{
  "_id": "6a48aaa9e06c18f0a6545fc9",
  "Package": "bbmix",
  "Title": "Bayesian Model for Genotyping using RNA-Seq",
  "Version": "1.0.0",
  "Authors@R": "c(\nperson(\"Elena\", \"Vigorito\", email = \"elena.vigorito@mrc-bsu.cam.ac.uk\",  role = c(\"aut\", \"cre\")),\nperson(\"Chris\", \"Wallace\", email=\"cew54@cam.ac.uk\", role=\"aut\"))",
  "Description": "The method models RNA-seq reads using a mixture of 3\nbeta-binomial distributions to generate posterior probabilities\nfor genotyping bi-allelic single nucleotide polymorphisms.\nElena Vigorito, Anne Barton, Costantino Pitzalis, Myles J.\nLewis and Chris Wallace (2023)\n<doi:10.1093/bioinformatics/btad393> \"BBmix: a Bayesian\nbeta-binomial mixture model for accurate genotyping from\nRNA-sequencing.\"",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "Biarch": "true",
  "SystemRequirements": "GNU make",
  "RoxygenNote": "7.1.0",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-04 06:08:10 UTC",
    "User": "root"
  },
  "Author": "Elena Vigorito [aut, cre], Chris Wallace [aut]",
  "Maintainer": "Elena Vigorito <elena.vigorito@mrc-bsu.cam.ac.uk>",
  "Config/pak/sysreqs": "make",
  "Repository": "https://evigorito.r-universe.dev",
  "Date/Publication": "2023-07-06 13:00:09 UTC",
  "RemoteUrl": "https://github.com/cran/bbmix",
  "RemoteRef": "HEAD",
  "RemoteSha": "ef559b819bb265c617d876930153cdaec644d189",
  "_user": "evigorito",
  "_type": "src",
  "_file": "bbmix_1.0.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/9efdb5cac32a65b70663d57bec943a29fad6502ce32c30929bb0ff0160f9f7bf",
  "_filesize": 373267,
  "_sha256": "9efdb5cac32a65b70663d57bec943a29fad6502ce32c30929bb0ff0160f9f7bf",
  "_expires": "2026-10-12T06:39:35.000Z",
  "_created": "2026-07-04T06:08:10.000Z",
  "_published": "2026-07-04T06:39:37.284Z",
  "_jobs": [
    {
      "job": 85108986107,
      "time": 229,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8079017501"
    },
    {
      "job": 85108986105,
      "time": 238,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8079018370"
    },
    {
      "job": 85108986130,
      "time": 246,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8079019911"
    },
    {
      "job": 85108986109,
      "time": 274,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8079023015"
    },
    {
      "job": 85108986128,
      "time": 199,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8079215520"
    },
    {
      "job": 85108986125,
      "time": 483,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8079044225"
    },
    {
      "job": 85108986113,
      "time": 148,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8079207535"
    },
    {
      "job": 85108986129,
      "time": 489,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8079048749"
    },
    {
      "job": 85108650717,
      "time": 298,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8078984428"
    },
    {
      "job": 85108986090,
      "time": 190,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 85108986137,
      "time": 265,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8079022096"
    },
    {
      "job": 85108986116,
      "time": 269,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8079022529"
    },
    {
      "job": 85108986122,
      "time": 270,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8079022993"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/evigorito/actions/runs/28697127061",
  "_status": "success",
  "_upstream": "https://github.com/cran/bbmix",
  "_commit": {
    "id": "ef559b819bb265c617d876930153cdaec644d189",
    "author": "Elena Vigorito <elena.vigorito@mrc-bsu.cam.ac.uk>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.0.0\n",
    "time": 1688648409
  },
  "_maintainer": {
    "name": "Elena Vigorito",
    "email": "elena.vigorito@mrc-bsu.cam.ac.uk",
    "login": "evigorito",
    "description": "",
    "uuid": 20164062
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "BH",
      "version": ">= 1.66.0",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.0",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "version": ">= 0.3.3.3.0",
      "role": "LinkingTo"
    },
    {
      "package": "rstan",
      "version": ">= 2.18.1",
      "role": "LinkingTo"
    },
    {
      "package": "rstantools",
      "role": "LinkingTo"
    },
    {
      "package": "StanHeaders",
      "version": ">= 2.18.0",
      "role": "LinkingTo"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.0",
      "role": "Imports"
    },
    {
      "package": "rstan",
      "version": ">= 2.18.1",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "rmutil",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "evigorito",
      "count": 1,
      "uuid": 20164062
    }
  ],
  "_userbio": {
    "uuid": 20164062,
    "type": "user",
    "name": "evigorito",
    "followers": 3
  },
  "_downloads": {
    "count": 328,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bbmix"
  },
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/bbmix.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "evigorito",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2023-07-06"
    }
  ],
  "_exports": [
    "call_gt",
    "ex_alt_hom",
    "fit_bb",
    "poolreads"
  ],
  "_help": [
    {
      "page": "bbmix-package",
      "title": "The 'bbmix' package.",
      "topics": [
        "bbmix-package",
        "bbmix"
      ]
    },
    {
      "page": "call_gt",
      "title": "Call genotypes using beta binomial after model training",
      "topics": [
        "call_gt"
      ]
    },
    {
      "page": "call_help",
      "title": "call gt helper, calculate mean dbetabinom from all posterior samples",
      "topics": [
        "call_help"
      ]
    },
    {
      "page": "ex_alt_hom",
      "title": "Exclude fSNPs with no alternative allele in any sample. Also exclude fSNPs if all samples are hom.",
      "topics": [
        "ex_alt_hom"
      ]
    },
    {
      "page": "fit_bb",
      "title": "Fit beta binomial distribution to allelic counts for homozygous reference, heterozygous, homozygous alternative",
      "topics": [
        "fit_bb"
      ]
    },
    {
      "page": "gt_help",
      "title": "call gt helper, get posterior mean, expected gt and sd expected gt across all samples",
      "topics": [
        "gt_help"
      ]
    },
    {
      "page": "poolreads",
      "title": "Pool randomly selected reads from different files",
      "topics": [
        "poolreads"
      ]
    }
  ],
  "_readme": "https://github.com/cran/bbmix/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "BH",
    "callr",
    "checkmate",
    "cli",
    "cpp11",
    "data.table",
    "desc",
    "distributional",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "inline",
    "isoband",
    "labeling",
    "lifecycle",
    "loo",
    "magrittr",
    "matrixStats",
    "numDeriv",
    "otel",
    "pillar",
    "pkgbuild",
    "pkgconfig",
    "posterior",
    "processx",
    "ps",
    "QuickJSR",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RcppParallel",
    "rlang",
    "rmutil",
    "rstan",
    "rstantools",
    "S7",
    "scales",
    "StanHeaders",
    "tensorA",
    "tibble",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "bbmix.Rmd",
      "filename": "bbmix.html",
      "title": "BBmix: genotyping using RNA-seq",
      "author": "Elena Vigorito and Chris Wallace",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Install  bbmix from GitLab:",
        "Running bbmix",
        "Calling genotypes with the model trained with external default sample (NA12878)",
        "Calling genotypes with the model trained with a sample of choice",
        "Calling genotypes with a pool of samples",
        "Calling genotypes output",
        "Quality control for  genotypes"
      ],
      "created": "2023-07-06 13:00:09",
      "modified": "2023-07-06 13:00:09",
      "commits": 1
    }
  ],
  "_score": 2.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "bbmix",
  "_universes": [
    "evigorito"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-07-04T06:11:42.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "ef559b819bb265c617d876930153cdaec644d189",
      "fileid": "https://r2.ropensci.org/a6281e42b7976c9cbdd0dfe980367148c1ba37005ba419d72385b4a20a7a22b5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/evigorito/actions/runs/28697127061"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-07-04T06:11:22.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "ef559b819bb265c617d876930153cdaec644d189",
      "fileid": "https://r2.ropensci.org/93edc8bdbf76c81feff7548d8dac80777e875bbb36babc5afcc68754cdac90a1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/evigorito/actions/runs/28697127061"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-07-04T06:11:50.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "ef559b819bb265c617d876930153cdaec644d189",
      "fileid": "https://r2.ropensci.org/84d86ff0f2455157bb07d314372dbbd790b9af3e68a3236072b7e828a8a1b576",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/evigorito/actions/runs/28697127061"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-07-04T06:11:48.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "ef559b819bb265c617d876930153cdaec644d189",
      "fileid": "https://r2.ropensci.org/f73bc09180d616b37a6f8763fd1373f6287dde1d07e3852c39d6b12c8eff25c3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/evigorito/actions/runs/28697127061"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-07-04T06:37:41.000Z",
      "arch": "aarch64",
      "commit": "ef559b819bb265c617d876930153cdaec644d189",
      "fileid": "https://r2.ropensci.org/acc5511afd8c164ce5d6b999771d2d02275362a46a9fec594afc4d81ef8caf5b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/evigorito/actions/runs/28697127061"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-07-04T06:12:54.000Z",
      "arch": "x86_64",
      "commit": "ef559b819bb265c617d876930153cdaec644d189",
      "fileid": "https://r2.ropensci.org/95d1b6f36bcb1876391e09e7e4583d4d3386b355d7307364d93fd6f53cfadde4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/evigorito/actions/runs/28697127061"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-07-04T06:37:01.000Z",
      "arch": "aarch64",
      "commit": "ef559b819bb265c617d876930153cdaec644d189",
      "fileid": "https://r2.ropensci.org/d3a9db83e122066adca870f11b7972c7c9fdca26fc29e5765c8ba4d4878993f7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/evigorito/actions/runs/28697127061"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-07-04T06:13:34.000Z",
      "arch": "x86_64",
      "commit": "ef559b819bb265c617d876930153cdaec644d189",
      "fileid": "https://r2.ropensci.org/aa92ce64aedd96a2b4010c2d9f8bd6c5b41f2713cff5264e05acf7345be44e0b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/evigorito/actions/runs/28697127061"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-07-04T06:10:44.000Z",
      "arch": "x86_64",
      "commit": "ef559b819bb265c617d876930153cdaec644d189",
      "fileid": "https://r2.ropensci.org/816cc0da0e21ab86bea76d15c3c7f2f57c551154f620dcb7b9c9118d09be28cd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/evigorito/actions/runs/28697127061"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-07-04T06:10:54.000Z",
      "arch": "x86_64",
      "commit": "ef559b819bb265c617d876930153cdaec644d189",
      "fileid": "https://r2.ropensci.org/f7da7cf22d0e9da9dd3c0d84fff0bd26485b6cb1f24446110ca811c5e5cc5e24",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/evigorito/actions/runs/28697127061"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-07-04T06:10:58.000Z",
      "arch": "x86_64",
      "commit": "ef559b819bb265c617d876930153cdaec644d189",
      "fileid": "https://r2.ropensci.org/31f2d638a46b60a067f6762699f2169cd9da462dabc9695bdf726f801f6bf1fc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/evigorito/actions/runs/28697127061"
    }
  ]
}