{ "_id": "6a339f333efcd9bda43a7954", "Package": "coRdon", "Type": "Package", "Title": "Codon Usage Analysis and Prediction of Gene Expressivity", "Version": "1.30.0", "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-release.r-universe.dev", "Date/Publication": "2026-04-28 12:48:23 UTC", "RemoteUrl": "https://github.com/bioc/coRdon", "RemoteRef": "RELEASE_3_23", "RemoteSha": "9aab9bdb3d1caeb0ea7caa3dead8f3d988b41879", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-18 07:14:17 UTC", "User": "root" }, "Author": "Anamaria Elek [cre, aut],\nMaja Kuzman [aut],\nKristian Vlahovicek [aut]", "Maintainer": "Anamaria Elek ", "MD5sum": "07711bbfef01e28dea8f2d0bcac71b0a", "_user": "bioc-release", "_type": "src", "_file": "coRdon_1.30.0.tar.gz", "_fileid": "d8d39c38676263234992e1e1fa6fdd4b0e8cfb4f934c67d00cb3d665b4bb1795", "_filesize": 2129044, "_sha256": "d8d39c38676263234992e1e1fa6fdd4b0e8cfb4f934c67d00cb3d665b4bb1795", "_created": "2026-06-18T07:14:17.000Z", "_published": "2026-06-18T07:33:07.074Z", "_jobs": [ { "job": 82075007084, "time": 158, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7716604313" }, { "job": 82075007074, "time": 235, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7716628356" }, { "job": 82075007066, "time": 220, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7716624185" }, { "job": 82075007097, "time": 218, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7716889731" }, { "job": 82075007032, "time": 130, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7716860932" }, { "job": 82074442738, "time": 220, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7716555479" }, { "job": 82075007023, "time": 119, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7716594749" }, { "job": 82075007077, "time": 171, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7716608777" }, { "job": 82075007083, "time": 151, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7716603544" }, { "job": 82075007102, "time": 188, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7716614021" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742984411", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/coRdon", "_commit": { "id": "9aab9bdb3d1caeb0ea7caa3dead8f3d988b41879", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380503 }, "_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": false, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_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", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 6, "_devurl": "https://github.com/bioinfohr/cordon", "_searchresults": 86, "_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/RELEASE_3_23/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": 8.028620047084129, "_indexed": false, "_nocasepkg": "cordon", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/coRdon", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.30.0", "date": "2026-06-18T07:17:10.000Z", "distro": "noble", "commit": "9aab9bdb3d1caeb0ea7caa3dead8f3d988b41879", "fileid": "7fa836bb189d308b5ede941835d5a6aeb90ed846db25b7c65d8b4ee41fe4e39c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742984411" }, { "r": "4.6.0", "os": "linux", "version": "1.30.0", "date": "2026-06-18T07:16:57.000Z", "distro": "noble", "commit": "9aab9bdb3d1caeb0ea7caa3dead8f3d988b41879", "fileid": "2ee93eca58035c644ed30820d631535cdc926de6735ded1295802577d3d20dde", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742984411" }, { "r": "4.5.3", "os": "mac", "version": "1.30.0", "date": "2026-06-18T07:31:12.000Z", "commit": "9aab9bdb3d1caeb0ea7caa3dead8f3d988b41879", "fileid": "d3db5ce12073ffc14b5c2cfda58a10a31d9f27b995bfe16fe9fa9dc28a1b9e44", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742984411" }, { "r": "4.6.0", "os": "mac", "version": "1.30.0", "date": "2026-06-18T07:30:20.000Z", "commit": "9aab9bdb3d1caeb0ea7caa3dead8f3d988b41879", "fileid": "e6aebc39a7bc36673af2cf7906b9f917c4749dd5f9bf416ec068f86ce6ecc45c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742984411" }, { "r": "4.6.0", "os": "wasm", "version": "1.30.0", "date": "2026-06-18T07:16:48.000Z", "commit": "9aab9bdb3d1caeb0ea7caa3dead8f3d988b41879", "fileid": "f397731d6eb9d9ff7bb057ff9eeed15144d1f28a4790aac3df7aadbc8736e128", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742984411" }, { "r": "4.7.0", "os": "win", "version": "1.30.0", "date": "2026-06-18T07:15:58.000Z", "commit": "9aab9bdb3d1caeb0ea7caa3dead8f3d988b41879", "fileid": "dedd31c9aecb37be551432a812d75c39701b825f4a7ce26b46616a23c1083f58", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742984411" }, { "r": "4.5.3", "os": "win", "version": "1.30.0", "date": "2026-06-18T07:15:43.000Z", "commit": "9aab9bdb3d1caeb0ea7caa3dead8f3d988b41879", "fileid": "9cee8f3882efd630e04887fe36bc6c913f371fded4f1d333077113f90236bc35", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742984411" }, { "r": "4.6.0", "os": "win", "version": "1.30.0", "date": "2026-06-18T07:16:32.000Z", "commit": "9aab9bdb3d1caeb0ea7caa3dead8f3d988b41879", "fileid": "46e5701178fb030959ba042709669016506f9af909c0554fcfcf04d824c8094d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742984411" } ] }