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    "alphabet.protein.gap",
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    "alphabet.rna.gap",
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    "subBoxes",
    "subLines",
    "suggestColors",
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      "page": "Alphabet",
      "title": "built alphabet",
      "topics": [
        "Alphabet"
      ]
    },
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      "title": "DNA alphabet",
      "topics": [
        "alphabet.dna"
      ]
    },
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      "title": "DNA alphabet with gaps",
      "topics": [
        "alphabet.dna.gap"
      ]
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      "title": "Amino acid alphabet",
      "topics": [
        "alphabet.protein"
      ]
    },
    {
      "page": "alphabet.protein.gap",
      "title": "Amino acid alphabet with gaps",
      "topics": [
        "alphabet.protein.gap"
      ]
    },
    {
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      "title": "RNA alphabet",
      "topics": [
        "alphabet.rna"
      ]
    },
    {
      "page": "alphabet.rna.gap",
      "title": "RNA alphabet with gaps",
      "topics": [
        "alphabet.rna.gap"
      ]
    },
    {
      "page": "colorchart",
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      ]
    },
    {
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      "title": "Rectangles of averaged colors",
      "topics": [
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      ]
    },
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      "topics": [
        "DLData"
      ]
    },
    {
      "page": "filter.by.conservation",
      "title": "Filters columns (sequence positions) by conservation",
      "topics": [
        "filter.by.conservation"
      ]
    },
    {
      "page": "filter.by.dependencies",
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      "topics": [
        "filter.by.dependencies"
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    },
    {
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      "title": "Filters columns (sequence positions) by gaps",
      "topics": [
        "filter.by.gaps"
      ]
    },
    {
      "page": "filterColumns",
      "title": "Filters data columns by some filter function",
      "topics": [
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      ]
    },
    {
      "page": "getDeps",
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      "topics": [
        "getDeps",
        "getDeps.data.frame",
        "getDeps.DLData"
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    {
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      "topics": [
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        "getPWM.DLData"
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    },
    {
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      "title": "Sequence logo",
      "topics": [
        "logo"
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    },
    {
      "page": "partition",
      "title": "Paritions data by most inter-dependent positions",
      "topics": [
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        "partition.DLData"
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    {
      "page": "plotBlocks",
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      "topics": [
        "plotBlocks",
        "plotBlocks.DLData",
        "plotBlocks.list"
      ]
    },
    {
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      ]
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        "plotDeplogo.DLData"
      ]
    },
    {
      "page": "plotDepmatrix",
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        "plotDepmatrix"
      ]
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        "replaceColors.DLData"
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        "revcom.DLData"
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      "topics": [
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      ]
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      "source": "DepLogo.Rmd",
      "filename": "DepLogo.html",
      "title": "DepLogo -- plotting dependency logos of sequence data",
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        "Dependencies and p-values",
        "Plotting dependency logos from data",
        "Tuning parameters",
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        "Adding plots of sequence weights/values",
        "Components of dependency logos and customization",
        "Visualizing pairwise dependencies",
        "Visualizing partitions of sequence data",
        "Visualizing summaries of sequence data",
        "References"
      ],
      "created": "2019-03-13 15:23:27",
      "modified": "2021-04-16 19:10:02",
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