refGenes.rda",
      "class": [
        "GeneRegionTrack"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "addAncestorGO",
      "title": "Add ancestor GO IDs",
      "topics": [
        "addAncestorGO"
      ]
    },
    {
      "page": "axisTrack",
      "title": "Example data for plotting annotation.",
      "topics": [
        "axisTrack",
        "cpgIslands",
        "refGenes"
      ]
    },
    {
      "page": "Axt-class",
      "title": "Class '\"Axt\"'",
      "topics": [
        "Axt",
        "Axt-class",
        "c,Axt-method",
        "length,Axt-method",
        "queryRanges",
        "queryRanges,Axt-method",
        "querySeqs",
        "querySeqs,Axt-method",
        "score,Axt-method",
        "symCount",
        "symCount,Axt-method",
        "targetRanges",
        "targetRanges,Axt-method",
        "targetSeqs",
        "targetSeqs,Axt-method",
        "[,Axt,ANY,ANY-method"
      ]
    },
    {
      "page": "axtChain",
      "title": "axtChain",
      "topics": [
        "axtChain"
      ]
    },
    {
      "page": "axtInfo",
      "title": "axtInfo function",
      "topics": [
        "axtInfo"
      ]
    },
    {
      "page": "binner",
      "title": "UCSC bin indexing system utility functions",
      "topics": [
        "binFromCoordRange",
        "binRangesFromCoordRange",
        "binRestrictionString"
      ]
    },
    {
      "page": "blatCNE",
      "title": "Wrapper function of blat for 'CNE' object",
      "topics": [
        "blatCNE"
      ]
    },
    {
      "page": "ceScan-methods",
      "title": "ceScan function",
      "topics": [
        "ceScan",
        "ceScan,Axt-method",
        "ceScan,CNE-method"
      ]
    },
    {
      "page": "chainMergeSort",
      "title": "chainMergeSort",
      "topics": [
        "chainMergeSort"
      ]
    },
    {
      "page": "chainNetSyntenic",
      "title": "chainNetSyntenic",
      "topics": [
        "chainNetSyntenic"
      ]
    },
    {
      "page": "chainPreNet",
      "title": "chainPreNet",
      "topics": [
        "chainPreNet"
      ]
    },
    {
      "page": "CNE-class",
      "title": "Class '\"CNE\"'",
      "topics": [
        "CNE",
        "CNE-class",
        "CNE12",
        "CNE12,CNE-method",
        "CNE21",
        "CNE21,CNE-method",
        "CNEFinal",
        "CNEFinal,CNE-method",
        "CNEMerged",
        "CNEMerged,CNE-method",
        "thresholds",
        "thresholds,CNE-method"
      ]
    },
    {
      "page": "CNEDanRer10Hg38",
      "title": "CNEHg38DanRer10 and CNEDanRer10Hg38 dataset",
      "topics": [
        "CNEDanRer10Hg38",
        "CNEHg38DanRer10"
      ]
    },
    {
      "page": "CNEDensity",
      "title": "CNEDensity function",
      "topics": [
        "CNEDensity",
        "CNEDensity,ANY,character,character,missing,missing-method",
        "CNEDensity,ANY,missing,character,character,character-method",
        "CNEDensity-methods"
      ]
    },
    {
      "page": "cneFinalListDanRer10Hg38",
      "title": "cneFinalListDanRer10Hg38 dataset",
      "topics": [
        "cneFinalListDanRer10Hg38"
      ]
    },
    {
      "page": "cneMerge",
      "title": "CNE merge function",
      "topics": [
        "cneMerge",
        "cneMerge,CNE,missing-method",
        "cneMerge,GRangePairs,GRangePairs-method"
      ]
    },
    {
      "page": "fetchChromSizes",
      "title": "fetchChromSizes function.",
      "topics": [
        "fetchChromSizes"
      ]
    },
    {
      "page": "fixCoordinates",
      "title": "Fix the coordinates in 'Axt' object",
      "topics": [
        "fixCoordinates",
        "fixCoordinates,Axt-method"
      ]
    },
    {
      "page": "GRangePairs-class",
      "title": "GRangePairs objects",
      "topics": [
        "c,GRangePairs-method",
        "class:GRangePairs",
        "coerce,GRangePairs,GRanges-method",
        "coerce,GRangePairs,GRangesList-method",
        "first,GRangePairs-method",
        "GRangePairs",
        "GRangePairs-class",
        "grglist,GRangePairs-method",
        "last",
        "last,GRangePairs-method",
        "second,GRangePairs-method",
        "seqinfo,GRangePairs-method",
        "seqnames,GRangePairs-method",
        "strand,GRangePairs-method",
        "swap",
        "swap,GRangePairs-method",
        "unique,GRangePairs-method",
        "unlist,GRangePairs-method"
      ]
    },
    {
      "page": "grangesPairsForDotplot",
      "title": "grangesPairsForDotplot",
      "topics": [
        "grangesPairsForDotplot"
      ]
    },
    {
      "page": "last",
      "title": "lastal wrapper",
      "topics": [
        "lastal"
      ]
    },
    {
      "page": "lastz",
      "title": "lastz wrapper",
      "topics": [
        "lastz"
      ]
    },
    {
      "page": "lavToPsl",
      "title": "lavToPsl",
      "topics": [
        "lavToPsl"
      ]
    },
    {
      "page": "makeAncoraFiles",
      "title": "makeAncoraFiles",
      "topics": [
        "makeAncoraFiles"
      ]
    },
    {
      "page": "makeAxtTracks",
      "title": "makeAxtTracks",
      "topics": [
        "makeAxtTracks"
      ]
    },
    {
      "page": "makeCNEDensity",
      "title": "Make 'Bed', 'bedGraph' and 'BigWig' files",
      "topics": [
        "makeCNEDensity"
      ]
    },
    {
      "page": "makeGRBs",
      "title": "makeGRBs",
      "topics": [
        "makeGRBs"
      ]
    },
    {
      "page": "matchDistribution",
      "title": "Plot the distribution of matched alignments.",
      "topics": [
        "matchDistribution",
        "matchDistribution,Axt-method"
      ]
    },
    {
      "page": "AssemblyStats",
      "title": "Assembly statistics.",
      "topics": [
        "N50",
        "N90"
      ]
    },
    {
      "page": "netToAxt",
      "title": "netToAxt",
      "topics": [
        "netToAxt"
      ]
    },
    {
      "page": "orgKEGGIds2EntrezIDs",
      "title": "Fetch mapping from KEGG IDs to Entrez IDs",
      "topics": [
        "orgKEGGIds2EntrezIDs"
      ]
    },
    {
      "page": "plotCNEDistribution",
      "title": "Plot sequential CNE number against CNE genomic location",
      "topics": [
        "plotCNEDistribution"
      ]
    },
    {
      "page": "plotCNEWidth",
      "title": "Plot the CNE widths distribution",
      "topics": [
        "plotCNEWidth"
      ]
    },
    {
      "page": "psubAxt",
      "title": "Parallel subset of Axt alignment",
      "topics": [
        "psubAxt"
      ]
    },
    {
      "page": "queryCNEData",
      "title": "Query the CNEData package to fetch the CNEs",
      "topics": [
        "queryCNEData"
      ]
    },
    {
      "page": "read.rmMask.GRanges",
      "title": "Read a RepeatMasker .out file",
      "topics": [
        "read.rmMask.GRanges"
      ]
    },
    {
      "page": "read.rmskFasta",
      "title": "Read a soft repeat masked fasta",
      "topics": [
        "read.rmskFasta"
      ]
    },
    {
      "page": "readAncora",
      "title": "Read the cne file from Ancora format.",
      "topics": [
        "readAncora"
      ]
    },
    {
      "page": "readAncoraIntoSQLite",
      "title": "Read Ancora legacy CNE format",
      "topics": [
        "readAncoraIntoSQLite"
      ]
    },
    {
      "page": "readAxt",
      "title": "Read 'Axt' file",
      "topics": [
        "readAxt"
      ]
    },
    {
      "page": "readBed",
      "title": "Read bed file",
      "topics": [
        "readBed"
      ]
    },
    {
      "page": "readCNERangesFromSQLite",
      "title": "readCNERangesFromSQLite function",
      "topics": [
        "readCNERangesFromSQLite"
      ]
    },
    {
      "page": "reverseCigar",
      "title": "reverseCigar function",
      "topics": [
        "reverseCigar"
      ]
    },
    {
      "page": "saveCNEToSQLite",
      "title": "Save CNE to SQLite",
      "topics": [
        "saveCNEToSQLite"
      ]
    },
    {
      "page": "scoringMatrix",
      "title": "scoringMatrix",
      "topics": [
        "scoringMatrix"
      ]
    },
    {
      "page": "subAxt-methods",
      "title": "Subset an 'Axt' object",
      "topics": [
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        "subAxt,Axt,character,integer,integer-method",
        "subAxt,Axt,character,missing,missing-method",
        "subAxt,Axt,character,numeric,numeric-method",
        "subAxt,Axt,GRanges,missing,missing-method",
        "subAxt-methods"
      ]
    },
    {
      "page": "Axt-util",
      "title": "Utility functions related to Axt alignment",
      "topics": [
        "summary",
        "summary,Axt-method"
      ]
    },
    {
      "page": "syntenicDotplot",
      "title": "Syntenic dotplot",
      "topics": [
        "syntenicDotplot",
        "syntenicDotplot,Axt-method",
        "syntenicDotplot,GRangePairs-method"
      ]
    },
    {
      "page": "writeAxt",
      "title": "'writeAxt' function",
      "topics": [
        "writeAxt"
      ]
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  "_readme": "https://github.com/bioc/CNEr/raw/HEAD/README.md",
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      "source": "CNEr.Rmd",
      "filename": "CNEr.html",
      "title": "CNE identification and visualisation",
      "author": "Ge Tan",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Workflow of the package",
        "CNE identification",
        "CNE visualisation",
        "Input",
        "axt alignment file",
        "Filtering information",
        "Creating a CNE class",
        "Scan axt alignments",
        "Merge CNEs",
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        "CNE length distribution",
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        "Output of bed and bedGraph files",
        "CNEs visualisation",
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      "created": "2015-10-08 13:39:08",
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      "filename": "PairwiseWholeGenomeAlignment.html",
      "title": "Pairwise whole genome alignment",
      "author": "Ge Tan",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "Chaining:",
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      "created": "2016-02-03 21:16:33",
      "modified": "2016-10-06 13:59:20",
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