{ "_id": "6a47ead5e06c18f0a652472e", "Package": "cubfits", "Version": "0.1-4", "Date": "2021-11-06", "Title": "Codon Usage Bias Fits", "Authors@R": "c(person(\"Wei-Chen\", \"Chen\", role = c(\"aut\", \"cre\"), email =\n\"wccsnow@gmail.com\"),\nperson(\"Russell\", \"Zaretzki\", role = \"aut\", email = \"rzaretzk@utk.edu\"),\nperson(\"William\", \"Howell\", role = \"aut\"),\nperson(\"Cedric\", \"Landerer\", role = \"aut\"),\nperson(\"Drew\", \"Schmidt\", role = \"aut\"),\nperson(\"Michael A.\", \"Gilchrist\", role = \"aut\", email = \"mikeg@utk.edu\"),\nperson(\"Preston\", \"Hewgley\", role = \"ctb\"),\nperson(\"Students\", \"REU13\", role = \"ctb\"))", "LazyLoad": "yes", "LazyData": "yes", "Description": "Estimating mutation and selection coefficients on\nsynonymous codon bias usage based on models of ribosome\noverhead cost (ROC). Multinomial logistic regression and Markov\nChain Monte Carlo are used to estimate and predict protein\nproduction rates with/without the presence of expressions and\nmeasurement errors. Work flows with examples for simulation,\nestimation and prediction processes are also provided with\nparallelization speedup. The whole framework is tested with\nyeast genome and gene expression data of Yassour, et al. (2009)\n.", "License": "Mozilla Public License 2.0", "BugReports": "https://github.com/snoweye/cubfits/issues", "URL": "https://github.com/snoweye/cubfits", "NeedsCompilation": "yes", "Maintainer": "Wei-Chen Chen ", "Repository": "https://snoweye.r-universe.dev", "Date/Publication": "2021-11-07 01:54:08 UTC", "RemoteUrl": "https://github.com/snoweye/cubfits", "RemoteRef": "HEAD", "RemoteSha": "7462d9f475ba4ceb18109fbc142f610ab93698b1", "Packaged": { "Date": "2026-07-03 16:56:38 UTC", "User": "root" }, "Author": "Wei-Chen Chen [aut, cre],\nRussell Zaretzki [aut],\nWilliam Howell [aut],\nCedric Landerer [aut],\nDrew Schmidt [aut],\nMichael A. Gilchrist [aut],\nPreston Hewgley [ctb],\nStudents REU13 [ctb]", "_user": "snoweye", "_type": "src", "_file": "cubfits_0.1-4.tar.gz", "_fileid": "https://r2.ropensci.org/4eb26169bdd161832caa352a75ea60a972146c0f9171ece4c043a4c3e889e40b", "_filesize": 1581892, "_sha256": "4eb26169bdd161832caa352a75ea60a972146c0f9171ece4c043a4c3e889e40b", "_expires": "2026-10-11T17:01:07.000Z", "_created": "2026-07-03T16:56:38.000Z", "_published": "2026-07-03T17:01:09.218Z", "_jobs": [ { "job": 85042920084, "time": 140, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8071680492" }, { "job": 85042920088, "time": 126, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8071676855" }, { "job": 85042920075, "time": 138, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8071680298" }, { "job": 85042920078, "time": 128, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8071677013" }, { "job": 85042920071, "time": 80, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8071665767" }, { "job": 85042920140, "time": 189, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8071691870" }, { "job": 85042920056, "time": 99, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8071670204" }, { "job": 85042920080, "time": 201, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8071694533" }, { "job": 85042582669, "time": 163, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8071646109" }, { "job": 85042920021, "time": 135, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8071678704" }, { "job": 85042920036, "time": 118, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8071674800" }, { "job": 85042920034, "time": 89, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8071667900" }, { "job": 85042920043, "time": 110, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8071672829" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/snoweye/actions/runs/28673721820", "_status": "success", "_upstream": "https://github.com/snoweye/cubfits", "_commit": { "id": "7462d9f475ba4ceb18109fbc142f610ab93698b1", "author": "snoweye ", "committer": "snoweye ", "message": "minor\n", "time": 1636250048 }, "_maintainer": { "name": "Wei-Chen Chen", "email": "wccsnow@gmail.com", "login": "snoweye", "description": "", "uuid": 2565440 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "coda", "role": "Depends" }, { "package": "foreach", "role": "Depends" }, { "package": "parallel", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "graphics", "role": "Depends" }, { "package": "utils", "role": "Depends" }, { "package": "seqinr", "role": "Suggests" }, { "package": "VGAM", "role": "Suggests" }, { "package": "EMCluster", "role": "Suggests" }, { "package": "pbdMPI", "version": ">= 0.3-1", "role": "Enhances" } ], "_owner": "snoweye", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 7, "_contributors": [ { "user": "snoweye", "count": 116, "uuid": 2565440 }, { "user": "clandere", "count": 38, "uuid": 7977755 }, { "user": "ozway", "count": 14, "uuid": 8481135 }, { "user": "wrathematics", "count": 4, "uuid": 2561297 } ], "_userbio": { "uuid": 2565440, "type": "user", "name": "Wei-Chen Chen", "followers": 53 }, "_downloads": { "count": 820, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/cubfits" }, "_devurl": "https://github.com/snoweye/cubfits", "_searchresults": 33, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/cubfits.html", "manual.pdf" ], "_homeurl": "https://github.com/snoweye/cubfits", "_realowner": "snoweye", "_cranurl": true, "_releases": [ { "version": "0.1-0", "date": "2014-05-19" }, { "version": "0.1-2", "date": "2016-01-25" }, { "version": "0.1-3", "date": "2017-04-30" }, { "version": "0.1-4", "date": "2021-11-07" } ], "_exports": [ "asl.optim", "calc_cai_values", "calc_scu_values", "calc_scuo_values", "codon.low2up", "codon.up2low", "convert.b.to.bVec", "convert.bVec.to.b", "convert.n.to.list", "convert.reu13.df.to.list", "convert.seq.data.to.string", "convert.y.to.list", "convert.y.to.scuo", "cp.workflow", "cubappr", "cubfits", "cubmultichain", "cubpred", "cubsinglechain", "dasl", "dasla", "dmixnormerr", "dna.low2up", "dna.up2low", "estimatePhi", "fitMultinom", "gen.n", "gen.phi.Obs", "gen.reu13.df", "gen.reu13.list", "gen.scuo", "gen.y", "get.expath", "get.workflow", "init.function", "mixnormerr.optim", "normalizeDataSet", "pasl", "pasla", "plotaddmodel", "plotbin", "plotbin.NSE", "plotBMatrixPosterior", "plotCUB", "plotCUB.NSE", "plotExpectedPhiTrace", "plotmodel", "plotprxy", "plotPTraces", "plotTraces", "prop.bin.roc", "prop.model.nse", "prop.model.roc", "qasl", "qasla", "rasl", "rasla", "read.phi.df", "read.seq", "readGenome", "rearrange.n", "rearrange.phi.Obs", "rearrange.reu13.df", "rearrange.y", "scuo.random", "simu.mixnormerr", "simu.orf", "simu.phi.Obs", "write.phi.df", "write.seq" ], "_datasets": [ { "name": ".CF.AC", "title": "Default Controlling Options", "object": "control", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": ".CF.CONF", "title": "Default Controlling Options", "object": "control", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": ".CF.CT", "title": "Default Controlling Options", "object": "control", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": ".CF.DP", "title": "Default Controlling Options", "object": "control", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": ".CF.GV", "title": "Default Controlling Options", "object": "global", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": ".CF.OP", "title": "Default Controlling Options", "object": "control", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": ".CF.PARAM", "title": "Default Controlling Options", "object": "control", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": ".CF.PT", "title": "Default Controlling Options", "object": "plot", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": ".CO.CT", "title": "Default Controlling Options", "object": "control_optim", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": ".cubfitsEnv", "title": "Default Controlling Options", "object": "envir", "class": [ "environment" ], "fields": [], "table": false, "tojson": false }, { "name": "b.Init", "title": "Datasets for Demonstrations", "object": "b.Init", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "ex.test", "title": "Datasets for Demonstrations", "object": "ex.test", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "ex.train", "title": "Datasets for Demonstrations", "object": "ex.train", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "yassour", "title": "Yassour 2009 Yeast Experiment Dataset", "object": "yassour", "class": [ "data.frame" ], "fields": [ "ORF", "YPD0.1", "YPD0.2", "YPD15.1", "YPD15.2" ], "rows": 6303, "table": true, "tojson": true }, { "name": "yassour.info", "title": "Posterior Results of Yassour 2009 Yeast Experiment Dataset", "object": "yassour.mcmc", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "yassour.PM.appr", "title": "Posterior Results of Yassour 2009 Yeast Experiment Dataset", "object": "yassour.mcmc", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "yassour.PM.fits", "title": "Posterior Results of Yassour 2009 Yeast Experiment Dataset", "object": "yassour.mcmc", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "00_cubfits-package", "title": "Codon Bias Usage Fits", "topics": [ "cubfits-package" ] }, { "page": "u4_asl", "title": "The Asymmetric Laplace Distribution", "topics": [ "asl.optim", "dasl", "dasla", "pasl", "pasla", "qasl", "qasla", "rasl", "rasla" ] }, { "page": "c2_convergence", "title": "Cedric Convergence Utilities", "topics": [ "cubmultichain", "cubsinglechain", "isConverged" ] }, { "page": "c1_io", "title": "Cedric IO Utilities", "topics": [ "normalizeDataSet", "readGenome" ] }, { "page": "c0_plot", "title": "Cedric Plot Utilities", "topics": [ "plotCUB", "plotExpectedPhiTrace", "plotPTraces", "plotTraces" ] }, { "page": "t4_cai", "title": "Function for Codon Adaptation Index (CAI)", "topics": [ "calc_cai_values" ] }, { "page": "yy_control", "title": "Default Controlling Options", "topics": [ ".CF.AC", ".CF.CONF", ".CF.CT", ".CF.DP", ".CF.GV", ".CF.OP", ".CF.PARAM", ".CF.PT", ".CO.CT", ".cubfitsEnv" ] }, { "page": "u2_convert", "title": "Convert Data Frame to Other Formats", "topics": [ "codon.low2up", "codon.up2low", "convert.b.to.bVec", "convert.bVec.to.b", "convert.n.to.list", "convert.reu13.df.to.list", "convert.seq.data.to.string", "convert.y.to.list", "convert.y.to.scuo", "DataConverting", "dna.low2up", "dna.up2low" ] }, { "page": "a2_cubappr", "title": "Codon Usage Bias Approximation for ORFs without Expression", "topics": [ "cubappr" ] }, { "page": "a1_cubfits", "title": "Codon Usage Bias Fits for Observed ORFs and Expression", "topics": [ "cubfits" ] }, { "page": "a3_cubpred", "title": "Codon Usage Bias Prediction for Observed ORFs", "topics": [ "cubpred" ] }, { "page": "xx_dataformat", "title": "Data Formats", "topics": [ "AllDataFormats", "b", "bVec", "n", "n.list", "phi.df", "phi.Obs", "reu13.df", "reu13.list", "scuo", "seq.data", "seq.string", "y", "y.list" ] }, { "page": "yy_dataset", "title": "Datasets for Demonstrations", "topics": [ "b.Init", "ex.test", "ex.train" ] }, { "page": "s2_estimatePhi", "title": "Initialization of Phi (Generic)", "topics": [ "estimatePhi" ] }, { "page": "s1_fitMultinom", "title": "Fit Multinomial Model (Generic)", "topics": [ "fitMultinom" ] }, { "page": "u1_gen", "title": "Generating Data Structure", "topics": [ "DataGenerating", "gen.n", "gen.phi.Obs", "gen.reu13.df", "gen.reu13.list", "gen.scuo", "gen.y" ] }, { "page": "s0_init.function", "title": "Initial Generic Functions of Codon Usage Bias Fits", "topics": [ "init.function" ] }, { "page": "u0_io", "title": "Input and Output Utility", "topics": [ "DataIO", "get.expath", "read.phi.df", "read.seq", "write.phi.df", "write.seq" ] }, { "page": "u5_mixnorm", "title": "Mixed Normal Optimization", "topics": [ "dmixnormerr", "mixnormerr.optim" ] }, { "page": "b1_plotbin", "title": "Plot Binning Results", "topics": [ "plotbin", "prop.bin.roc" ] }, { "page": "b2_plotmodel", "title": "Plot Fitted Models", "topics": [ "plotaddmodel", "plotmodel", "prop.model.roc" ] }, { "page": "b0_plotprxy", "title": "Predictive X-Y Plot", "topics": [ "plotprxy" ] }, { "page": "yy_yassour_PM", "title": "Posterior Results of Yassour 2009 Yeast Experiment Dataset", "topics": [ "yassour.info", "yassour.PM.appr", "yassour.PM.fits" ] }, { "page": "vv_print", "title": "Functions for Printing Objects According to Classes", "topics": [ "print.mixnormerr" ] }, { "page": "t3_scuo.random", "title": "Generate Randomized SCUO Index", "topics": [ "scuo.random" ] }, { "page": "u3_rearrange", "title": "Rearrange Data Structure by ORF Names", "topics": [ "rearrange.n", "rearrange.phi.Obs", "rearrange.reu13.df", "rearrange.y" ] }, { "page": "t2_scuo", "title": "Function for Synonymous Codon Usage Order (SCUO) Index", "topics": [ "calc_scuo_values" ] }, { "page": "t5_scu", "title": "Function for Selection on Codon Usage (SCU)", "topics": [ "calc_scu_values" ] }, { "page": "t1_simulation", "title": "Simulate ORFs and Expression Data", "topics": [ "simu.mixnormerr", "simu.orf", "simu.phi.Obs" ] }, { "page": "yy_yassour", "title": "Yassour 2009 Yeast Experiment Dataset", "topics": [ "yassour" ] } ], "_rundeps": [ "coda", "codetools", "foreach", "iterators", "lattice" ], "_vignettes": [ { "source": "cubfits-guide.Rnw", "filename": "cubfits-guide.pdf", "title": "cubfits-guide", "engine": "utils::Sweave", "headings": [ "Acknowledgement", "1. Introduction", "2. Main Functions", "3. Parallel Speedup", "4. Work Flows", "5. Utilities", "6. FAQs", "7. Miscellaneous", "References" ], "created": "2014-04-02 16:33:20", "modified": "2017-04-29 21:14:53", "commits": 7 } ], "_score": 4.8407332346118075, "_indexed": true, "_nocasepkg": "cubfits", "_universes": [ "snoweye" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1-4", "date": "2026-07-03T16:59:04.000Z", "distro": "resolute", "arch": "aarch64", "commit": "7462d9f475ba4ceb18109fbc142f610ab93698b1", "fileid": "https://r2.ropensci.org/441561ad00f5135531b843aa5de0a78a2fb83e824c35dd7086fd851113da1abd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/snoweye/actions/runs/28673721820" }, { "r": "4.7.0", "os": "linux", "version": "0.1-4", "date": "2026-07-03T16:58:44.000Z", "distro": "resolute", "arch": "x86_64", "commit": "7462d9f475ba4ceb18109fbc142f610ab93698b1", "fileid": "https://r2.ropensci.org/f556057959d626a7aba2a1b375d5741614b04ef4351c9e4b575b609067fd831b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/snoweye/actions/runs/28673721820" }, { "r": "4.6.1", "os": "linux", "version": "0.1-4", "date": "2026-07-03T16:59:06.000Z", "distro": "resolute", "arch": "aarch64", "commit": "7462d9f475ba4ceb18109fbc142f610ab93698b1", "fileid": "https://r2.ropensci.org/1ef2e61e722678284930e36f637b971d400529e941fc873eedd0ed62ceb9161a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/snoweye/actions/runs/28673721820" }, { "r": "4.6.1", "os": "linux", "version": "0.1-4", "date": "2026-07-03T16:58:45.000Z", "distro": "resolute", "arch": "x86_64", "commit": "7462d9f475ba4ceb18109fbc142f610ab93698b1", "fileid": "https://r2.ropensci.org/f25e88afeccad0fb8673c837cce9af5522653e231518fc8b5fed71a4e6335898", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/snoweye/actions/runs/28673721820" }, { "r": "4.5.3", "os": "mac", "version": "0.1-4", "date": "2026-07-03T16:58:06.000Z", "arch": "aarch64", "commit": "7462d9f475ba4ceb18109fbc142f610ab93698b1", "fileid": "https://r2.ropensci.org/383495af56f422b59b3ee8ccd1fdce06160bf484798da79277d141124ad10aaa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/snoweye/actions/runs/28673721820" }, { "r": "4.5.3", "os": "mac", "version": "0.1-4", "date": "2026-07-03T16:59:34.000Z", "arch": "x86_64", "commit": "7462d9f475ba4ceb18109fbc142f610ab93698b1", "fileid": "https://r2.ropensci.org/b4c572e1d5762ece7cd79302b9a7656177eb302d6dc13c4f0b9a53201ac22bcf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/snoweye/actions/runs/28673721820" }, { "r": "4.6.1", "os": "mac", "version": "0.1-4", "date": "2026-07-03T16:58:19.000Z", "arch": "aarch64", "commit": "7462d9f475ba4ceb18109fbc142f610ab93698b1", "fileid": "https://r2.ropensci.org/957ae8f1254fc9486f855fc683fa969e2120819ba12147e4428faf6ad14d3200", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/snoweye/actions/runs/28673721820" }, { "r": "4.6.1", "os": "mac", "version": "0.1-4", "date": "2026-07-03T16:59:42.000Z", "arch": "x86_64", "commit": "7462d9f475ba4ceb18109fbc142f610ab93698b1", "fileid": "https://r2.ropensci.org/ded75b8bedbdd959199362c9d22f1ffd98f147ebb26de35a007fe659146dc306", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/snoweye/actions/runs/28673721820" }, { "r": "4.6.0", "os": "wasm", "version": "0.1-4", "date": "2026-07-03T16:59:15.000Z", "arch": "emscripten", "commit": "7462d9f475ba4ceb18109fbc142f610ab93698b1", "fileid": "https://r2.ropensci.org/89d8040466a2fc7ed0aef573b61a197249e83d832c7f80cdddcde8fbb236566d", "status": "success", "buildurl": "https://github.com/r-universe/snoweye/actions/runs/28673721820" }, { "r": "4.7.0", "os": "win", "version": "0.1-4", "date": "2026-07-03T16:58:13.000Z", "arch": "x86_64", "commit": "7462d9f475ba4ceb18109fbc142f610ab93698b1", "fileid": "https://r2.ropensci.org/b590b4409948fac7c03920d41534b2a64fd423ca1c25a276f3603e24ecc4e96e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/snoweye/actions/runs/28673721820" }, { "r": "4.5.3", "os": "win", "version": "0.1-4", "date": "2026-07-03T16:57:53.000Z", "arch": "x86_64", "commit": "7462d9f475ba4ceb18109fbc142f610ab93698b1", "fileid": "https://r2.ropensci.org/ffc51bb4ca50423bbc06a0d632707f2b12a1fcc4c66931ed5233722ed0f8ea5f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/snoweye/actions/runs/28673721820" }, { "r": "4.6.1", "os": "win", "version": "0.1-4", "date": "2026-07-03T16:58:10.000Z", "arch": "x86_64", "commit": "7462d9f475ba4ceb18109fbc142f610ab93698b1", "fileid": "https://r2.ropensci.org/bb2fc6c48d08d0ed3fa8a9b7c981b13c7babb4a8e930b8a9987ebb47474e6210", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/snoweye/actions/runs/28673721820" } ] }