{
  "_id": "6a1ad5801d7bb097a09e4fce",
  "Package": "coRdon",
  "Type": "Package",
  "Title": "Codon Usage Analysis and Prediction of Gene Expressivity",
  "Version": "1.31.0",
  "Authors@R": "c(person(given = \"Anamaria\",\nfamily = \"Elek\",\nrole = c(\"cre\", \"aut\"),\nemail = \"anamariaelek@gmail.com\"),\nperson(given = \"Maja\",\nfamily = \"Kuzman\",\nrole = \"aut\",\nemail = \"mkuzman@mail.bioinfo.hr\"),\nperson(given = \"Kristian\",\nfamily = \"Vlahovicek\",\nrole = \"aut\",\nemail = \"kristian@bioinfo.hr\"))",
  "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.",
  "License": "Artistic-2.0",
  "LazyData": "TRUE",
  "biocViews": "Software, Metagenomics, GeneExpression, GeneSetEnrichment,\nGenePrediction, Visualization, KEGG, Pathways, Genetics\nCellBiology, BiomedicalInformatics, ImmunoOncology",
  "RoxygenNote": "6.1.1",
  "Collate": "'coRdon.R' 'genCode-class.R' 'codonTable-class.R'\n'functions.R' 'codonUsage.R' 'codonUsage-expressivity.R'\n'codonUsage-visualization.R' 'crossTab-class.R' 'data.R'\n'enrichment-visualization.R' 'enrichment.R' 'readSet.R'",
  "VignetteBuilder": "knitr",
  "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",
  "RemoteUrl": "https://github.com/bioc/coRdon",
  "RemoteRef": "HEAD",
  "RemoteSha": "86ceb2eb0aa2b17857715aa21eee685de933caff",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 08:46:56 UTC",
    "User": "root"
  },
  "Author": "Anamaria Elek [cre, aut],\nMaja Kuzman [aut],\nKristian Vlahovicek [aut]",
  "Maintainer": "Anamaria Elek <anamariaelek@gmail.com>",
  "MD5sum": "87d0633d748590d165aed31fed4618f3",
  "_user": "bioc",
  "_type": "src",
  "_file": "coRdon_1.31.0.tar.gz",
  "_fileid": "203722e5009b9ff0fc81a88ab85dd360f2dfc750e2aa40493b70d66b71b87028",
  "_filesize": 2127483,
  "_sha256": "203722e5009b9ff0fc81a88ab85dd360f2dfc750e2aa40493b70d66b71b87028",
  "_created": "2026-05-30T08:46:56.000Z",
  "_published": "2026-05-30T12:18:08.017Z",
  "_jobs": [
    {
      "job": 78637543828,
      "time": 164,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306952215"
    },
    {
      "job": 78637543824,
      "time": 251,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306961171"
    },
    {
      "job": 78637543848,
      "time": 225,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306958548"
    },
    {
      "job": 78637543833,
      "time": 120,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7308105431"
    },
    {
      "job": 78637543831,
      "time": 151,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7308107357"
    },
    {
      "job": 78637329899,
      "time": 233,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306936035"
    },
    {
      "job": 78637543827,
      "time": 116,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306947540"
    },
    {
      "job": 78637543843,
      "time": 167,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306952602"
    },
    {
      "job": 78637543849,
      "time": 150,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7306950989"
    },
    {
      "job": 78637543834,
      "time": 173,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306953226"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 10
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679527697",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/coRdon",
  "_commit": {
    "id": "86ceb2eb0aa2b17857715aa21eee685de933caff",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380504
  },
  "_maintainer": {
    "name": "Anamaria Elek",
    "email": "anamariaelek@gmail.com",
    "login": "anamariaelek",
    "description": "",
    "uuid": 20280755
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.31.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.30.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "metagenomics",
    "geneexpression",
    "genesetenrichment",
    "geneprediction",
    "visualization",
    "kegg",
    "pathways",
    "genetics\ncellbiology",
    "biomedicalinformatics",
    "immunooncology"
  ],
  "_stars": 23,
  "_contributors": [
    {
      "user": "anamariaelek",
      "count": 83,
      "uuid": 20280755
    },
    {
      "user": "bioinfohr",
      "count": 27,
      "uuid": 13433744
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "makuzman",
      "count": 1,
      "uuid": 37149324
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 590,
    "source": "https://www.bioconductor.org/packages/stats/bioc/coRdon"
  },
  "_mentions": 6,
  "_devurl": "https://github.com/bioinfohr/cordon",
  "_searchresults": 69,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/coRdon.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/bioinfohr/cordon",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "B",
    "Bplot",
    "CAI",
    "codonCounts",
    "codonTable",
    "contable",
    "crossTab",
    "E",
    "ENC",
    "ENCprime",
    "enrichBarplot",
    "enrichMAplot",
    "enrichMatrix",
    "enrichment",
    "Fop",
    "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": [
        "intraBplot",
        "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"
      ]
    },
    {
      "page": "show-codonTable",
      "title": "Display the object of 'codonTable' class.",
      "topics": [
        "show,codonTable-method",
        "show-codonTable"
      ]
    },
    {
      "page": "show-crossTab",
      "title": "Display the object of 'crossTab' class.",
      "topics": [
        "show,crossTab-method",
        "show-crossTab"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/coRdon/raw/HEAD/README.md",
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "Biostrings",
    "cli",
    "cpp11",
    "crayon",
    "data.table",
    "dplyr",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "IRanges",
    "isoband",
    "labeling",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "RColorBrewer",
    "rlang",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "stringi",
    "stringr",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "coRdon.Rmd",
      "filename": "coRdon.html",
      "title": "Codon usage (CU) analysis in R",
      "author": "Anamaria Elek",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Loading sequences",
        "Calculate CU bias",
        "Visualisation of CU bias",
        "Predict genes' expressivity",
        "Functional annotation",
        "Visualisation of enrichment",
        "Integration",
        "Session info"
      ],
      "created": "2018-03-26 07:03:57",
      "modified": "2018-10-18 13:01:59",
      "commits": 12
    }
  ],
  "_score": 7.932970686577818,
  "_indexed": true,
  "_nocasepkg": "cordon",
  "_universes": [
    "bioc",
    "anamariaelek",
    "bioinfohr"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-05-30T08:50:07.000Z",
      "distro": "noble",
      "commit": "86ceb2eb0aa2b17857715aa21eee685de933caff",
      "fileid": "4bf521b040c5af8d1b6cb8a3b88f58b1d335a6b6ff8dff46145e1dd4c110fb62",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679527697"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-05-30T08:49:43.000Z",
      "distro": "noble",
      "commit": "86ceb2eb0aa2b17857715aa21eee685de933caff",
      "fileid": "530d23f371a2269202f1e0b3f212240ead954ba5e0010ab6f68e1ea6561a7b55",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679527697"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-05-30T12:16:31.000Z",
      "commit": "86ceb2eb0aa2b17857715aa21eee685de933caff",
      "fileid": "db7e423a2c4475d7ff8a381039001b2efa15271999e64a108b2c01acf37b125a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679527697"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-05-30T12:16:44.000Z",
      "commit": "86ceb2eb0aa2b17857715aa21eee685de933caff",
      "fileid": "0af557cabfea8abcb7118a7c5bd52a9fe818094fb6a9bd5adb8c0be6f9c94ffc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679527697"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.31.0",
      "date": "2026-05-30T08:49:17.000Z",
      "commit": "86ceb2eb0aa2b17857715aa21eee685de933caff",
      "fileid": "fb3ee9267a677a43daa0ad0947a363ac94ea980711b95a90431a7db061a66a56",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679527697"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-05-30T08:48:22.000Z",
      "commit": "86ceb2eb0aa2b17857715aa21eee685de933caff",
      "fileid": "9627b460232fbbac1f3adc0659cdba6b636be06b71b37c00c913bd5bf9d6309c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679527697"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-05-30T08:48:21.000Z",
      "commit": "86ceb2eb0aa2b17857715aa21eee685de933caff",
      "fileid": "49fe9a7216860aae1227b07b8ea571faef94717b5d5ef53bf8386323f00ef6d4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679527697"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-05-30T08:48:28.000Z",
      "commit": "86ceb2eb0aa2b17857715aa21eee685de933caff",
      "fileid": "04071526a96e7a547f790fa9b915b252c946c11ffbde66e7b681be83b93b6d64",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679527697"
    }
  ]
}