{
  "_id": "6abe55b699f7aa8c6aa557df",
  "Package": "mzID",
  "Type": "Package",
  "Title": "An mzIdentML parser for R",
  "Version": "1.51.0",
  "Authors@R": "c(person(given = \"Laurent\", family = \"Gatto\",\nemail = \"laurent.gatto@uclouvain.be\",\ncomment = c(ORCID = \"0000-0002-1520-2268\"),\nrole = c(\"ctb\", \"cre\")),\nperson(given = \"Thomas\", family = \"Pedersen\",\nemail = \"thomasp85@gmail.com\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-6977-7147\")),\nperson(given = \"Vladislav\", family = \"Petyuk\",\nrole = c(\"ctb\")))",
  "Description": "A parser for mzIdentML files implemented using the XML\npackage. The parser tries to be general and able to handle all\ntypes of mzIdentML files with the drawback of having less\n'pretty' output than a vendor specific parser. Please contact\nthe maintainer with any problems and supply an mzIdentML file\nso the problems can be fixed quickly.",
  "License": "GPL (>= 2)",
  "LazyLoad": "yes",
  "biocViews": "ImmunoOncology, DataImport, MassSpectrometry, Proteomics",
  "VignetteBuilder": "knitr",
  "Collate": "'aaa.R' 'generics.R' 'mzIDpsm.R' 'mzIDpeptides.R'\n'mzIDparameters.R' 'mzIDevidence.R' 'mzIDdatabase.R' 'mzID.R'\n'mzIDCollection.R' 'mzID-constructor.R' 'mzID-package.R'",
  "RoxygenNote": "5.0.1",
  "Config/pak/sysreqs": "libxml2-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:09 UTC",
  "RemoteUrl": "https://github.com/bioc/mzID",
  "RemoteRef": "HEAD",
  "RemoteSha": "61b447eeb1e17247ce8cb09969a8339c32714b0c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-01 12:17:11 UTC",
    "User": "root"
  },
  "Author": "Laurent Gatto [ctb, cre] (ORCID:\n<https://orcid.org/0000-0002-1520-2268>),\nThomas Pedersen [aut] (ORCID: <https://orcid.org/0000-0002-6977-7147>),\nVladislav Petyuk [ctb]",
  "Maintainer": "Laurent Gatto <laurent.gatto@uclouvain.be>",
  "_user": "bioc",
  "_type": "src",
  "_file": "mzID_1.51.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/b491e1d58e5940bc201423c16e6448236efd15a31584ff0064304f58319c8d5c",
  "_filesize": 734068,
  "_sha256": "b491e1d58e5940bc201423c16e6448236efd15a31584ff0064304f58319c8d5c",
  "_expires": "2027-01-09T12:44:36.000Z",
  "_created": "2026-10-01T12:17:11.000Z",
  "_published": "2026-10-01T12:44:38.274Z",
  "_bioccheck": {
    "error": 1,
    "warning": 4,
    "note": 10
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/36860380683",
  "_status": "success",
  "_upstream": "https://github.com/bioc/mzID",
  "_commit": {
    "id": "61b447eeb1e17247ce8cb09969a8339c32714b0c",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777379889
  },
  "_maintainer": {
    "name": "Laurent Gatto",
    "email": "laurent.gatto@uclouvain.be",
    "login": "lgatto",
    "mastodon": "@lgatto@fediscience.org",
    "orcid": "0000-0002-1520-2268",
    "description": "Open science, reproducible research, bioinformatics, computational biology, proteomics, more omics, emacs, a lot of R, running and parenting.\n",
    "uuid": 384198
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 110364162868,
      "time": 154,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11160649078"
    },
    {
      "job": 110364162906,
      "time": 234,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11161473531"
    },
    {
      "job": 110364162972,
      "time": 237,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11161493540"
    },
    {
      "job": 110364162814,
      "time": 144,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11162732643"
    },
    {
      "job": 110364162721,
      "time": 116,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11162437536"
    },
    {
      "job": 110362962457,
      "time": 195,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11161252701"
    },
    {
      "job": 110364162710,
      "time": 109,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11160603986"
    },
    {
      "job": 110364162843,
      "time": 83,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11161602860"
    },
    {
      "job": 110364162796,
      "time": 69,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11161318076"
    },
    {
      "job": 110364162765,
      "time": 82,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11161068616"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "XML",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "iterators",
      "role": "Imports"
    },
    {
      "package": "ProtGenerics",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 41,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-14",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.51.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.50.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "dataimport",
    "massspectrometry",
    "proteomics"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 471,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 6814,
    "source": "https://www.bioconductor.org/packages/stats/bioc/mzID"
  },
  "_mentions": 4,
  "_searchresults": 47,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/mzID.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "evidence",
    "files",
    "flatten",
    "id",
    "idScanMap",
    "mzID",
    "mzIDCollection",
    "mzIDdatabase",
    "mzIDevidence",
    "mzIDparameters",
    "mzIDpeptides",
    "mzIDpsm",
    "parameters",
    "removeDecoy",
    "software"
  ],
  "_help": [
    {
      "page": "mzID-package",
      "title": "A parser for the mzIdentML file format",
      "topics": [
        "mzID-package"
      ]
    },
    {
      "page": "flatten",
      "title": "Flatten an mzID related class into a table",
      "topics": [
        "flatten",
        "flatten,mzID-method",
        "flatten,mzIDCollection-method",
        "flatten,mzIDpeptides-method",
        "flatten,mzIDpsm-method"
      ]
    },
    {
      "page": "mzID",
      "title": "Parse an mzIdentML file",
      "topics": [
        "mzID"
      ]
    },
    {
      "page": "mzID-class",
      "title": "A class to contain data from mzIdentML-files",
      "topics": [
        "c,mzID-method",
        "database,mzID-method",
        "evidence,mzID-method",
        "files,mzID-method",
        "id,mzID-method",
        "idScanMap,mzID-method",
        "length,mzID-method",
        "modifications,mzID-method",
        "mzID-class",
        "parameters,mzID-method",
        "peptides,mzID-method",
        "removeDecoy,mzID-method",
        "scans,mzID-method",
        "show,mzID-method",
        "software,mzID-method"
      ]
    },
    {
      "page": "mzID-getters",
      "title": "Getter functions for identification data",
      "topics": [
        "evidence",
        "files",
        "id",
        "idScanMap",
        "mzID-getters",
        "parameters",
        "software"
      ]
    },
    {
      "page": "mzIDCollection",
      "title": "Create a new mzIDCollection",
      "topics": [
        "mzIDCollection"
      ]
    },
    {
      "page": "mzIDCollection-class",
      "title": "A class to handle a set of mzID objects",
      "topics": [
        "as.list.mzIDCollection",
        "c,mzIDCollection-method",
        "database,mzIDCollection-method",
        "evidence,mzIDCollection-method",
        "files,mzIDCollection-method",
        "id,mzIDCollection-method",
        "idScanMap,mzIDCollection-method",
        "length,mzIDCollection-method",
        "modifications,mzIDCollection-method",
        "mzIDCollection-class",
        "names,mzIDCollection-method",
        "names<-,mzIDCollection,character-method",
        "parameters,mzIDCollection-method",
        "peptides,mzIDCollection-method",
        "removeDecoy,mzIDCollection-method",
        "scans,mzIDCollection-method",
        "show,mzIDCollection-method",
        "software,mzIDCollection-method",
        "[,mzIDCollection,character,missing,missing-method",
        "[,mzIDCollection,logical,missing,missing-method",
        "[,mzIDCollection,numeric,missing,missing-method",
        "[[,mzIDCollection,character,missing-method",
        "[[,mzIDCollection,numeric,missing-method"
      ]
    },
    {
      "page": "mzIDdatabase",
      "title": "A constructor for the mzIDdatabase class",
      "topics": [
        "mzIDdatabase"
      ]
    },
    {
      "page": "mzIDdatabase-class",
      "title": "A class to store database information from an mzIdentML file",
      "topics": [
        "database,mzIDdatabase-method",
        "length,mzIDdatabase-method",
        "mzIDdatabase-class",
        "show,mzIDdatabase-method"
      ]
    },
    {
      "page": "mzIDevidence",
      "title": "A constructor for the mzIDevidence class",
      "topics": [
        "mzIDevidence"
      ]
    },
    {
      "page": "mzIDevidence-class",
      "title": "A class to store peptide evidence information from an mzIdentML file",
      "topics": [
        "evidence,mzIDevidence-method",
        "length,mzIDevidence-method",
        "mzIDevidence-class",
        "show,mzIDevidence-method"
      ]
    },
    {
      "page": "mzIDparameters",
      "title": "A constructor for the mzIDparameters class",
      "topics": [
        "mzIDparameters"
      ]
    },
    {
      "page": "mzIDparameters-class",
      "title": "A Class to store analysis information from the mzIdentML file",
      "topics": [
        "files,mzIDparameters-method",
        "length,mzIDparameters-method",
        "mzIDparameters-class",
        "parameters,mzIDparameters-method",
        "show,mzIDparameters-method",
        "software,mzIDparameters-method"
      ]
    },
    {
      "page": "mzIDpeptides",
      "title": "A constructor for the mzIDpeptides class",
      "topics": [
        "mzIDpeptides"
      ]
    },
    {
      "page": "mzIDpeptides-class",
      "title": "A class to store peptide information from an mzIdentML file",
      "topics": [
        "length,mzIDpeptides-method",
        "modifications,mzIDpeptides-method",
        "mzIDpeptides-class",
        "peptides,mzIDpeptides-method",
        "show,mzIDpeptides-method"
      ]
    },
    {
      "page": "mzIDpsm",
      "title": "A constructor for the mzIDpsm class",
      "topics": [
        "mzIDpsm"
      ]
    },
    {
      "page": "mzIDpsm-class",
      "title": "A class to store psm information from an mzIdentML file",
      "topics": [
        "id,mzIDpsm-method",
        "idScanMap,mzIDpsm-method",
        "length,mzIDpsm-method",
        "mzIDpsm-class",
        "scans,mzIDpsm-method",
        "show,mzIDpsm-method"
      ]
    },
    {
      "page": "removeDecoy",
      "title": "Remove decoy identification",
      "topics": [
        "removeDecoy"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/mzID/raw/HEAD/README.md",
  "_rundeps": [
    "codetools",
    "doParallel",
    "foreach",
    "iterators",
    "plyr",
    "ProtGenerics",
    "Rcpp",
    "XML"
  ],
  "_vignettes": [
    {
      "source": "HOWTO_mzID.Rnw",
      "filename": "HOWTO_mzID.pdf",
      "title": "Using mzID",
      "engine": "knitr",
      "headings": [],
      "created": "2013-09-17 21:45:26",
      "modified": "2016-04-21 10:49:45",
      "commits": 3
    }
  ],
  "_score": 8.373556348990618,
  "_indexed": true,
  "_nocasepkg": "mzid",
  "_universes": [
    "bioc",
    "lgatto"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.51.0",
      "date": "2026-10-01T12:21:03.000Z",
      "distro": "resolute",
      "commit": "61b447eeb1e17247ce8cb09969a8339c32714b0c",
      "fileid": "https://r2.ropensci.org/66972e98e65d3ca87b4d186daac04a7df3f58cefb0788ac230a6f31fd6beaa79",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36860380683"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.51.0",
      "date": "2026-10-01T12:21:00.000Z",
      "distro": "resolute",
      "commit": "61b447eeb1e17247ce8cb09969a8339c32714b0c",
      "fileid": "https://r2.ropensci.org/dd11cb61ca02a30d0a063b0c4487c26ccbe7d48d1d13aea4d5068a163247def7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36860380683"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.51.0",
      "date": "2026-10-01T12:43:34.000Z",
      "commit": "61b447eeb1e17247ce8cb09969a8339c32714b0c",
      "fileid": "https://r2.ropensci.org/b2779a6cfcbfd2a46b5f087907373fd89c4a1cb18d699b43169d2f3227da1a3c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36860380683"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.51.0",
      "date": "2026-10-01T12:43:07.000Z",
      "commit": "61b447eeb1e17247ce8cb09969a8339c32714b0c",
      "fileid": "https://r2.ropensci.org/dca60459a66568d373ef91ef6532baefa62acaa92eb647db3f90a5ba99bfe815",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36860380683"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.51.0",
      "date": "2026-10-01T12:19:16.000Z",
      "commit": "61b447eeb1e17247ce8cb09969a8339c32714b0c",
      "fileid": "https://r2.ropensci.org/b44dcea09382c44860dffc8ea8c2fa7ec766c25ad08d37010981b8cd6f3bd098",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36860380683"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.51.0",
      "date": "2026-10-01T12:18:21.000Z",
      "commit": "61b447eeb1e17247ce8cb09969a8339c32714b0c",
      "fileid": "https://r2.ropensci.org/8fba854256517ce9cfe59f4226bb545da968b67ddf2d260027458f14128a9330",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36860380683"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.51.0",
      "date": "2026-10-01T12:18:10.000Z",
      "commit": "61b447eeb1e17247ce8cb09969a8339c32714b0c",
      "fileid": "https://r2.ropensci.org/93b8cf66f07d7ad6b6242bf05ae5508d7c0cfa40c6a097879c294004c5030800",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36860380683"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.51.0",
      "date": "2026-10-01T12:18:22.000Z",
      "commit": "61b447eeb1e17247ce8cb09969a8339c32714b0c",
      "fileid": "https://r2.ropensci.org/59a006d425a5374debaa80b6edcfbd1f1f22a57744cea29a70f47d9c58a7c265",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36860380683"
    }
  ]
}