{ "_id": "6a1af2e11d7bb097a09f7f1f", "Package": "sscu", "Type": "Package", "Title": "Strength of Selected Codon Usage", "Version": "2.43.0", "Date": "2016-12-1", "Author": "Yu Sun", "Maintainer": "Yu Sun ", "Description": "The package calculates the indexes for selective stength\nin codon usage in bacteria species. (1) The package can\ncalculate the strength of selected codon usage bias (sscu, also\nnamed as s_index) based on Paul Sharp's method. The method take\ninto account of background mutation rate, and focus only on\nfour pairs of codons with universal translational advantages in\nall bacterial species. Thus the sscu index is comparable among\ndifferent species. (2) The package can detect the strength of\ntranslational accuracy selection by Akashi's test. The test\ntabulating all codons into four categories with the feature as\nconserved/variable amino acids and optimal/non-optimal codons.\n(3) Optimal codon lists (selected codons) can be calculated by\neither op_highly function (by using the highly expressed genes\ncompared with all genes to identify optimal codons), or\nop_corre_CodonW/op_corre_NCprime function (by correlative\nmethod developed by Hershberg & Petrov). Users will have a list\nof optimal codons for further analysis, such as input to the\nAkashi's test. (4) The detailed codon usage information, such\nas RSCU value, number of optimal codons in the highly/all gene\nset, as well as the genomic gc3 value, can be calculate by the\noptimal_codon_statistics and genomic_gc3 function. (5)\nFurthermore, we added one test function low_frequency_op in the\npackage. The function try to find the low frequency optimal\ncodons, among all the optimal codons identified by the\nop_highly function.", "VignetteBuilder": "knitr", "LazyLoad": "yes", "License": "GPL (>= 2)", "biocViews": "Genetics, GeneExpression, WholeGenome", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:43:08 UTC", "RemoteUrl": "https://github.com/bioc/sscu", "RemoteRef": "HEAD", "RemoteSha": "e95a31e1d3ba3bca627341ec3004baf225b2c40d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:44:49 UTC", "User": "root" }, "MD5sum": "3854307e0e7c8768f1f1d0f11ec84b48", "_user": "bioc", "_type": "src", "_file": "sscu_2.43.0.tar.gz", "_fileid": "c592d02831d1b7ac31880f6c25d98faf727d81b28deb02bbad9e8ef65d4d5a79", "_filesize": 1519230, "_sha256": "c592d02831d1b7ac31880f6c25d98faf727d81b28deb02bbad9e8ef65d4d5a79", "_created": "2026-05-30T09:44:49.000Z", "_published": "2026-05-30T14:23:29.415Z", "_jobs": [ { "job": 78640513353, "time": 155, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307449213" }, { "job": 78640513349, "time": 170, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307450523" }, { "job": 78640513352, "time": 237, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7307457085" }, { "job": 78640513396, "time": 146, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7308838074" }, { "job": 78640513383, "time": 120, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7308835393" }, { "job": 78639882113, "time": 175, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307276700" }, { "job": 78640513354, "time": 112, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307445404" }, { "job": 78640513388, "time": 149, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7307447274" }, { "job": 78640513394, "time": 130, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7307447586" }, { "job": 78640513393, "time": 143, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7307448732" } ], "_bioccheck": { "error": 3, "warning": 1, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676862132", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/sscu", "_commit": { "id": "e95a31e1d3ba3bca627341ec3004baf225b2c40d", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380188 }, "_maintainer": { "name": "Yu Sun", "email": "sunyu1357@gmail.com", "login": "sunyu1357", "description": "", "uuid": 6084933 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3", "role": "Depends" }, { "package": "Biostrings", "version": ">= 2.36.4", "role": "Imports" }, { "package": "seqinr", "version": ">= 3.1-3", "role": "Imports" }, { "package": "BiocGenerics", "version": ">= 0.16.1", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.43.0", "bioc": "3.24" }, { "branch": "release", "version": "2.42.0", "bioc": "3.23" } ], "_topics": [ "genetics", "geneexpression", "wholegenome" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 412, "source": "https://www.bioconductor.org/packages/stats/bioc/sscu" }, "_mentions": 1, "_searchresults": 4, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/sscu.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "akashi_test", "genomic_gc3", "low_frequency_op", "op_corre_CodonW", "op_corre_NCprime", "op_highly", "op_highly_stats", "s_index" ], "_help": [ { "page": "sscu-package", "title": "Strength of Selected Codon Usage", "topics": [ "sscu-package" ] }, { "page": "akashi_test", "title": "akashi test for codon usage", "topics": [ "akashi_test" ] }, { "page": "genomic_gc3", "title": "genomic gc3 for an multifasta genomic file", "topics": [ "genomic_gc3" ] }, { "page": "low_frequency_op", "title": "the function identify low frequency optimal codons", "topics": [ "low_frequency_op" ] }, { "page": "op_corre_CodonW", "title": "Identify optimal codons by using the correlative method from Hershberg & Petrov, the input file is from CodonW", "topics": [ "op_corre_CodonW" ] }, { "page": "op_corre_NCprime", "title": "Identify optimal codons by using the correlative method from Hershberg & Petrov, the input file is from NCprime", "topics": [ "op_corre_NCprime" ] }, { "page": "op_highly", "title": "Identify optimal codons by using the highly expressed genes method", "topics": [ "optimal_codons", "op_highly", "selected_codons" ] }, { "page": "op_highly_stats", "title": "statistics for the optimal codons", "topics": [ "optimal_codons_table", "optimal_codon_statistics", "op_highly_stats" ] }, { "page": "s_index", "title": "S index (Strength of Selected Codon Usage)", "topics": [ "s_index" ] } ], "_rundeps": [ "ade4", "BiocGenerics", "Biostrings", "crayon", "generics", "IRanges", "lattice", "MASS", "nlme", "pixmap", "Rcpp", "RcppArmadillo", "S4Vectors", "segmented", "Seqinfo", "seqinr", "sp", "XVector" ], "_score": 2.3010299956639813, "_indexed": true, "_nocasepkg": "sscu", "_universes": [ "bioc", "sunyu1357" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.43.0", "date": "2026-05-30T10:15:03.000Z", 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