{
  "_id": "6a193a84acfb0bcc41dd3f33",
  "Package": "mzID",
  "Type": "Package",
  "Title": "An mzIdentML parser for R",
  "Version": "1.50.0",
  "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-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:09 UTC",
  "RemoteUrl": "https://github.com/bioc/mzID",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "2f84f81777555179b3f3f605c6e0e6e9906d4792",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 06:25:29 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>",
  "MD5sum": "e19e70d26db4ad6ca5eec7a0f48cf031",
  "_user": "bioc-release",
  "_type": "src",
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  "_created": "2026-05-29T06:25:29.000Z",
  "_published": "2026-05-29T07:04:36.574Z",
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    "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",
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    "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
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  "_registered": true,
  "_dependencies": [
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      "role": "Depends"
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    },
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    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
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  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 38,
  "_updates": [
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      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-14",
      "n": 1
    },
    {
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      "bioc": "3.24"
    },
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      "bioc": "3.23"
    }
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    "immunooncology",
    "dataimport",
    "massspectrometry",
    "proteomics"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 5099,
    "source": "https://www.bioconductor.org/packages/stats/bioc/mzID"
  },
  "_mentions": 4,
  "_searchresults": 38,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/mzID.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_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"
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    },
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      "topics": [
        "mzIDparameters"
      ]
    },
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      "page": "mzIDparameters-class",
      "title": "A Class to store analysis information from the mzIdentML file",
      "topics": [
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        "length,mzIDparameters-method",
        "mzIDparameters-class",
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    },
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      "title": "A class to store peptide information from an mzIdentML file",
      "topics": [
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      "title": "A class to store psm information from an mzIdentML file",
      "topics": [
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        "idScanMap,mzIDpsm-method",
        "length,mzIDpsm-method",
        "mzIDpsm-class",
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        "show,mzIDpsm-method"
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    },
    {
      "page": "removeDecoy",
      "title": "Remove decoy identification",
      "topics": [
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      ]
    }
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