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  "Type": "Package",
  "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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  "biocViews": "Software, Metagenomics, GeneExpression, GeneSetEnrichment,\nGenePrediction, Visualization, KEGG, Pathways, Genetics\nCellBiology, BiomedicalInformatics, ImmunoOncology",
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  "URL": "https://github.com/BioinfoHR/coRdon",
  "BugReports": "https://github.com/BioinfoHR/coRdon/issues",
  "Config/pak/sysreqs": "libicu-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:48:24 UTC",
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    "User": "root"
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  "Author": "Anamaria Elek [cre, aut],\nMaja Kuzman [aut],\nKristian Vlahovicek [aut]",
  "Maintainer": "Anamaria Elek <anamariaelek@gmail.com>",
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  "_created": "2026-07-04T23:02:00.000Z",
  "_published": "2026-07-04T23:11:24.335Z",
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    "note": 9
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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    "Bplot",
    "CAI",
    "codonCounts",
    "codonTable",
    "contable",
    "crossTab",
    "E",
    "ENC",
    "ENCprime",
    "enrichBarplot",
    "enrichMAplot",
    "enrichMatrix",
    "enrichment",
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    "GCB",
    "getCOG",
    "getID",
    "getKO",
    "getlen",
    "getSeqAnnot",
    "getVariable",
    "intraBplot",
    "MCB",
    "MELP",
    "MILC",
    "readSet",
    "reduceCrossTab",
    "SCUO",
    "setCOG",
    "setKO",
    "show"
  ],
  "_datasets": [
    {
      "name": "HD59",
      "title": "Codon usage in healthy human gut microbiome.",
      "object": "HD59",
      "class": [
        "codonTable"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "HD59_KO",
      "title": "Codon usage based KO enrichment analysis results from the healthy human gut microbiome. For more information, see '?HD59'.",
      "object": "HD59_KO",
      "class": [
        "AnnotatedDataFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "HD59_PATHWAYS",
      "title": "Codon usage based KEGG Pathway enrichment analysis results from a healthy human gut microbiome. For more information, see '?HD59'.",
      "object": "HD59_PATHWAYS",
      "class": [
        "AnnotatedDataFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "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": [
        "AnnotatedDataFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "LD94_PATHWAYS",
      "title": "Codon usage based KEGG Pathway enrichment analysis results from an gut microbiome of an individual with liver cirrhosis. For more information, see '?LD94'.",
      "object": "LD94_PATHWAYS",
      "class": [
        "AnnotatedDataFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_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"
      ]
    },
    {
      "page": "codonUsage",
      "title": "Calculate CU measures.",
      "topics": [
        "B",
        "B,codonTable-method",
        "codonUsage",
        "ENC",
        "ENC,codonTable-method",
        "ENCprime",
        "ENCprime,codonTable-method",
        "MCB",
        "MCB,codonTable-method",
        "MILC",
        "MILC,codonTable-method",
        "SCUO",
        "SCUO,codonTable-method"
      ]
    },
    {
      "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"
      ]
    },
    {
      "page": "coRdon",
      "title": "coRdon: codon usage analysis in R",
      "topics": [
        "coRdon-package",
        "coRdon"
      ]
    },
    {
      "page": "crossTab-class",
      "title": "An S4 class 'crossTab'",
      "topics": [
        "contable",
        "contable,crossTab-method",
        "crossTab",
        "crossTab,character,numeric-method",
        "crossTab-class",
        "getSeqAnnot",
        "getSeqAnnot,crossTab-method",
        "getVariable",
        "getVariable,crossTab-method"
      ]
    },
    {
      "page": "enrichBarplot",
      "title": "Barplot of enriched and depleted annotations.",
      "topics": [
        "enrichBarplot",
        "enrichBarplot,AnnotatedDataFrame-method",
        "enrichBarplot,list-method"
      ]
    },
    {
      "page": "enrichMAplot",
      "title": "MA plot of enriched annotations.",
      "topics": [
        "enrichMAplot",
        "enrichMAplot,AnnotatedDataFrame-method",
        "enrichMAplot,list-method"
      ]
    },
    {
      "page": "enrichMatrix",
      "title": "Extract chosen enrichment values to a matrix.",
      "topics": [
        "enrichMatrix",
        "enrichMatrix,list-method"
      ]
    },
    {
      "page": "enrichment",
      "title": "Enrichment analysis for codon usage (CU) data.",
      "topics": [
        "enrichment",
        "enrichment,crossTab-method"
      ]
    },
    {
      "page": "genCode-class",
      "title": "An S4 class 'genCode'",
      "topics": [
        "genCode",
        "genCode,ANY-method",
        "genCode-class"
      ]
    },
    {
      "page": "HD59",
      "title": "Codon usage in healthy human gut microbiome.",
      "topics": [
        "HD59"
      ]
    },
    {
      "page": "HD59_KO",
      "title": "Codon usage based KO enrichment analysis results from the healthy human gut microbiome. For more information, see `?HD59`.",
      "topics": [
        "HD59_KO"
      ]
    },
    {
      "page": "HD59_PATHWAYS",
      "title": "Codon usage based KEGG Pathway enrichment analysis results from a healthy human gut microbiome. For more information, see `?HD59`.",
      "topics": [
        "HD59_PATHWAYS"
      ]
    },
    {
      "page": "intraBplot",
      "title": "Intra-samples Karlin B plot",
      "topics": [
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        "intraBplot,codonTable,codonTable-method"
      ]
    },
    {
      "page": "LD94",
      "title": "Codon usage in human gut microbiome in liver cirrhosis.",
      "topics": [
        "LD94"
      ]
    },
    {
      "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": [
        "LD94_KO"
      ]
    },
    {
      "page": "LD94_PATHWAYS",
      "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"
      ]
    },
    {
      "page": "length-codonTable",
      "title": "Length of 'codonTable' object.",
      "topics": [
        "length,codonTable-method",
        "length-codonTable"
      ]
    },
    {
      "page": "length-crossTab",
      "title": "Length of 'crossTab' object.",
      "topics": [
        "length,crossTab-method",
        "length-crossTab"
      ]
    },
    {
      "page": "readSet",
      "title": "Read set of sequences.",
      "topics": [
        "readSet"
      ]
    },
    {
      "page": "reduceCrossTab",
      "title": "Reduce 'crossTab'.",
      "topics": [
        "reduceCrossTab",
        "reduceCrossTab,crossTab,character-method"
      ]
    },
    {
      "page": "RPKOs",
      "title": "KEGG Orthology (KO) annotations for ribosomal genes.",
      "topics": [
        "RPKOs"
      ]
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    {
      "page": "show-codonTable",
      "title": "Display the object of 'codonTable' class.",
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        "show-codonTable"
      ]
    },
    {
      "page": "show-crossTab",
      "title": "Display the object of 'crossTab' class.",
      "topics": [
        "show,crossTab-method",
        "show-crossTab"
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      "headings": [
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        "Loading sequences",
        "Calculate CU bias",
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        "Functional annotation",
        "Visualisation of enrichment",
        "Integration",
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      "modified": "2018-10-18 13:01:59",
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