{
  "_id": "6a37c60d3efcd9bda442edf2",
  "Package": "metaMS",
  "Type": "Package",
  "Title": "MS-based metabolomics annotation pipeline",
  "Version": "1.48.0",
  "Authors@R": "c(person(\"Ron\", \"Wehrens\", role = \"aut\", comment =\nc(\"author of GC-MS part\", \"Initial Maintainer\"), email = \"ron.wehrens@gmail.com\"),\nperson(\"Pietro\", \"Franceschi\", role = \"aut\", comment = \"author\nof LC-MS part\"), person(\"Nir\", \"Shahaf\", role = \"ctb\"),\nperson(\"Matthias\", \"Scholz\", role = \"ctb\"), person(\"Georg\",\n\"Weingart\", role = \"ctb\", comment = \"development of GC-MS\napproach\"), person(\"Elisabete\", \"Carvalho\", role = \"ctb\",\ncomment = \"testing and feedback of GC-MS pipeline\"), person(\"Yann\", \"Guitton\", role=c(\"ctb\",\"cre\"), email=\"yann.guitton@gmail.com\", comment=c(ORCID = \"0000-0002-4479-0636\")), person(\"Julien\", \"Saint-Vanne\", role=\"ctb\"))",
  "Description": "MS-based metabolomics data processing and compound\nannotation pipeline.",
  "URL": "https://github.com/yguitton/metaMS",
  "License": "GPL (>= 2)",
  "biocViews": "ImmunoOncology, MassSpectrometry, Metabolomics",
  "Encoding": "UTF-8",
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  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libnetcdf-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:59 UTC",
  "RemoteUrl": "https://github.com/bioc/metaMS",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "82c42f6391d550263161d60bf1d232d5b8b003a3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-21 10:58:00 UTC",
    "User": "root"
  },
  "Author": "Ron Wehrens [aut] (author of GC-MS part, Initial Maintainer),\nPietro Franceschi [aut] (author of LC-MS part),\nNir Shahaf [ctb],\nMatthias Scholz [ctb],\nGeorg Weingart [ctb] (development of GC-MS approach),\nElisabete Carvalho [ctb] (testing and feedback of GC-MS pipeline),\nYann Guitton [ctb, cre] (ORCID:\n<https://orcid.org/0000-0002-4479-0636>),\nJulien Saint-Vanne [ctb]",
  "Maintainer": "Yann Guitton <yann.guitton@gmail.com>",
  "MD5sum": "3b97d4daf3b603a8559daa8578e9ff49",
  "_user": "bioc-release",
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  "_created": "2026-06-21T10:58:00.000Z",
  "_published": "2026-06-21T11:07:57.453Z",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
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    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
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    "uuid": 5373737,
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      "package": "graphics",
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      "package": "stats",
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    {
      "package": "utils",
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    {
      "package": "metaMSdata",
      "role": "Suggests"
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  "_owner": "bioc",
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  "_topics": [
    "immunooncology",
    "massspectrometry",
    "metabolomics"
  ],
  "_stars": 15,
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    "name": "Bioconductor",
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_mentions": 13,
  "_devurl": "https://github.com/yguitton/metams",
  "_searchresults": 16,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/metaMS.html",
    "extra/NEWS.html",
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    "extra/readme.md",
    "manual.pdf"
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  "_homeurl": "https://github.com/yguitton/metams",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addRI",
    "alignmentLC",
    "AnnotateFeature",
    "AnnotateTable",
    "construct.msp",
    "constructExpPseudoSpectra",
    "createSTDdbGC",
    "createSTDdbLC",
    "filter.msp",
    "generateStdDBGC",
    "generateStdDBLC",
    "getAnnotationLC",
    "getAnnotationMat",
    "getFeatureInfo",
    "getPeakTable",
    "matchExpSpec",
    "matchSamples2DB",
    "matchSamples2Samples",
    "metaMSsettings",
    "metaSetting",
    "metaSetting<-",
    "peakDetection",
    "plotPseudoSpectrum",
    "processStandards",
    "read.msp",
    "readStdInfo",
    "runCAMERA",
    "runGC",
    "runLC",
    "show",
    "to.msp",
    "treat.DB",
    "write.msp"
  ],
  "_datasets": [
    {
      "name": "DB",
      "title": "Information on three chemical standards measured in GC-MS (liquid injection)",
      "object": "threeStdsDB",
      "file": "threeStdsDB.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "errf",
      "title": "Mass error surface for Waters Synapt Q-TOF spectrometers",
      "object": "errf",
      "file": "errf.RData",
      "class": [
        "lm"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "exptable",
      "title": "Sample table for the generation of a database of standards (LCMS)",
      "object": "exptable",
      "file": "exptable.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ChemSpiderID",
        "compound",
        "formula",
        "M.ref",
        "mz.observed",
        "RTman",
        "stdFile"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "GCresults",
      "title": "Results of metaMS for a small GC-MS data set",
      "object": "GCresults",
      "file": "GCresults.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "LCDBtest",
      "title": "Sample DB for LC-MS annotation",
      "object": "LCDBtest",
      "file": "LCDBtest.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "LCresults",
      "title": "Result metaMS for a small LC-MS data set",
      "object": "LCresults",
      "file": "LCresults.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "Orbitrap.RP",
      "title": "Example settings for 'metaMS'",
      "object": "FEMsettings",
      "file": "FEMsettings.RData",
      "class": [
        "metaMSsettings"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "smallDB",
      "title": "Information on three chemical standards measured in GC-MS (liquid injection)",
      "object": "threeStdsNIST",
      "file": "threeStdsNIST.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "stdInfo",
      "title": "Information on three chemical standards measured in GC-MS (liquid injection)",
      "object": "threeStdsInfo",
      "file": "threeStdsInfo.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CAS",
        "Name",
        "RTman",
        "ChemspiderID",
        "SMILES",
        "InChI",
        "csLinks",
        "monoMW",
        "stdFile"
      ],
      "rows": 3,
      "table": true,
      "tojson": true
    },
    {
      "name": "Synapt.NP",
      "title": "Example settings for 'metaMS'",
      "object": "FEMsettings",
      "file": "FEMsettings.RData",
      "class": [
        "metaMSsettings"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "Synapt.RP",
      "title": "Example settings for 'metaMS'",
      "object": "FEMsettings",
      "file": "FEMsettings.RData",
      "class": [
        "metaMSsettings"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "TSQXLS.GC",
      "title": "Example settings for 'metaMS'",
      "object": "FEMsettings",
      "file": "FEMsettings.RData",
      "class": [
        "metaMSsettings"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "metaMS-package",
      "title": "Analysis pipeline for MS-based metabolomics data",
      "topics": [
        "metaMS-package",
        "metaMS"
      ]
    },
    {
      "page": "addRI",
      "title": "Add retention index information to an msp object",
      "topics": [
        "addRI"
      ]
    },
    {
      "page": "alignmentLC",
      "title": "LC alignment",
      "topics": [
        "alignmentLC"
      ]
    },
    {
      "page": "AnnotateTable",
      "title": "Annotate a Peaktable",
      "topics": [
        "AnnotateFeature",
        "AnnotateTable"
      ]
    },
    {
      "page": "annotations2tab",
      "title": "Conversion of a list of annotation results into a table",
      "topics": [
        "annotations2tab",
        "makeAnnotation"
      ]
    },
    {
      "page": "constructExpPseudoSpectra",
      "title": "Create a list of all pseudospectra found in a GC-MS experiment of several samples.",
      "topics": [
        "constructExpPseudoSpectra"
      ]
    },
    {
      "page": "createSTDdbGC",
      "title": "Create an in-house database for GC-MS annotation",
      "topics": [
        "createSTDdbGC",
        "generateStdDBGC"
      ]
    },
    {
      "page": "createSTDdbLC",
      "title": "Create an in-house database for LC-MS annotation",
      "topics": [
        "createSTDdbLC",
        "generateStdDBLC"
      ]
    },
    {
      "page": "errf",
      "title": "Mass error surface for Waters Synapt Q-TOF spectrometers",
      "topics": [
        "errf"
      ]
    },
    {
      "page": "exptable",
      "title": "Sample table for the generation of a database of standards (LCMS)",
      "topics": [
        "exptable"
      ]
    },
    {
      "page": "FEMsettings",
      "title": "Example settings for 'metaMS'",
      "topics": [
        "FEMsettings",
        "Orbitrap.RP",
        "Synapt.NP",
        "Synapt.RP",
        "TSQXLS.GC"
      ]
    },
    {
      "page": "GCresults",
      "title": "Results of metaMS for a small GC-MS data set",
      "topics": [
        "GCresults"
      ]
    },
    {
      "page": "getAnnotationLC",
      "title": "Get LC annotation",
      "topics": [
        "getAnnotationLC"
      ]
    },
    {
      "page": "getAnnotationMat",
      "title": "Obtain relative quantitative annotation results for GC-MS",
      "topics": [
        "getAnnotationMat",
        "relInt"
      ]
    },
    {
      "page": "getFeatureInfo",
      "title": "Construct an object containing all meta-information of the annotated pseudospectra (GC-MS).",
      "topics": [
        "getFeatureInfo"
      ]
    },
    {
      "page": "getPeakTable",
      "title": "Extract a peak table from an xcms or CAMERA object",
      "topics": [
        "getPeakTable"
      ]
    },
    {
      "page": "LCDBtest",
      "title": "Sample DB for LC-MS annotation",
      "topics": [
        "LCDBtest"
      ]
    },
    {
      "page": "LCresults",
      "title": "Result metaMS for a small LC-MS data set",
      "topics": [
        "LCresults",
        "LCxset"
      ]
    },
    {
      "page": "match2ExtDB",
      "title": "Match GC-MS spectra to an external reference DB",
      "topics": [
        "match2ExtDB"
      ]
    },
    {
      "page": "matchExpSpec",
      "title": "Match a GC-MS pseudospectrum to a database with a weighted crossproduct criterion.",
      "topics": [
        "matchExpSpec"
      ]
    },
    {
      "page": "matchSamples2DB",
      "title": "Match pseudospectra from several samples to an in-house DB (GC-MS)",
      "topics": [
        "matchSamples2DB"
      ]
    },
    {
      "page": "matchSamples2Samples",
      "title": "Compare pseudospectra across samples (GC-MS)",
      "topics": [
        "match.unannot.patterns",
        "matchSamples2Samples"
      ]
    },
    {
      "page": "metaMSsettings-class",
      "title": "Class '\"metaMSsettings\"'",
      "topics": [
        "metaMSsettings",
        "metaMSsettings-class",
        "show,metaMSsettings-method"
      ]
    },
    {
      "page": "metaSetting-methods",
      "title": "Get or set values in metaMSsettings objects",
      "topics": [
        "metaSetting",
        "metaSetting,metaMSsettings-method",
        "metaSetting<-",
        "metaSetting<-,metaMSsettings-method"
      ]
    },
    {
      "page": "msp",
      "title": "Functions to handle msp-type objects (GC-MS)",
      "topics": [
        "construct.msp",
        "filter.msp",
        "msp",
        "read.msp",
        "SearchNIST",
        "to.msp",
        "write.msp",
        "xset2msp"
      ]
    },
    {
      "page": "peakDetection",
      "title": "Wrapper for XCMS peak detection, to be used for both GC-MS and LC-MS data.",
      "topics": [
        "peakDetection"
      ]
    },
    {
      "page": "plotPseudoSpectrum",
      "title": "Plot a pseudospectrum.",
      "topics": [
        "plotPseudoSpectrum"
      ]
    },
    {
      "page": "printString",
      "title": "Functions for metaMS-formatted text output",
      "topics": [
        "printInfo",
        "printString",
        "printWarning"
      ]
    },
    {
      "page": "processStandards",
      "title": "Process input files containing raw data for pure standards.",
      "topics": [
        "processStandards"
      ]
    },
    {
      "page": "readStdInfo",
      "title": "Read information of GC injections of standards from a csv file",
      "topics": [
        "readStdInfo"
      ]
    },
    {
      "page": "removeDoubleMasses",
      "title": "Remove double m/z entries in a pseudospectrum",
      "topics": [
        "removeDoubleMasses"
      ]
    },
    {
      "page": "runCAMERA",
      "title": "The CAMERA element in the metaMS pipeline",
      "topics": [
        "runCAMERA"
      ]
    },
    {
      "page": "runGC",
      "title": "Wrapper for processing of GC-MS data files",
      "topics": [
        "runGC"
      ]
    },
    {
      "page": "runLC",
      "title": "Wrapper for processing of LC-MS data files",
      "topics": [
        "runLC"
      ]
    },
    {
      "page": "threeStdsDB",
      "title": "Information on three chemical standards measured in GC-MS (liquid injection)",
      "topics": [
        "DB",
        "smallDB",
        "stdInfo",
        "threeStdsDB",
        "threeStdsInfo",
        "threeStdsNIST"
      ]
    },
    {
      "page": "treat.DB",
      "title": "Scaling of pseudospectra in an msp object",
      "topics": [
        "treat.DB"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/metaMS/raw/RELEASE_3_23/README.md",
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