{
  "_id": "6a10476facfb0bcc41c9ef39",
  "Package": "MetaboCoreUtils",
  "Title": "Core Utils for Metabolomics Data",
  "Version": "1.21.1",
  "Description": "MetaboCoreUtils defines metabolomics-related core\nfunctionality provided as low-level functions to allow a data\nstructure-independent usage across various R packages. This\nincludes functions to calculate between ion (adduct) and\ncompound mass-to-charge ratios and masses or functions to work\nwith chemical formulas. The package provides also a set of\nadduct definitions and information on some commercially\navailable internal standard mixes commonly used in MS\nexperiments.",
  "Authors@R": "c(person(given = \"Johannes\", family = \"Rainer\",\nemail = \"Johannes.Rainer@eurac.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-6977-7147\")),\nperson(given = \"Michael\", family = \"Witting\",\nemail = \"michael.witting@helmholtz-muenchen.de\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-1462-4426\")),\nperson(given = \"Andrea\", family = \"Vicini\",\nemail = \"andrea.vicini@eurac.edu\",\nrole = \"aut\"),\nperson(given = \"Liesa\", family = \"Salzer\",\nemail = \"liesa.salzer@helmholtz-muenchen.de\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0003-0761-0656\")),\nperson(given = \"Sebastian\", family = \"Gibb\",\nemail = \"mail@sebastiangibb.de\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0001-7406-4443\")),\nperson(given = \"Michael\", family = \"Stravs\",\nemail = \"stravsmi@eawag.ch\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-1426-8572\")),\nperson(given = \"Roger\", family = \"Gine\",\nemail = \"alrgibe9@gmail.com\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-0288-9619\")),\nperson(given = \"William\", family = \"Kumler\",\nemail = \"wkumler@uw.edu\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-5022-8009\")),\nperson(given = \"Philippine\", family = \"Louail\",\nemail = \"philippine.louail@eurac.edu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0009-0007-5429-6846\")),\nperson(given = \"Gabriele\", family = \"Tomè\",\nemail = \"gabriele.tome@eurac.edu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-3976-6068\",\nfnd = \"MetaRbolomics4Galaxy project (CUP: D53C25001030003) co-funded by the Autonomous Province of Bolzano under the Joint Projects South Tyrol–Germany 2025 program.\"))\n)",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "BugReports": "https://github.com/RforMassSpectrometry/MetaboCoreUtils/issues",
  "URL": "https://github.com/RforMassSpectrometry/MetaboCoreUtils",
  "biocViews": "Infrastructure, Metabolomics, MassSpectrometry",
  "Roxygen": "list(markdown=TRUE)",
  "RoxygenNote": "7.3.3",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-30 05:55:35 UTC",
  "RemoteUrl": "https://github.com/bioc/MetaboCoreUtils",
  "RemoteRef": "HEAD",
  "RemoteSha": "1e25732196a281aea891b040bfe6efe07841411e",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-10 09:33:45 UTC",
    "User": "root"
  },
  "Author": "Johannes Rainer [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-6977-7147>),\nMichael Witting [aut] (ORCID: <https://orcid.org/0000-0002-1462-4426>),\nAndrea Vicini [aut],\nLiesa Salzer [ctb] (ORCID: <https://orcid.org/0000-0003-0761-0656>),\nSebastian Gibb [aut] (ORCID: <https://orcid.org/0000-0001-7406-4443>),\nMichael Stravs [ctb] (ORCID: <https://orcid.org/0000-0002-1426-8572>),\nRoger Gine [aut] (ORCID: <https://orcid.org/0000-0003-0288-9619>),\nWilliam Kumler [aut] (ORCID: <https://orcid.org/0000-0002-5022-8009>),\nPhilippine Louail [aut] (ORCID:\n<https://orcid.org/0009-0007-5429-6846>),\nGabriele Tomè [aut] (ORCID: <https://orcid.org/0000-0002-3976-6068>,\nfnd: MetaRbolomics4Galaxy project (CUP: D53C25001030003) co-funded\nby the Autonomous Province of Bolzano under the Joint Projects\nSouth Tyrol–Germany 2025 program.)",
  "Maintainer": "Johannes Rainer <Johannes.Rainer@eurac.edu>",
  "MD5sum": "1398f556a7ebd50da32c85f958d81a5a",
  "_user": "bioc",
  "_type": "src",
  "_file": "MetaboCoreUtils_1.21.1.tar.gz",
  "_fileid": "0c763c2a1e3f2b38da52f4946239720e8e89733c0e6bcad730a7928bb77bc887",
  "_filesize": 1202411,
  "_sha256": "0c763c2a1e3f2b38da52f4946239720e8e89733c0e6bcad730a7928bb77bc887",
  "_created": "2026-05-10T09:33:45.000Z",
  "_published": "2026-05-22T12:09:19.252Z",
  "_jobs": [
    {
      "job": 77376403371,
      "time": 147,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6902703832"
    },
    {
      "job": 77376403207,
      "time": 213,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6902710699"
    },
    {
      "job": 77376403630,
      "time": 211,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6902710482"
    },
    {
      "job": 77376403488,
      "time": 92,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6902779125"
    },
    {
      "job": 77376403405,
      "time": 119,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6902786053"
    },
    {
      "job": 77376403297,
      "time": 186,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6902687944"
    },
    {
      "job": 77376402786,
      "time": 128,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7160114953"
    },
    {
      "job": 77376403254,
      "time": 102,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6902704496"
    },
    {
      "job": 77376403880,
      "time": 112,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6902705120"
    },
    {
      "job": 77376403505,
      "time": 112,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6902700023"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 6
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25625252006",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/MetaboCoreUtils",
  "_commit": {
    "id": "1e25732196a281aea891b040bfe6efe07841411e",
    "author": "Johannes Rainer <johannes.rainer@gmail.com>",
    "committer": "Johannes Rainer <johannes.rainer@gmail.com>",
    "message": "tests: fix precision\n",
    "time": 1777528535
  },
  "_maintainer": {
    "name": "Johannes Rainer",
    "email": "johannes.rainer@eurac.edu",
    "login": "jorainer",
    "mastodon": "@jorainer@fediscience.org",
    "bluesky": "@jorainer.bsky.social",
    "linkedin": "in/jorainer",
    "orcid": "0000-0002-6977-7147",
    "uuid": 5506112
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "MsCoreUtils",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "robustbase",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 65,
  "_updates": [
    {
      "week": "2025-19",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2025-47",
      "n": 1
    },
    {
      "week": "2026-07",
      "n": 1
    },
    {
      "week": "2026-16",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 5
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.21.1",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.20.1",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "infrastructure",
    "metabolomics",
    "massspectrometry",
    "mass-spectrometry"
  ],
  "_stars": 9,
  "_contributors": [
    {
      "user": "jorainer",
      "count": 163,
      "uuid": 5506112
    },
    {
      "user": "philouail",
      "count": 38,
      "uuid": 127301965
    },
    {
      "user": "michaelwitting",
      "count": 35,
      "uuid": 2734706
    },
    {
      "user": "sgibb",
      "count": 20,
      "uuid": 1828443
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "andreavicini",
      "count": 12,
      "uuid": 36991461
    },
    {
      "user": "rogerginber",
      "count": 7,
      "uuid": 45530914
    },
    {
      "user": "liesasalzer",
      "count": 6,
      "uuid": 61467853
    },
    {
      "user": "nturaga",
      "count": 6,
      "uuid": 2746443
    },
    {
      "user": "gabrieletome",
      "count": 3,
      "uuid": 39188419
    },
    {
      "user": "meowcat",
      "count": 3,
      "uuid": 1563881
    },
    {
      "user": "lgatto",
      "count": 1,
      "uuid": 384198
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 3340,
    "source": "https://www.bioconductor.org/packages/stats/bioc/MetaboCoreUtils"
  },
  "_devurl": "https://github.com/rformassspectrometry/metabocoreutils",
  "_searchresults": 101,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/MetaboCoreUtils.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/rformassspectrometry/metabocoreutils",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addElements",
    "adductCharge",
    "adductFormula",
    "adductNames",
    "adducts",
    "adjust_lm",
    "betaValues",
    "calculateKm",
    "calculateKmd",
    "calculateMass",
    "calculateRkmd",
    "containsElements",
    "convertMtime",
    "correctRindex",
    "countElements",
    "fit_lm",
    "formula2mz",
    "guessSource",
    "indexRtime",
    "internalStandardMixNames",
    "internalStandards",
    "isotopicSubstitutionMatrix",
    "isotopologues",
    "isRkmd",
    "mass2mz",
    "mclosest",
    "multiplyElements",
    "mz2mass",
    "nameMapping",
    "pasteElements",
    "percentMissing",
    "rowBlank",
    "rowDratio",
    "rowPercentMissing",
    "rowRsd",
    "rsd",
    "softwareMapping",
    "softwareMappingSchema",
    "standardizeFormula",
    "standardizeSingleCharge",
    "subtractElements",
    "translate"
  ],
  "_help": [
    {
      "page": "addElements",
      "title": "Combine chemical formulae",
      "topics": [
        "addElements"
      ]
    },
    {
      "page": "adductCharge",
      "title": "Get the charge of an adduct",
      "concept": [
        "adduct related functions"
      ],
      "topics": [
        "adductCharge"
      ]
    },
    {
      "page": "adductFormula",
      "title": "Calculate a table of adduct (ionic) formulas",
      "concept": [
        "adduct related functions"
      ],
      "topics": [
        "adductFormula"
      ]
    },
    {
      "page": "adductNames",
      "title": "Retrieve names of supported adducts",
      "concept": [
        "adduct related functions"
      ],
      "topics": [
        "adductNames",
        "adducts"
      ]
    },
    {
      "page": "betaValues",
      "title": "Peak shape quality: beta parameters",
      "topics": [
        "betaValues"
      ]
    },
    {
      "page": "calculateKendrickMass",
      "title": "Kendrick mass defects",
      "topics": [
        "calculateKendrickMass",
        "calculateKm",
        "calculateKmd",
        "calculateRkmd",
        "isRkmd"
      ]
    },
    {
      "page": "calculateMass",
      "title": "Calculate exact mass",
      "topics": [
        "calculateMass"
      ]
    },
    {
      "page": "containsElements",
      "title": "Check if one formula is contained in another",
      "topics": [
        "containsElements"
      ]
    },
    {
      "page": "convertMtime",
      "title": "Convert migration times to effective mobility",
      "topics": [
        "convertMtime"
      ]
    },
    {
      "page": "correctRindex",
      "title": "2-point correction of RIs",
      "topics": [
        "correctRindex"
      ]
    },
    {
      "page": "countElements",
      "title": "Count elements in a chemical formula",
      "topics": [
        "countElements"
      ]
    },
    {
      "page": "fit_lm",
      "title": "Linear model-based normalization of abundance matrices",
      "topics": [
        "adjust_lm",
        "fit_lm"
      ]
    },
    {
      "page": "formula2mz",
      "title": "Calculate mass-to-charge ratio from a formula",
      "concept": [
        "adduct related functions"
      ],
      "topics": [
        "formula2mz"
      ]
    },
    {
      "page": "guessSource",
      "title": "Guess the source of names",
      "concept": [
        "name translation functions"
      ],
      "topics": [
        "guessSource"
      ]
    },
    {
      "page": "indexRtime",
      "title": "Convert retention times to retention indices",
      "topics": [
        "indexRtime"
      ]
    },
    {
      "page": "internalStandardMixNames",
      "title": "Get names of internal standard mixes provided by the package",
      "topics": [
        "internalStandardMixNames"
      ]
    },
    {
      "page": "internalStandards",
      "title": "Get definitions for internal standards",
      "topics": [
        "internalStandards"
      ]
    },
    {
      "page": "isotopicSubstitutionMatrix",
      "title": "Definitions of isotopic substitutions",
      "topics": [
        "isotopicSubstitutionMatrix"
      ]
    },
    {
      "page": "isotopologues",
      "title": "Identfying isotopologue peaks in MS data",
      "topics": [
        "isotopologues"
      ]
    },
    {
      "page": "mass2mz",
      "title": "Calculate mass-to-charge ratio",
      "concept": [
        "adduct related functions"
      ],
      "topics": [
        "mass2mz"
      ]
    },
    {
      "page": "mclosest",
      "title": "Extract closest values in a pairwise manner between two matrices",
      "topics": [
        "mclosest"
      ]
    },
    {
      "page": "multiplyElements",
      "title": "Multiply chemical formulas by a scalar",
      "topics": [
        "multiplyElements"
      ]
    },
    {
      "page": "mz2mass",
      "title": "Calculate neutral mass",
      "concept": [
        "adduct related functions"
      ],
      "topics": [
        "mz2mass"
      ]
    },
    {
      "page": "nameMapping",
      "title": "Get mapping vector between two software",
      "concept": [
        "name translation functions"
      ],
      "topics": [
        "nameMapping"
      ]
    },
    {
      "page": "pasteElements",
      "title": "Create chemical formula from a named vector",
      "topics": [
        "pasteElements"
      ]
    },
    {
      "page": "quality_assessment",
      "title": "Basic quality assessment functions for metabolomics",
      "topics": [
        "percentMissing",
        "quality_assessment",
        "rowBlank",
        "rowDratio",
        "rowPercentMissing",
        "rowRsd",
        "rsd"
      ]
    },
    {
      "page": "softwareMapping",
      "title": "Get supported software for name translation",
      "concept": [
        "name translation functions"
      ],
      "topics": [
        "softwareMapping"
      ]
    },
    {
      "page": "softwareMappingSchema",
      "title": "Get mapping schema for name translation",
      "concept": [
        "name translation functions"
      ],
      "topics": [
        "softwareMappingSchema"
      ]
    },
    {
      "page": "standardizeFormula",
      "title": "Standardize a chemical formula",
      "topics": [
        "standardizeFormula"
      ]
    },
    {
      "page": "standardizeSingleCharge",
      "title": "Fix short-hand charge notation in adduct definition",
      "concept": [
        "adduct related functions"
      ],
      "topics": [
        "standardizeSingleCharge"
      ]
    },
    {
      "page": "subtractElements",
      "title": "subtract two chemical formula",
      "topics": [
        "subtractElements"
      ]
    },
    {
      "page": "translate",
      "title": "Translate names based on a provided mapping",
      "concept": [
        "name translation functions"
      ],
      "topics": [
        "translate"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/MetaboCoreUtils/raw/HEAD/logo.png",
  "_readme": "https://github.com/bioc/MetaboCoreUtils/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "clue",
    "cluster",
    "codetools",
    "cpp11",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "lambda.r",
    "MASS",
    "MsCoreUtils",
    "Rcpp",
    "S4Vectors",
    "snow"
  ],
  "_vignettes": [
    {
      "source": "MetaboCoreUtils.Rmd",
      "filename": "MetaboCoreUtils.html",
      "title": "Core Utils for Metabolomics Data",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Examples",
        "Conversion between ion m/z and compound masses",
        "Working with chemical formulas",
        "Kendrick mass defect calculation",
        "Retention time indexing",
        "Linear model-based adjustment of LC-MS feature abundances",
        "Basic quality assessment and pre-filtering of metabolomics data",
        "Contributions",
        "Session information",
        "References"
      ],
      "created": "2021-01-25 10:42:02",
      "modified": "2024-04-13 17:20:43",
      "commits": 14
    }
  ],
  "_score": 10.290858901273937,
  "_indexed": true,
  "_nocasepkg": "metabocoreutils",
  "_universes": [
    "bioc",
    "jorainer",
    "rformassspectrometry"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.21.1",
      "date": "2026-05-10T09:37:01.000Z",
      "distro": "noble",
      "commit": "1e25732196a281aea891b040bfe6efe07841411e",
      "fileid": "756cba2e88a5b68af137cb8f7055be681ab8f8fa0b73942ced79f307742333e0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625252006"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.21.1",
      "date": "2026-05-10T09:36:58.000Z",
      "distro": "noble",
      "commit": "1e25732196a281aea891b040bfe6efe07841411e",
      "fileid": "a49823f9a516311fb32fc0e504ded3ec190e6d79b61315fafde1aaef84e62ad0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625252006"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.21.1",
      "date": "2026-05-10T09:48:54.000Z",
      "commit": "1e25732196a281aea891b040bfe6efe07841411e",
      "fileid": "321ed46eb6cfc507b83a444c8fd20623882be6ef3f935262a25851c08627afe0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625252006"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.21.1",
      "date": "2026-05-10T09:49:57.000Z",
      "commit": "1e25732196a281aea891b040bfe6efe07841411e",
      "fileid": "bab29f3c2f07ff7cc72bb5f50f802729e164e9a0f7d1d39fc8d5fd6cfec78f4a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625252006"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.21.1",
      "date": "2026-05-10T09:36:01.000Z",
      "commit": "1e25732196a281aea891b040bfe6efe07841411e",
      "fileid": "25da7eca9f9bc4d6e17273e61498f5bdb4fb6f49c8ac08e87923e15fa3aa9edf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625252006"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.21.1",
      "date": "2026-05-10T09:35:55.000Z",
      "commit": "1e25732196a281aea891b040bfe6efe07841411e",
      "fileid": "ccd079ba6842aa6d81fe879122d9ff40efa033dfb88c654c6d04591693d04f5b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625252006"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.21.1",
      "date": "2026-05-10T09:35:15.000Z",
      "commit": "1e25732196a281aea891b040bfe6efe07841411e",
      "fileid": "fd48455c6a6d5ebd72edbf9116c51d4b36f5d730170a1274220070542cecccb8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625252006"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.21.1",
      "date": "2026-05-22T12:08:59.000Z",
      "commit": "1e25732196a281aea891b040bfe6efe07841411e",
      "fileid": "b4246ad33e1c2b9f259cb1e1fb0fc186ed0a425506e9df333fe4865904f36d7e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625252006"
    }
  ]
}