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  "Package": "CAMERA",
  "Version": "1.68.0",
  "Date": "2025-05-09",
  "Title": "Collection of annotation related methods for mass spectrometry\ndata",
  "Author": "Carsten Kuhl, Ralf Tautenhahn, Hendrik Treutler, Steffen\nNeumann {ckuhl|htreutle|sneumann}@ipb-halle.de,\nrtautenh@scripps.edu",
  "Maintainer": "Steffen Neumann <sneumann@ipb-halle.de>",
  "Description": "Annotation of peaklists generated by xcms, rule based\nannotation of isotopes and adducts, isotope validation, EIC\ncorrelation based tagging of unknown adducts and fragments",
  "License": "GPL (>= 2)",
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  "URL": "http://msbi.ipb-halle.de/msbi/CAMERA/",
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    "metabolomics"
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  "_homeurl": "https://github.com/sneumann/camera",
  "_realowner": "bioc",
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  "_exports": [
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    "annotateDiffreport",
    "calcCaS",
    "calcCiS",
    "calcIsotopes",
    "calcPC",
    "calcPC.hcs",
    "calcPC.lpc",
    "cleanParallel",
    "combinexsAnnos",
    "compoundLibraries",
    "compoundQuantiles",
    "findAdducts",
    "findIsotopes",
    "findIsotopesWithValidation",
    "findKendrickMasses",
    "findNeutralLoss",
    "findNeutralLossSpecs",
    "generateRules",
    "getAllPeakEICs",
    "getAtomCount",
    "getIsotopeCluster",
    "getIsotopeProportion",
    "getPeaklist",
    "getpspectra",
    "getReducedPeaklist",
    "groupCorr",
    "groupDen",
    "groupFWHM",
    "massWindowSizes",
    "plotEICs",
    "plotPsSpectrum",
    "pspec2metfrag",
    "pspec2metfusion",
    "readLists",
    "setDefaultLists",
    "setDefaultParams",
    "setParams",
    "show",
    "xsAnnotate"
  ],
  "_datasets": [
    {
      "name": "mm14",
      "title": "Extract of marker mixture 14 LC/MS data",
      "object": "mm14",
      "file": "mm14.rda",
      "class": [
        "xcmsSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "annotate-methods",
      "title": "Automatic deconvolution/annotation of LC/ESI-MS data",
      "topics": [
        "annotate",
        "annotate,xcmsSet-method"
      ]
    },
    {
      "page": "annotateDiffreport",
      "title": "Automatic deconvolution/annotation of LC/ESI-MS data",
      "topics": [
        "annotateDiffreport",
        "annotateDiffreport,xsAnnotate-methods"
      ]
    },
    {
      "page": "calcCaS-methods",
      "title": "EIC correlation grouping of LC/ESI-MS data",
      "topics": [
        "calcCaS",
        "calcCaS,xsAnnotate-method"
      ]
    },
    {
      "page": "calcCiS-methods",
      "title": "Calculate peak distance matrix after EIC correlation",
      "topics": [
        "calcCiS",
        "calcCiS,xsAnnotate-method"
      ]
    },
    {
      "page": "calcIsotopes-methods",
      "title": "Calculate isotope distance matrix from xsAnnotate object",
      "topics": [
        "calcIsotopes",
        "calcIsotopes,xsAnnotate-method"
      ]
    },
    {
      "page": "calcPC-methods",
      "title": "Peakclustering into pseudospectra according to a distance matrix",
      "topics": [
        "calcPC",
        "calcPC,calcPC-method",
        "calcPC,xsAnnotate-method"
      ]
    },
    {
      "page": "calcPC.hcs-methods",
      "title": "Peakclustering into pseudospectra with the highly connected subgraphs approach",
      "topics": [
        "calcPC.hcs",
        "calcPC.hcs,xsAnnotate-method"
      ]
    },
    {
      "page": "calcPC.lpc-methods",
      "title": "Peakclustering into pseudospectra with the label-propagation-community algorithm",
      "topics": [
        "calcPC.lpc",
        "calcPC.lpc,xsAnnotate-method"
      ]
    },
    {
      "page": "cleanParallel",
      "title": "Cleans up with spawned slave processes after use",
      "topics": [
        "cleanParallel"
      ]
    },
    {
      "page": "combinexsAnnos",
      "title": "Check CAMERA ion species annotation due to matching with opposite ion mode",
      "topics": [
        "combinexsAnnos"
      ]
    },
    {
      "page": "compoundLibraries",
      "title": "The supported compound databases",
      "topics": [
        "compoundLibraries"
      ]
    },
    {
      "page": "compoundQuantiles",
      "title": "compoundQuantiles constructor",
      "topics": [
        "compoundQuantiles"
      ]
    },
    {
      "page": "compoundQuantiles-class",
      "title": "Class compoundQuantiles encapsulates compound statistics from different databases.",
      "topics": [
        "compoundQuantiles-class"
      ]
    },
    {
      "page": "findAdducts-methods",
      "title": "Calculate Adducts and Annotate LC/ESI-MS Spectra",
      "topics": [
        "findAdducts",
        "findAdducts,xsAnnotate-method"
      ]
    },
    {
      "page": "findIsotopes-methods",
      "title": "Deconvolute/Annotate LC/ESI-MS data",
      "topics": [
        "findIsotopes",
        "findIsotopes,xsAnnotate-method"
      ]
    },
    {
      "page": "findIsotopesWithValidation-methods",
      "title": "Deconvolute/Annotate LC/ESI-MS data",
      "topics": [
        "findIsotopesWithValidation",
        "findIsotopesWithValidation,xsAnnotate-method"
      ]
    },
    {
      "page": "findKendrickMasses",
      "title": "Find specfic mass defects using Kendrick mass scales",
      "topics": [
        "findKendrickMasses"
      ]
    },
    {
      "page": "findNeutralLoss",
      "title": "Find pseudospectra that contains a specific neutral loss",
      "topics": [
        "findNeutralLoss"
      ]
    },
    {
      "page": "findNeutralLossSpecs",
      "title": "Find pseudospectra that contains a specific neutral loss",
      "topics": [
        "findNeutralLossSpecs"
      ]
    },
    {
      "page": "getAllPeakEICs-methods",
      "title": "Generate EIC information from raw data",
      "topics": [
        "getAllPeakEICs",
        "getAllPeakEICs,xsAnnotate-method"
      ]
    },
    {
      "page": "getAtomCount-compoundQuantiles-method",
      "title": "The number of atoms of the given element",
      "topics": [
        "getAtomCount",
        "getAtomCount,compoundQuantiles-method"
      ]
    },
    {
      "page": "getIsotopeCluster",
      "title": "Retrieve the annotatad isotopes",
      "topics": [
        "getIsotopeCluster"
      ]
    },
    {
      "page": "getIsotopeProportion-compoundQuantiles-method",
      "title": "The proportion of the intensities of two isotope peaks",
      "topics": [
        "getIsotopeProportion",
        "getIsotopeProportion,compoundQuantiles-method"
      ]
    },
    {
      "page": "getPeaklist-methods",
      "title": "Generate the annotatad peaklist",
      "topics": [
        "getPeaklist",
        "getPeaklist,xsAnnotate-method"
      ]
    },
    {
      "page": "getpspectra",
      "title": "Retrieve a peaklist of one or more pseudospectra",
      "topics": [
        "getpspectra"
      ]
    },
    {
      "page": "getReducedPeaklist-methods",
      "title": "Generate reduced peaklist from the annotatad peaklist",
      "topics": [
        "getReducedPeaklist",
        "getReducedPeaklist,xsAnnotate-method"
      ]
    },
    {
      "page": "groupCorr-methods",
      "title": "EIC correlation grouping of LC/ESI-MS data",
      "topics": [
        "groupCorr",
        "groupCorr,xsAnnotate-method"
      ]
    },
    {
      "page": "groupDen-methods",
      "title": "Density-Grouping of LC/ESI-MS data",
      "topics": [
        "groupDen",
        "groupDen,xsAnnotate-method"
      ]
    },
    {
      "page": "groupFWHM-methods",
      "title": "FWHM-Grouping of LC/ESI-MS data",
      "topics": [
        "groupFWHM",
        "groupFWHM,xsAnnotate-method"
      ]
    },
    {
      "page": "massWindowSizes",
      "title": "The supported mass window sizes",
      "topics": [
        "massWindowSizes"
      ]
    },
    {
      "page": "mm14",
      "title": "Extract of marker mixture 14 LC/MS data",
      "topics": [
        "mm14"
      ]
    },
    {
      "page": "plotEIC.xsAnnotate",
      "title": "Plot extracted ion chromatograms from (multiple) Pseudospectra",
      "topics": [
        "plotEICs",
        "plotEICs,xsAnnotate-method",
        "plotEICs.xsAnnotate"
      ]
    },
    {
      "page": "plotPsSpectrum.xsAnnotate",
      "title": "Plot a Pseudospectrum",
      "topics": [
        "plotPsSpectrum",
        "plotPsSpectrum,xsAnnotate-method",
        "plotPsSpectrum.xsAnnotate"
      ]
    },
    {
      "page": "psDist-methods",
      "title": "Distance methods for xsAnnotate",
      "topics": [
        "psDist",
        "psDist,CAMERA-method",
        "psDist-methods"
      ]
    },
    {
      "page": "pspec2metfrag",
      "title": "Export the putative fragments as MetFrag query files",
      "topics": [
        "pspec2metfrag",
        "pspec2metfusion"
      ]
    },
    {
      "page": "ruleSet-class",
      "title": "Class 'ruleSet'",
      "topics": [
        "class:ruleSet",
        "generateRules",
        "generateRules,ruleSet-method",
        "readLists",
        "readLists,ruleSet-method",
        "ruleSet-class",
        "setDefaultLists",
        "setDefaultLists,ruleSet-method",
        "setDefaultParams",
        "setDefaultParams,ruleSet-method",
        "setParams",
        "setParams,ruleSet,numeric,numeric,numeric,numeric,numeric,numeric,character,character-method",
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    },
    {
      "page": "xsAnnotate",
      "title": "xsAnnotate constructor for an provided xcmsSet object",
      "topics": [
        "xsAnnotate"
      ]
    },
    {
      "page": "xsAnnotate-class",
      "title": "Class xsAnnotate, a class for annotated peak data",
      "topics": [
        "show,xsAnnotate-method",
        "xsAnnotate-class"
      ]
    }
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