{ "_id": "6a497b436d67900babdf6e64", "Package": "vhcub", "Title": "Virus-Host Codon Usage Co-Adaptation Analysis", "Version": "1.0.0", "Authors@R": "c(\nperson(given = \"Ali\",family = \"Mostafa Anwar\",role = c(\"aut\", \"cre\"),email = \"ali.mo.anwar@std.agr.cu.edu.eg\"),\nperson(given = \"Mohamed\",family = \"Soudy\",email = \"MohmedSoudy2009@gmail.com\", role = \"aut\"))", "Author": "Ali Mostafa Anwar [aut, cre], Mohamed Soudy [aut]", "Maintainer": "Ali Mostafa Anwar ", "Description": "Analyze the co-adaptation of codon usage between a virus\nand its host,calculate various codon usage bias measurements\nas; effective number of codons (ENc) Novembre (2002)\n, codon adaptation\nindex (CAI) Sharp and Li (1987) ,\nrelative codon deoptimization index (RCDI) Puigbò et al (2010)\n, similarity index (SiD) Zhou et al\n(2013) , synonymous codon\nusage orderliness (SCUO) Wan et al (2004)\n and, relative synonymous codon\nusage (RSCU) Sharp et al (1986) .\nAlso, it provides a statistical dinucleotide over- and\nunderrepresentation with three different models. Implement\nseveral methods for visualization of codon usage as\nENc.GC3plot() and PR2.plot().", "License": "GPL-3", "Encoding": "UTF-8", "biocViews": "", "RoxygenNote": "6.1.1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 21:25:45 UTC", "User": "root" }, "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://aliyoussef96.r-universe.dev", "Date/Publication": "2025-07-05 11:02:55 UTC", "RemoteUrl": "https://github.com/aliyoussef96/vhcub", "RemoteRef": "HEAD", "RemoteSha": "49f58dab1d0abd4e5700686f1e10f0c21d702137", "_user": "aliyoussef96", "_type": "src", "_file": "vhcub_1.0.0.tar.gz", "_fileid": "https://r2.ropensci.org/81a180585ad5bad2786d63da4229d3c61852dc1f9013359ba0eca7c40dbad39f", "_filesize": 226015, "_sha256": "81a180585ad5bad2786d63da4229d3c61852dc1f9013359ba0eca7c40dbad39f", "_expires": "2026-10-12T21:29:37.000Z", "_created": "2026-07-04T21:25:45.000Z", "_published": "2026-07-04T21:29:39.324Z", "_jobs": [ { "job": 85168297951, "time": 191, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "8085587385" }, { "job": 85168297947, "time": 181, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8085586192" }, { "job": 85168297940, "time": 171, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "8085582452" }, { "job": 85168297938, "time": 165, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8085581760" }, { "job": 85168074499, "time": 204, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8085565067" }, { "job": 85168297952, "time": 150, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8085582557" }, { "job": 85168297948, "time": 129, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "8085580191" }, { "job": 85168297970, "time": 126, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "8085579878" }, { "job": 85168297955, "time": 122, "config": "windows-release", "r": "4.6.1", "check": "WARNING", "artifact": "8085579446" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/aliyoussef96/actions/runs/28720053198", "_status": "success", "_upstream": "https://github.com/aliyoussef96/vhcub", "_commit": { "id": "49f58dab1d0abd4e5700686f1e10f0c21d702137", "author": "Ali Youssef ", "committer": "GitHub ", "message": "Update README.md", "time": 1751713375 }, "_maintainer": { "name": "Ali Mostafa Anwar", "email": "ali.mo.anwar@std.agr.cu.edu.eg" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "Biostrings", "role": "Imports" }, { "package": "coRdon", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "seqinr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "aliyoussef96", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-27", "n": 1 } ], "_tags": [], "_stars": 5, "_contributors": [ { "user": "aliyoussef96", "count": 64, "uuid": 42375503 } ], "_userbio": { "uuid": 42375503, "type": "user", "name": "Ali Youssef", "followers": 46 }, "_downloads": { "count": 275, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/vhcub" }, "_mentions": 1, "_devurl": "https://github.com/aliyoussef96/vhcub", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/vhcub.html", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/aliyoussef96/vhcub", "_realowner": "aliyoussef96", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2019-11-15" } ], "_exports": [ "CAI.values", "dinuc.base", "dinuc.codon", "dinuc.syncodon", "ENc.GC3plot", "ENc.values", "fasta.read", "GC.content", "PR2.plot", "RCDI.values", "RSCU.values", "SCUO.values", "SiD.value" ], "_help": [ { "page": "CAI.values", "title": "Codon Adaptation Index (CAI)", "topics": [ "CAI.values" ] }, { "page": "dinuc.base", "title": "Statistical dinucleotide over- and underrepresentation (base model).", "topics": [ "dinuc.base" ] }, { "page": "dinuc.codon", "title": "Statistical dinucleotide over- and underrepresentation (codon model).", "topics": [ "dinuc.codon" ] }, { "page": "dinuc.syncodon", "title": "Statistical dinucleotide over- and underrepresentation (syncodon model).", "topics": [ "dinuc.syncodon" ] }, { "page": "ENc.GC3plot", "title": "ENc-GC3 scatterplot.", "topics": [ "ENc.GC3plot" ] }, { "page": "ENc.values", "title": "Effective Number of Codons (ENc).", "topics": [ "ENc.values" ] }, { "page": "fasta.read", "title": "Read fasta formate and convert it to data frame", "topics": [ "fasta.read" ] }, { "page": "GC.content", "title": "GC content", "topics": [ "GC.content" ] }, { "page": "PR2.plot", "title": "Parity rule 2 (PR2) plot", "topics": [ "PR2.plot" ] }, { "page": "RCDI.values", "title": "Relative Codon Deoptimization Index (RCDI)", "topics": [ "RCDI.values" ] }, { "page": "RSCU.values", "title": "Relative Synonymous Codon Usage (RSCU)", "topics": [ "RSCU.values" ] }, { "page": "SCUO.values", "title": "Synonymous codon usage eorderliness (SCUO)", "topics": [ "SCUO.values" ] }, { "page": "SiD.value", "title": "Similarity Index (SiD)", "topics": [ "SiD.value" ] }, { "page": "vhcub", "title": "vhcub: A package to analysis the co-adaptation of codon usage between a virus and its host.", "topics": [ "vhcub-package", "vhcub" ] } ], "_pkglogo": "https://github.com/aliyoussef96/vhcub/raw/HEAD/logo.png", "_readme": "https://github.com/aliyoussef96/vhcub/raw/HEAD/README.md", "_rundeps": [ "ade4", "Biobase", "BiocGenerics", "Biostrings", "cli", "coRdon", "cpp11", "crayon", "data.table", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "IRanges", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "nlme", "pillar", "pixmap", "pkgconfig", "purrr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "S4Vectors", "S7", "scales", "segmented", "Seqinfo", "seqinr", "sp", "stringi", "stringr", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XVector" ], "_score": 3.3979400086720375, "_indexed": true, "_nocasepkg": "vhcub", "_universes": [ "aliyoussef96" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-07-04T21:28:10.000Z", "distro": "resolute", "commit": "49f58dab1d0abd4e5700686f1e10f0c21d702137", "fileid": "https://r2.ropensci.org/baeea28ad0fe2768b9b19d64e15819ca62a911a250f60bc3f6ea93cce2d8e3ad", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/aliyoussef96/actions/runs/28720053198" }, { "r": "4.6.1", "os": "linux", "version": "1.0.0", "date": "2026-07-04T21:28:06.000Z", "distro": "resolute", "commit": "49f58dab1d0abd4e5700686f1e10f0c21d702137", "fileid": "https://r2.ropensci.org/47d9d71b04eeef93251ba6b791f42bcf7666a3422c66e60eaa0978de27ccdd58", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/aliyoussef96/actions/runs/28720053198" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-07-04T21:27:57.000Z", "commit": "49f58dab1d0abd4e5700686f1e10f0c21d702137", "fileid": "https://r2.ropensci.org/4cc8dc5e5b1da57a5c6c0e68c1f86c165b2770bb4a902950c936bbf0e5bd70bf", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/aliyoussef96/actions/runs/28720053198" }, { "r": "4.6.1", "os": "mac", "version": "1.0.0", "date": "2026-07-04T21:27:46.000Z", "commit": "49f58dab1d0abd4e5700686f1e10f0c21d702137", "fileid": "https://r2.ropensci.org/f44eedda6af3fbef758eaa7f4b7db67ee9281b1a723602a3429523679a875143", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/aliyoussef96/actions/runs/28720053198" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-07-04T21:28:36.000Z", "commit": "49f58dab1d0abd4e5700686f1e10f0c21d702137", "fileid": "https://r2.ropensci.org/ce4296f918697b655f24e8a62113b93c63a071c75e88f1cbcc8da27553cbcf2b", "status": "success", "buildurl": "https://github.com/r-universe/aliyoussef96/actions/runs/28720053198" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-07-04T21:27:08.000Z", "commit": "49f58dab1d0abd4e5700686f1e10f0c21d702137", "fileid": "https://r2.ropensci.org/b424d73bc0663f952efadaf80434cddddb90eb31f1ca0d849a44a66a4ee24db6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/aliyoussef96/actions/runs/28720053198" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-07-04T21:27:15.000Z", "commit": "49f58dab1d0abd4e5700686f1e10f0c21d702137", "fileid": "https://r2.ropensci.org/ecbef9677562be615f2106811f5d64d0207545b59fb141424741e31a99e1265f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/aliyoussef96/actions/runs/28720053198" }, { "r": "4.6.1", "os": "win", "version": "1.0.0", "date": "2026-07-04T21:27:01.000Z", "commit": "49f58dab1d0abd4e5700686f1e10f0c21d702137", "fileid": "https://r2.ropensci.org/612f626432218c59c2bb1af3f503e39ae0e106fd97d50a1b1d96d6df3cb6bbb6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/aliyoussef96/actions/runs/28720053198" } ] }