{ "_id": "6a103b73acfb0bcc41c9b7ea", "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://rformassspectrometry.r-universe.dev", "Date/Publication": "2026-04-30 05:55:35 UTC", "RemoteUrl": "https://github.com/rformassspectrometry/metabocoreutils", "RemoteRef": "HEAD", "RemoteSha": "1e25732196a281aea891b040bfe6efe07841411e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 11:03:31 UTC", "User": "root" }, "Author": "Johannes Rainer [aut, cre] (ORCID:\n),\nMichael Witting [aut] (ORCID: ),\nAndrea Vicini [aut],\nLiesa Salzer [ctb] (ORCID: ),\nSebastian Gibb [aut] (ORCID: ),\nMichael Stravs [ctb] (ORCID: ),\nRoger Gine [aut] (ORCID: ),\nWilliam Kumler [aut] (ORCID: ),\nPhilippine Louail [aut] (ORCID:\n),\nGabriele Tomè [aut] (ORCID: ,\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 ", "MD5sum": "99b695bd34574c88c472a2af7e32ec22", "_user": "rformassspectrometry", "_type": "src", "_file": "MetaboCoreUtils_1.21.1.tar.gz", "_fileid": "e97bb89793e23d2d6e605fefe4f5e7a08eca8439f72c0334dc9083eded4f52ab", "_filesize": 1202413, "_sha256": "e97bb89793e23d2d6e605fefe4f5e7a08eca8439f72c0334dc9083eded4f52ab", "_created": "2026-05-11T11:03:31.000Z", "_published": "2026-05-22T11:18:11.239Z", "_distro": "noble", "_jobs": [ { "job": 77368975003, "time": 203, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6916821281" }, { "job": 77368975509, "time": 155, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6916805527" }, { "job": 77368975330, "time": 113, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6916792117" }, { "job": 77368975499, "time": 118, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6916793692" }, { "job": 77368974684, "time": 251, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6916754285" }, { "job": 77368974648, "time": 117, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7159217122" }, { "job": 77368975317, "time": 121, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6916794279" }, { "job": 77368975253, "time": 133, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6916798629" }, { "job": 77368975299, "time": 131, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6916798273" } ], "_buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/25666062095", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/rformassspectrometry/metabocoreutils", "_commit": { "id": "1e25732196a281aea891b040bfe6efe07841411e", "author": "Johannes Rainer ", "committer": "Johannes Rainer ", "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 }, "_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": "rformassspectrometry", "_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": 51361942, "type": "organization", "name": "RforMassSpectrometry", "description": "R packages for mass spectrometry" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/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": true, "_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/rformassspectrometry/metabocoreutils/raw/HEAD/logo.png", "_readme": "https://github.com/rformassspectrometry/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": 9.767112434462373, "_indexed": false, "_nocasepkg": "metabocoreutils", "_universes": [ "rformassspectrometry" ], "_indexurl": "https://bioc.r-universe.dev/MetaboCoreUtils", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.1", "date": "2026-05-11T11:06:39.000Z", "distro": "noble", "commit": "1e25732196a281aea891b040bfe6efe07841411e", "fileid": "cd701657ce7232ff8374852cb0f10a10a4856c1ed091957a1b805762c6f25edd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/25666062095" }, { "r": "4.6.0", "os": "linux", "version": "1.21.1", "date": "2026-05-11T11:05:53.000Z", "distro": "noble", "commit": "1e25732196a281aea891b040bfe6efe07841411e", "fileid": "b467e7fca8cd3272abe6dff03cd8eea031d4f066782f53566e9c7ed3bf84f040", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/25666062095" }, { "r": "4.5.3", "os": "mac", "version": "1.21.1", "date": "2026-05-11T11:05:16.000Z", "commit": "1e25732196a281aea891b040bfe6efe07841411e", "fileid": "cb1a551b79a4068ab5b2a929496318a9292f47c32320e31e8bae9f53e705a1b4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/25666062095" }, { "r": "4.6.0", "os": "mac", "version": "1.21.1", "date": "2026-05-11T11:05:24.000Z", "commit": "1e25732196a281aea891b040bfe6efe07841411e", "fileid": "66fa9291e1f77dcd2f15442e2012a6274a8bdcb089d7eec6ac88a8f17e5b968c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/25666062095" }, { "r": "4.7.0", "os": "win", "version": "1.21.1", "date": "2026-05-11T11:05:11.000Z", "commit": "1e25732196a281aea891b040bfe6efe07841411e", "fileid": "10a4d48b873ffc98885ac3a598b4581d0850adbfc11623684e93573824c6289e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/25666062095" }, { "r": "4.5.3", "os": "win", "version": "1.21.1", "date": "2026-05-11T11:05:26.000Z", "commit": "1e25732196a281aea891b040bfe6efe07841411e", "fileid": "a844f6bdfcb9f38dc48a766d187514fdee5cab04ca4346ca8be5dced819b9a4c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/25666062095" }, { "r": "4.6.0", "os": "win", "version": "1.21.1", "date": "2026-05-11T11:05:24.000Z", "commit": "1e25732196a281aea891b040bfe6efe07841411e", "fileid": "af73ec88f92d16a73955f14cf58fd08e627cf6b531002ccd3991263a80703e55", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/25666062095" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.1", "date": "2026-05-22T11:17:55.000Z", "commit": "1e25732196a281aea891b040bfe6efe07841411e", "fileid": "09b3c465b1dba1cb35f74f1e3bbcd3243fbffc7d566085ab0f65290895983d45", "status": "success", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/25666062095" } ] }