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  "Title": "Codon Usage Analysis and Prediction of Gene Expressivity",
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  "Description": "Tool for analysis of codon usage in various unannotated or\nKEGG/COG annotated DNA sequences. Calculates different measures\nof CU bias and CU-based predictors of gene expressivity, and\nperforms gene set enrichment analysis for annotated sequences.\nImplements several methods for visualization of CU and\nenrichment analysis results.",
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  "Date/Publication": "2026-04-28 12:48:23 UTC",
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    "CAI",
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    "codonTable",
    "contable",
    "crossTab",
    "E",
    "ENC",
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    "getID",
    "getKO",
    "getlen",
    "getSeqAnnot",
    "getVariable",
    "intraBplot",
    "MCB",
    "MELP",
    "MILC",
    "readSet",
    "reduceCrossTab",
    "SCUO",
    "setCOG",
    "setKO",
    "show"
  ],
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      "name": "HD59",
      "title": "Codon usage in healthy human gut microbiome.",
      "object": "HD59",
      "class": [
        "codonTable"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
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      "title": "Codon usage based KO enrichment analysis results from the healthy human gut microbiome. For more information, see '?HD59'.",
      "object": "HD59_KO",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
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      "title": "Codon usage based KEGG Pathway enrichment analysis results from a healthy human gut microbiome. For more information, see '?HD59'.",
      "object": "HD59_PATHWAYS",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
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      "name": "LD94",
      "title": "Codon usage in human gut microbiome in liver cirrhosis.",
      "object": "LD94",
      "class": [
        "codonTable"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "LD94_KO",
      "title": "Codon usage based KO enrichment analysis results from an gut microbiome of an individual with liver cirrhosis. For more information, see '?LD94'.",
      "object": "LD94_KO",
      "class": [
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      ],
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      "table": false,
      "tojson": false
    },
    {
      "name": "LD94_PATHWAYS",
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      "object": "LD94_PATHWAYS",
      "class": [
        "AnnotatedDataFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
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  "_help": [
    {
      "page": "subset",
      "title": "Subset 'codonTable' object.",
      "topics": [
        "subset.codonTable",
        "[,codonTable-method",
        "[[,codonTable-method"
      ]
    },
    {
      "page": "bplot",
      "title": "Karlin B plot",
      "topics": [
        "Bplot",
        "Bplot,character,character,matrix-method",
        "Bplot,numeric,numeric,missing-method"
      ]
    },
    {
      "page": "codonTable-class",
      "title": "An S4 class 'codonTable'",
      "topics": [
        "codonCounts",
        "codonCounts,codonTable-method",
        "codonTable",
        "codonTable,data.frame-method",
        "codonTable,DNAStringSet-method",
        "codonTable,matrix-method",
        "codonTable-class",
        "getCOG",
        "getCOG,codonTable-method",
        "getID",
        "getID,codonTable-method",
        "getKO",
        "getKO,codonTable-method",
        "getlen",
        "getlen,codonTable-method",
        "setCOG",
        "setCOG,codonTable-method",
        "setKO",
        "setKO,codonTable-method"
      ]
    },
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      "page": "codonUsage",
      "title": "Calculate CU measures.",
      "topics": [
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        "B,codonTable-method",
        "codonUsage",
        "ENC",
        "ENC,codonTable-method",
        "ENCprime",
        "ENCprime,codonTable-method",
        "MCB",
        "MCB,codonTable-method",
        "MILC",
        "MILC,codonTable-method",
        "SCUO",
        "SCUO,codonTable-method"
      ]
    },
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      "page": "codonUsage-expressivity",
      "title": "Calculate CU expressivity measures.",
      "topics": [
        "CAI",
        "CAI,codonTable-method",
        "codonUsage-expressivity",
        "E",
        "E,codonTable-method",
        "Fop",
        "Fop,codonTable-method",
        "GCB",
        "GCB,codonTable-method",
        "MELP",
        "MELP,codonTable-method"
      ]
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      "title": "coRdon: codon usage analysis in R",
      "topics": [
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        "coRdon"
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      "title": "An S4 class 'crossTab'",
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        "contable,crossTab-method",
        "crossTab",
        "crossTab,character,numeric-method",
        "crossTab-class",
        "getSeqAnnot",
        "getSeqAnnot,crossTab-method",
        "getVariable",
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    {
      "page": "enrichBarplot",
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      "topics": [
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        "enrichBarplot,AnnotatedDataFrame-method",
        "enrichBarplot,list-method"
      ]
    },
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      "topics": [
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        "enrichMAplot,AnnotatedDataFrame-method",
        "enrichMAplot,list-method"
      ]
    },
    {
      "page": "enrichMatrix",
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      "topics": [
        "enrichMatrix",
        "enrichMatrix,list-method"
      ]
    },
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      "title": "Enrichment analysis for codon usage (CU) data.",
      "topics": [
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        "enrichment,crossTab-method"
      ]
    },
    {
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      "title": "An S4 class 'genCode'",
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        "genCode,ANY-method",
        "genCode-class"
      ]
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      "topics": [
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      "topics": [
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    },
    {
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      "topics": [
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    },
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    {
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      "title": "Codon usage in human gut microbiome in liver cirrhosis.",
      "topics": [
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    {
      "page": "LD94_KO",
      "title": "Codon usage based KO enrichment analysis results from an gut microbiome of an individual with liver cirrhosis. For more information, see `?LD94`.",
      "topics": [
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    },
    {
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      "title": "Codon usage based KEGG Pathway enrichment analysis results from an gut microbiome of an individual with liver cirrhosis. For more information, see `?LD94`.",
      "topics": [
        "LD94_PATHWAYS"
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    },
    {
      "page": "length-codonTable",
      "title": "Length of 'codonTable' object.",
      "topics": [
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        "length-codonTable"
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      "topics": [
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        "length-crossTab"
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      "topics": [
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      "topics": [
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      "topics": [
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      "page": "show-codonTable",
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        "Functional annotation",
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