{ "_id": "6a1a74401d7bb097a09d14ec", "Package": "queeems", "Version": "1.1.0", "Date": "2025-04-28", "License": "GPL-3 + file LICENSE", "Authors@R": "c(person(\"Hassan\", \"Sadiq\", role=c(\"aut\",\"cre\",\"cph\",\"fnd\"),\nemail=\"hassan.t.sadiq@gmail.com\",\ncomment=c(ORCID=\"0000-0003-0192-7134\")))", "Title": "Quantify the Extent of Evolutionary Evidence in Molecular\nSequences", "Description": "Biological inferences obtained from molecular data are\nonly as good as the extent of evolutionary signatures retained\nin the genetic data. Techniques available to quantify these\nsignatures are largely targeted towards phylogeny\nreconstruction and they often rely on adhoc hypothesis tests of\nsignificance. I present a Bayesian function that assesses\nwhether a set of genetic sequences are saturated. That is, it\nis useful for determining whether the evolutionary information\nin the sequences has eroded with time. Site specific Bayes\nfactors are generated with respect to codon bases to allow for\nstraightforward applications in extensive computational biology\ninquiries, including natural selection analyses.", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "biocViews": "Alignment, Bayesian, Classification, DataImport, Genetics,\nMathematicalBiology, ResearchField, Sequencing,\nSequenceMatching, Software, StatisticalMethod, WorkflowStep", "Contact": "", "URL": "https://github.com/thsadiq/queeems", "BugReports": "https://github.com/thsadiq/queeems/issues", "Packaged": { "Date": "2026-05-29 10:16:47 UTC", "User": "root" }, "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:07:17 UTC", "RemoteUrl": "https://github.com/bioc/queeems", "RemoteRef": "HEAD", "RemoteSha": "54d1ec1b37ed1e581a5b410e73cbefc218e9df26", "NeedsCompilation": "no", "Author": "Hassan Sadiq [aut, cre, cph, fnd] (ORCID:\n)", "Maintainer": "Hassan Sadiq ", "MD5sum": "148ed7bd483cf2534f98c3fab2aedba4", "_user": "bioc", "_type": "src", "_file": "queeems_1.1.0.tar.gz", "_fileid": "4551581ae112e39ebfa8dc186e84adf8cb8933a7957484a15da8ce3f00278e5e", "_filesize": 953926, "_sha256": "4551581ae112e39ebfa8dc186e84adf8cb8933a7957484a15da8ce3f00278e5e", "_created": "2026-05-29T10:16:47.000Z", "_published": "2026-05-30T05:23:12.494Z", "_jobs": [ { "job": 78626323029, "time": 162, "config": "bioc-checks", "r": "4.6.0", "check": "OK", "artifact": "7288424632" }, { "job": 78626323030, "time": 212, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7288439360" }, { "job": 78626323100, "time": 293, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7288464499" }, { "job": 78626322965, "time": 199, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7290195677" }, { "job": 78626323041, "time": 151, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7290269679" }, { "job": 78626322811, "time": 242, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7288376069" }, { "job": 78626323039, "time": 111, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7288409947" }, { "job": 78626322879, "time": 175, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7305644818" }, { "job": 78626323053, "time": 155, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7288422601" }, { "job": 78626322985, "time": 194, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7288434113" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 0 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26631483954", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/queeems", "_commit": { "id": "54d1ec1b37ed1e581a5b410e73cbefc218e9df26", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381637 }, "_maintainer": { "name": "Hassan Sadiq", "email": "hassan.t.sadiq@gmail.com", "login": "thsadiq", "description": "Mathematical statistics lecturer. Research interests: computational molecular biology (focus = natural selection modelling) and interesting data analyses!", "uuid": 177087441, "orcid": "0000-0003-0192-7134" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "Biostrings", "role": "Depends" }, { "package": "gtools", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-24", "n": 11 }, { "week": "2026-08", "n": 1 }, { "week": "2026-09", "n": 2 }, { "week": "2026-10", "n": 4 }, { "week": "2026-11", "n": 3 }, { "week": "2026-12", "n": 3 }, { "week": "2026-13", "n": 2 }, { "week": "2026-17", "n": 6 }, 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"Counts Indicating Protein Base Prevalence", "topics": [ "baseFrequency" ] }, { "page": "baseSummary-class", "title": "Protein Base Composition Numerics", "topics": [ "basecensus", "basecensus,baseSummary-method", "baseSummary", "baseSummary-class", "datatype", "datatype,baseSummary-method", "nseqs", "nseqs,baseSummary-method", "show,baseSummary-method" ] }, { "page": "bstringCodons", "title": "Convert a BStringSet Object to Codon Sequences", "topics": [ "bstringCodons", "bstringCodons,BStringSet-method", "bstringCodons.BStringSet" ] }, { "page": "citing-class", "title": "Useful Package Citations", "topics": [ "citing", "citing-class", "show, citing-method" ] }, { "page": "CnCs", "title": "Synonymous and Non-Synonymous Codon Match Counts", "topics": [ "CnCs" ] }, { "page": "cncsentropy", "title": "Global [Non-]Synonymous Entropy Index for Protein Sequence", "topics": [ "cncsentropy" ] }, { "page": "cncsframe-class", "title": "Synonymous and Non-Synonymous Frequencies", "topics": [ "cncsframe", "cncsframe-class", "nonvaries", "nonvaries,cncsframe-method", "nORs", "nORs,cncsframe-method", "nsfreqs", "nsfreqs,cncsframe-method", "nucbalance", "nucbalance,cncsframe-method", "show,cncsframe-method", "wildtriplets", "wildtriplets,cncsframe-method" ] }, { "page": "codondifferindex", "title": "Molecular Entropy Estimated from Codon Mismatches", "topics": [ "codondifferindex" ] }, { "page": "codonDissimilarity", "title": "Codon Census Matrix Matched by Nucleotide Dissimilarity", "topics": [ "codonDissimilarity", "codonDissimilarity,BStringSet,numeric-method", "codonDissimilarity.BStringSet" ] }, { "page": "diffNucBinary", "title": "Compare Codon Pairs to Identify Nucleotide Mismatch", "topics": [ "diffNucBinary" ] }, { "page": "entropyindex", "title": "Obtain Entropy Indices", "topics": [ "entropyindex", "si.renyi", "si.shannon" ] }, { "page": "fubarweights", "title": "FUBAR-like Weights", "topics": [ "fubarweights" ] }, { "page": "geneindex-class", "title": "Protein Information Entropy Handling", "topics": [ "geneindex", "geneindex-class", "gentropy", "gentropy,geneindex-method", "informula", "informula,geneindex-method", "nonvaries,geneindex-method", "renyiA", "renyiA,geneindex-method", "show,geneindex-method", "sitecount", "sitecount,geneindex-method", "useSyn", "useSyn,geneindex-method" ] }, { "page": "mnomLogl", "title": "Approximate Log-Likelihood of a Multinomial Variable", "topics": [ "mnomLogl" ] }, { "page": "molentropy", "title": "Molecular Entropy Generated Independently per Base Site", "topics": [ "molentropy" ] }, { "page": "n2cFreqs", "title": "Generate Codon Frequencies from Nucleotide Frequencies", "topics": [ "n2cFreqs" ] }, { "page": "nonSynonymous", "title": "Identify Synonymous and Non-Synonymous Codons", "topics": [ "nonSynonymous" ] }, { "page": "queeems", "title": "Quantify the Extent of Evolutionary Evidence in Molecular Sequences", "topics": [ "queeems-package", "queeems" ] }, { "page": "queeemsExtdata", "title": "Paths to 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