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  "Date": "2024-04-23",
  "Title": "CNE Detection and Visualization",
  "Description": "Large-scale identification and advanced visualization of\nsets of conserved noncoding elements.",
  "Author": "Ge Tan <ge_tan@live.com>",
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  "Date/Publication": "2026-04-28 12:38:38 UTC",
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    "axtInfo",
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    "binRangesFromCoordRange",
    "binRestrictionString",
    "blatCNE",
    "ceScan",
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    "lastal",
    "lastz",
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    "makeCNEDensity",
    "makeGRBs",
    "matchDistribution",
    "N50",
    "N90",
    "netToAxt",
    "plotCNEDistribution",
    "plotCNEWidth",
    "psubAxt",
    "queryRanges",
    "querySeqs",
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    "read.rmskFasta",
    "readAncora",
    "readAncoraIntoSQLite",
    "readAxt",
    "readBed",
    "readCNERangesFromSQLite",
    "reverseCigar",
    "saveCNEToSQLite",
    "score",
    "scoringMatrix",
    "second",
    "seqinfo",
    "seqnames",
    "strand",
    "subAxt",
    "summary",
    "swap",
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    "syntenicDotplot",
    "targetRanges",
    "targetSeqs",
    "thresholds",
    "unique",
    "writeAxt"
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      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
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      "name": "CNEDanRer10Hg38",
      "title": "CNEHg38DanRer10 and CNEDanRer10Hg38 dataset",
      "object": "CNEDanRer10Hg38",
      "file": "CNEDanRer10Hg38.rda",
      "class": [
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      "fields": [],
      "table": false,
      "tojson": false
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      "name": "cneFinalListDanRer10Hg38",
      "title": "cneFinalListDanRer10Hg38 dataset",
      "object": "cneFinalListDanRer10Hg38",
      "file": "cneFinalListDanRer10Hg38.rda",
      "class": [
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      "table": false,
      "tojson": false
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      "name": "CNEHg38DanRer10",
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      "object": "CNEHg38DanRer10",
      "file": "CNEHg38DanRer10.rda",
      "class": [
        "list"
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      "table": false,
      "tojson": false
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      "class": [
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      "table": false,
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      "name": "refGenes",
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      "table": false,
      "tojson": false
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      "topics": [
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      "title": "Example data for plotting annotation.",
      "topics": [
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        "cpgIslands",
        "refGenes"
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    {
      "page": "Axt-class",
      "title": "Class '\"Axt\"'",
      "topics": [
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        "Axt-class",
        "c,Axt-method",
        "length,Axt-method",
        "queryRanges",
        "queryRanges,Axt-method",
        "querySeqs",
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      "topics": [
        "axtInfo"
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      "topics": [
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        "binRangesFromCoordRange",
        "binRestrictionString"
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    {
      "page": "blatCNE",
      "title": "Wrapper function of blat for 'CNE' object",
      "topics": [
        "blatCNE"
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    {
      "page": "ceScan-methods",
      "title": "ceScan function",
      "topics": [
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        "ceScan,Axt-method",
        "ceScan,CNE-method"
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    {
      "page": "chainMergeSort",
      "title": "chainMergeSort",
      "topics": [
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    },
    {
      "page": "chainNetSyntenic",
      "title": "chainNetSyntenic",
      "topics": [
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    },
    {
      "page": "chainPreNet",
      "title": "chainPreNet",
      "topics": [
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    {
      "page": "CNE-class",
      "title": "Class '\"CNE\"'",
      "topics": [
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        "CNE-class",
        "CNE12",
        "CNE12,CNE-method",
        "CNE21",
        "CNE21,CNE-method",
        "CNEFinal",
        "CNEFinal,CNE-method",
        "CNEMerged",
        "CNEMerged,CNE-method",
        "thresholds",
        "thresholds,CNE-method"
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    {
      "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": [
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        "matchDistribution,Axt-method"
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    },
    {
      "page": "AssemblyStats",
      "title": "Assembly statistics.",
      "topics": [
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        "N90"
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      "page": "netToAxt",
      "title": "netToAxt",
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      "page": "orgKEGGIds2EntrezIDs",
      "title": "Fetch mapping from KEGG IDs to Entrez IDs",
      "topics": [
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    {
      "page": "plotCNEDistribution",
      "title": "Plot sequential CNE number against CNE genomic location",
      "topics": [
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    },
    {
      "page": "plotCNEWidth",
      "title": "Plot the CNE widths distribution",
      "topics": [
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    {
      "page": "psubAxt",
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    {
      "page": "queryCNEData",
      "title": "Query the CNEData package to fetch the CNEs",
      "topics": [
        "queryCNEData"
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    },
    {
      "page": "read.rmMask.GRanges",
      "title": "Read a RepeatMasker .out file",
      "topics": [
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    },
    {
      "page": "read.rmskFasta",
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      "topics": [
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    {
      "page": "readAncora",
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      "page": "readAncoraIntoSQLite",
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      "page": "readAxt",
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      "page": "readBed",
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      "page": "readCNERangesFromSQLite",
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      "page": "scoringMatrix",
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      "page": "syntenicDotplot",
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      "page": "writeAxt",
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