{
  "_id": "6a195158acfb0bcc41ddfb05",
  "Package": "MouseFM",
  "Type": "Package",
  "Title": "In-silico methods for genetic finemapping in inbred mice",
  "Version": "1.22.0",
  "Authors@R": "c(person(\"Matthias\", \"Munz\", role = c(\"aut\", \"cre\"), \nemail = \"matthias.munz@gmx.de\", comment = c(ORCID = \"0000-0002-4728-3357\")),\nperson(\"Inken\", \"Wohlers\", role = c(\"aut\"),\nemail = \"inken.wohlers@uni-luebeck.de.de\", comment = c(ORCID = \"0000-0003-4004-0464\")),\nperson(\"Hauke\", \"Busch\", role = c(\"aut\"),\nemail = \"hauke.busch@uni-luebeck.de.de\", comment = c(ORCID = \"0000-0003-4763-4521\"))\n)",
  "Description": "This package provides methods for genetic finemapping in\ninbred mice by taking advantage of their very high homozygosity\nrate (>95%).",
  "Encoding": "UTF-8",
  "BugReports": "https://github.com/matmu/MouseFM/issues",
  "License": "GPL-3",
  "VignetteBuilder": "knitr",
  "biocViews": "Genetics, SNP, GeneTarget, VariantAnnotation,\nGenomicVariation, MultipleComparison, SystemsBiology,\nMathematicalBiology, PatternLogic, GenePrediction,\nBiomedicalInformatics, FunctionalGenomics",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "libicu-dev libpng-dev libxml2-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:57:31 UTC",
  "RemoteUrl": "https://github.com/bioc/MouseFM",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "ebfdc4412922ed9b8eeb4f9472bf59c6d287076a",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 07:33:35 UTC",
    "User": "root"
  },
  "Author": "Matthias Munz [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-4728-3357>),\nInken Wohlers [aut] (ORCID: <https://orcid.org/0000-0003-4004-0464>),\nHauke Busch [aut] (ORCID: <https://orcid.org/0000-0003-4763-4521>)",
  "Maintainer": "Matthias Munz <matthias.munz@gmx.de>",
  "MD5sum": "d5ce00ca9d0f03236eacc5ea109a1344",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "MouseFM_1.22.0.tar.gz",
  "_fileid": "d7467affcb867ba88bbf0285836a4667ff9d931bd90c20c9dbbea11e4a657d47",
  "_filesize": 254930,
  "_sha256": "d7467affcb867ba88bbf0285836a4667ff9d931bd90c20c9dbbea11e4a657d47",
  "_created": "2026-05-29T07:33:35.000Z",
  "_published": "2026-05-29T08:42:00.019Z",
  "_jobs": [
    {
      "job": 78457976920,
      "time": 177,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7285543269"
    },
    {
      "job": 78457976949,
      "time": 384,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7285604179"
    },
    {
      "job": 78457976937,
      "time": 320,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7285585202"
    },
    {
      "job": 78457977008,
      "time": 191,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7286653733"
    },
    {
      "job": 78457976951,
      "time": 207,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286656316"
    },
    {
      "job": 78457365060,
      "time": 260,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7285492583"
    },
    {
      "job": 78457976943,
      "time": 125,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7285528902"
    },
    {
      "job": 78457976961,
      "time": 251,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7285564210"
    },
    {
      "job": 78457976970,
      "time": 251,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7285564157"
    },
    {
      "job": 78457976934,
      "time": 214,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7285553621"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 9
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624328711",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/MouseFM",
  "_commit": {
    "id": "ebfdc4412922ed9b8eeb4f9472bf59c6d287076a",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777381051
  },
  "_maintainer": {
    "name": "Matthias Munz",
    "email": "matthias.munz@gmx.de",
    "login": "matmu",
    "description": "",
    "uuid": 94687,
    "orcid": "0000-0002-4728-3357"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "curl",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "gtools",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "rlist",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "biomaRt",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-30",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-12",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.23.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.22.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "genetics",
    "snp",
    "genetarget",
    "variantannotation",
    "genomicvariation",
    "multiplecomparison",
    "systemsbiology",
    "mathematicalbiology",
    "patternlogic",
    "geneprediction",
    "biomedicalinformatics",
    "functionalgenomics",
    "finemap",
    "gene-candidates",
    "inbred-mice",
    "inbred-strains",
    "mouse",
    "qtl",
    "qtl-mapping"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "matmu",
      "count": 87,
      "uuid": 94687
    },
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 8,
      "uuid": 2746443
    },
    {
      "user": "hpages",
      "count": 1,
      "uuid": 8810451
    },
    {
      "user": "lshep",
      "count": 1,
      "uuid": 18724380
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 312,
    "source": "https://www.bioconductor.org/packages/stats/bioc/MouseFM"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/matmu/mousefm",
  "_searchresults": 15,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/MouseFM.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/matmu/mousefm",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "annotate_consequences",
    "annotate_mouse_genes",
    "avail_chromosomes",
    "avail_consequences",
    "avail_strains",
    "df2GRanges",
    "fetch",
    "finemap",
    "get_top",
    "getURL",
    "GRanges2df",
    "prio",
    "ref_genome",
    "setURL",
    "vis_reduction_factors"
  ],
  "_help": [
    {
      "page": "annotate_consequences",
      "title": "Annotate with consequences",
      "topics": [
        "annotate_consequences"
      ]
    },
    {
      "page": "annotate_mouse_genes",
      "title": "Annotate with genes",
      "topics": [
        "annotate_mouse_genes"
      ]
    },
    {
      "page": "avail_chromosomes",
      "title": "Available chromosomes",
      "topics": [
        "avail_chromosomes"
      ]
    },
    {
      "page": "avail_consequences",
      "title": "Available consequences",
      "topics": [
        "avail_consequences"
      ]
    },
    {
      "page": "avail_strains",
      "title": "Available strains",
      "topics": [
        "avail_strains"
      ]
    },
    {
      "page": "df2GRanges",
      "title": "Data frame to GenomicRanges::GRanges object",
      "topics": [
        "df2GRanges"
      ]
    },
    {
      "page": "fetch",
      "title": "Fetch",
      "topics": [
        "fetch"
      ]
    },
    {
      "page": "finemap",
      "title": "Finemapping of genetic regions",
      "topics": [
        "finemap"
      ]
    },
    {
      "page": "get_top",
      "title": "Best strain combinations",
      "topics": [
        "get_top"
      ]
    },
    {
      "page": "getURL",
      "title": "Get backend service url",
      "topics": [
        "getURL"
      ]
    },
    {
      "page": "GRanges2df",
      "title": "GenomicRanges::GRanges object to data frame",
      "topics": [
        "GRanges2df"
      ]
    },
    {
      "page": "prio",
      "title": "Prioritization of inbred mouse strains for refining genetic regions",
      "topics": [
        "prio"
      ]
    },
    {
      "page": "ref_genome",
      "title": "Reference genome version",
      "topics": [
        "ref_genome"
      ]
    },
    {
      "page": "setURL",
      "title": "Set backend service url",
      "topics": [
        "setURL"
      ]
    },
    {
      "page": "vis_reduction_factors",
      "title": "Visualize",
      "topics": [
        "vis_reduction_factors"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/MouseFM/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "AnnotationDbi",
    "askpass",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "dplyr",
    "farver",
    "fastmap",
    "filelock",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "gtools",
    "hms",
    "httr",
    "httr2",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lifecycle",
    "magrittr",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "rlang",
    "rlist",
    "RSQLite",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "fetch.Rmd",
      "filename": "fetch.html",
      "title": "Fetch homozygous genotypes of inbred mouse strains",
      "author": "Matthias Munz",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Loading package",
        "Example function calls",
        "Output of Session Info"
      ],
      "created": "2020-05-18 12:39:07",
      "modified": "2020-06-08 08:31:14",
      "commits": 3
    },
    {
      "source": "finemap.Rmd",
      "filename": "finemap.html",
      "title": "Finemapping of genetic regions in inbred mice",
      "author": "Matthias Munz",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Loading package",
        "Example function calls",
        "Output of Session Info"
      ],
      "created": "2020-05-18 08:33:25",
      "modified": "2020-06-08 08:31:14",
      "commits": 6
    },
    {
      "source": "prio.Rmd",
      "filename": "prio.html",
      "title": "Prioritization of inbred mouse strains for resolving genetic regions",
      "author": "Matthias Munz",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Loading package",
        "Example function calls",
        "Output of Session Info"
      ],
      "created": "2020-05-18 08:33:25",
      "modified": "2020-06-08 08:31:14",
      "commits": 5
    }
  ],
  "_score": 5.556302500767288,
  "_indexed": false,
  "_nocasepkg": "mousefm",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/MouseFM",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.22.0",
      "date": "2026-05-29T07:38:12.000Z",
      "distro": "noble",
      "commit": "ebfdc4412922ed9b8eeb4f9472bf59c6d287076a",
      "fileid": "0b0b2e392a775550da38765318e5644ac8d665318f1d0e7dfa1a82e75358b328",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624328711"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.22.0",
      "date": "2026-05-29T07:36:40.000Z",
      "distro": "noble",
      "commit": "ebfdc4412922ed9b8eeb4f9472bf59c6d287076a",
      "fileid": "23c7072fed90404cc75fca3410facd5fcccddfeea59e2b8281b17c4fa09deaa4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624328711"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.22.0",
      "date": "2026-05-29T08:39:29.000Z",
      "commit": "ebfdc4412922ed9b8eeb4f9472bf59c6d287076a",
      "fileid": "239d64e843a2851a66e5e883cd8421cbc52fcb2f64e6985a4dac1c719d40757d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624328711"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.22.0",
      "date": "2026-05-29T08:39:31.000Z",
      "commit": "ebfdc4412922ed9b8eeb4f9472bf59c6d287076a",
      "fileid": "8757f3a400fd79d88c30ac11c1815c99d71301c0d749ce46cfc879384d502a8f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624328711"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.22.0",
      "date": "2026-05-29T07:36:07.000Z",
      "commit": "ebfdc4412922ed9b8eeb4f9472bf59c6d287076a",
      "fileid": "f09be8f49e881bf6373c670ceeea4536c0d8286f32ba82a95a3fe108ac472358",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624328711"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.22.0",
      "date": "2026-05-29T07:35:19.000Z",
      "commit": "ebfdc4412922ed9b8eeb4f9472bf59c6d287076a",
      "fileid": "279c7c3d4dcca9aff99ac33992767d7dc430f1a1d609e34345f4cf9e8b088ded",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624328711"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.22.0",
      "date": "2026-05-29T07:35:11.000Z",
      "commit": "ebfdc4412922ed9b8eeb4f9472bf59c6d287076a",
      "fileid": "42b426b216c8abbf85a8ba9e9e39740afde4c39ed5a9505dee76af89b0380f2a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624328711"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.22.0",
      "date": "2026-05-29T07:35:08.000Z",
      "commit": "ebfdc4412922ed9b8eeb4f9472bf59c6d287076a",
      "fileid": "112f7a74c913d3c82ef7321ea39a426a578f97f64a24568c101935012616dc4e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624328711"
    }
  ]
}