{
  "_id": "6a1b071e1d7bb097a0a044bd",
  "Package": "TargetSearch",
  "Type": "Package",
  "Title": "A package for the analysis of GC-MS metabolite profiling data",
  "Version": "2.14.0",
  "Date": "2025-08-04",
  "Authors@R": "c(person(\"Alvaro\", \"Cuadros-Inostroza\", role=c(\"aut\", \"cre\"),\nemail=\"acuadros+bioc@gmail.com\"),\nperson(\"Jan\", \"Lisec\", role=\"aut\"),\nperson(\"Henning\", \"Redestig\", role=\"aut\"),\nperson(\"Matt\", \"Hannah\", role=\"aut\"))",
  "Maintainer": "Alvaro Cuadros-Inostroza <acuadros+bioc@gmail.com>",
  "VignetteBuilder": "knitr",
  "Description": "This packages provides a flexible, fast and accurate\nmethod for targeted pre-processing of GC-MS data. The user\nprovides a (often very large) set of GC chromatograms and a\nmetabolite library of targets. The package will automatically\nsearch those targets in the chromatograms resulting in a data\nmatrix that can be used for further data analysis.",
  "biocViews": "MassSpectrometry, Preprocessing, DecisionTree,\nImmunoOncology",
  "License": "GPL (>= 2)",
  "URL": "https://github.com/acinostroza/TargetSearch",
  "BugReports": "https://github.com/acinostroza/TargetSearch/issues",
  "Config/pak/sysreqs": "libnetcdf-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:33:53 UTC",
  "RemoteUrl": "https://github.com/bioc/TargetSearch",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "3c7a3e6e4966e532b0dcda109fb28f61c1d84821",
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  "Packaged": {
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  "Author": "Alvaro Cuadros-Inostroza [aut, cre],\nJan Lisec [aut],\nHenning Redestig [aut],\nMatt Hannah [aut]",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
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    "manual.pdf"
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  "_homeurl": "https://github.com/acinostroza/targetsearch",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
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    "baselineCorrection",
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    "CDFfiles<-",
    "CDFpath",
    "CDFpath<-",
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    "fileFormat",
    "fileFormat<-",
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    "fixRIcorrection",
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    "ImportLibrary.msp",
    "ImportLibrary.tab",
    "ImportSamples",
    "ImportSamplesFromDir",
    "Intensity",
    "Intensity<-",
    "libData",
    "libData<-",
    "libId",
    "libName",
    "libName<-",
    "libRI",
    "libRI<-",
    "libUID",
    "libUID<-",
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    "medianRILib",
    "medRI",
    "medRI<-",
    "ncdf4_convert",
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    "ncdf4_data_extract",
    "ncdf4_plot_peak",
    "ncdf4_update_ri",
    "ncdf4Convert",
    "NetCDFPeakFinding",
    "peakCDFextraction",
    "peakFind",
    "plotAllRIdev",
    "plotAllSpectra",
    "plotFAME",
    "plotPeak",
    "plotPeakRI",
    "plotPeakSimple",
    "plotRefSpectra",
    "plotRIdev",
    "plotSpectra",
    "Profile",
    "ProfileCleanUp",
    "profileInfo",
    "profileInfo<-",
    "profileInt",
    "profileInt<-",
    "profileRI",
    "profileRI<-",
    "profileRT",
    "profileRT<-",
    "quantMass",
    "quantMass<-",
    "quantMatrix",
    "refLib",
    "retIndex",
    "retIndex<-",
    "retTime",
    "retTime<-",
    "ri_data_extract",
    "ri_plot_peak",
    "ri2rt",
    "RIcorrect",
    "RIdev",
    "RIdev<-",
    "RIfiles",
    "RIfiles<-",
    "riMatrix",
    "rimLimits",
    "rimLimits<-",
    "rimMass",
    "rimMass<-",
    "rimStandard",
    "rimStandard<-",
    "RIpath",
    "RIpath<-",
    "rt2ri",
    "sampleData",
    "sampleData<-",
    "sampleDays",
    "sampleDays<-",
    "sampleNames",
    "sampleNames<-",
    "sampleRI",
    "selMass",
    "selMass<-",
    "show",
    "spectra",
    "spectra<-",
    "TargetSearchGUI",
    "text2bin",
    "topMass",
    "topMass<-",
    "tsUpdate",
    "updateRI",
    "Write.Results",
    "writeLibText",
    "writeMSP"
  ],
  "_datasets": [
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      "title": "Example GC-MS data for TargetSearch Package",
      "object": "TSExample",
      "file": "TSExample.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
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        "7235eg22"
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      "table": true,
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      "title": "Example GC-MS data for TargetSearch Package",
      "object": "TSExample",
      "file": "TSExample.rda",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "peakData",
      "title": "Example GC-MS data for TargetSearch Package",
      "object": "TSExample",
      "file": "TSExample.rda",
      "class": [
        "tsMSdata"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
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      "title": "Example GC-MS data for TargetSearch Package",
      "object": "TSExample",
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      "class": [
        "tsLib"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
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      "title": "Example GC-MS data for TargetSearch Package",
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        "array"
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      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
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      "title": "Example GC-MS data for TargetSearch Package",
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      "class": [
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      "fields": [],
      "table": false,
      "tojson": false
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  "_help": [
    {
      "page": "TargetSearch-package",
      "title": "A targeted approach for GC-MS data.",
      "topics": [
        "TargetSearch-package",
        "TargetSearch"
      ]
    },
    {
      "page": "baseline",
      "title": "Baseline correction - wrapper function",
      "topics": [
        "baseline"
      ]
    },
    {
      "page": "baselineCorrection",
      "title": "Baseline correction - Chang's method",
      "topics": [
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      ]
    },
    {
      "page": "baselineCorrectionQuant",
      "title": "Baseline correction - quantiles method",
      "topics": [
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      ]
    },
    {
      "page": "checkRimLim",
      "title": "Visually check retention index marker limits",
      "topics": [
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      ]
    },
    {
      "page": "FAMEoutliers",
      "title": "FAME outlier detection",
      "topics": [
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      ]
    },
    {
      "page": "FindAllPeaks",
      "title": "Extract peaks from chromatogram files - low level function",
      "topics": [
        "FindAllPeaks"
      ]
    },
    {
      "page": "FindPeaks",
      "title": "Extract peaks from chromatogram files",
      "topics": [
        "FindPeaks"
      ]
    },
    {
      "page": "fixRI",
      "title": "Fixing Retention Time Index Correction",
      "topics": [
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      ]
    },
    {
      "page": "ImportFameSettings",
      "title": "Retention time markers settings",
      "topics": [
        "ImportFameSettings"
      ]
    },
    {
      "page": "ImportLibrary",
      "title": "Library import",
      "topics": [
        "ImportLibrary",
        "ImportLibrary.msp",
        "ImportLibrary.tab"
      ]
    },
    {
      "page": "ImportSamples",
      "title": "Sample definitions",
      "topics": [
        "ImportSamples",
        "ImportSamplesFromDir"
      ]
    },
    {
      "page": "makeIndex",
      "title": "Make an index vector out of selective/top masses",
      "topics": [
        "makeIndex"
      ]
    },
    {
      "page": "medianRILib",
      "title": "Median RI library correction",
      "topics": [
        "medianRILib"
      ]
    },
    {
      "page": "ncdf4_convert",
      "title": "Convert from a NetCDF file format 3 to format 4",
      "topics": [
        "ncdf4_convert"
      ]
    },
    {
      "page": "ncdf4_convert_from_path",
      "title": "Convert CDF files to CDF4 from a path automatically",
      "topics": [
        "ncdf4_convert_from_path"
      ]
    },
    {
      "page": "ncdf4_data_extract",
      "title": "Extract data ranges from a NetCDF file format 4",
      "topics": [
        "ncdf4_data_extract"
      ]
    },
    {
      "page": "ncdf4_plot_peak",
      "title": "Plot peaks from ncdf4 files",
      "topics": [
        "ncdf4_plot_peak"
      ]
    },
    {
      "page": "ncdf4_update_ri",
      "title": "Update retention time index on a NCDF4 file",
      "topics": [
        "ncdf4_update_ri"
      ]
    },
    {
      "page": "ncdf4Convert-method",
      "title": "Method for converting CDF-3 files to CDF-4",
      "topics": [
        "ncdf4Convert",
        "ncdf4Convert,tsSample-method"
      ]
    },
    {
      "page": "NetCDFPeakFinding",
      "title": "Peak picking algorithm from CDF files",
      "topics": [
        "NetCDFPeakFinding"
      ]
    },
    {
      "page": "peakCDFextraction",
      "title": "NetCDF to R",
      "topics": [
        "peakCDFextraction"
      ]
    },
    {
      "page": "peakFind",
      "title": "Intensities and RI matrices",
      "topics": [
        "peakFind"
      ]
    },
    {
      "page": "plotFAME",
      "title": "Plot a standard marker",
      "topics": [
        "plotFAME"
      ]
    },
    {
      "page": "plotPeak",
      "title": "Plot peaks",
      "topics": [
        "plotPeak"
      ]
    },
    {
      "page": "plotPeakRI",
      "title": "Plot peak RI across samples",
      "topics": [
        "plotPeakRI"
      ]
    },
    {
      "page": "plotPeakSimple",
      "title": "Plot peaks - simple (old) interface",
      "topics": [
        "plotPeakSimple"
      ]
    },
    {
      "page": "plotRefSpectra",
      "title": "Plot reference spectrum of a compound",
      "topics": [
        "plotRefSpectra"
      ]
    },
    {
      "page": "plotRIdev",
      "title": "Plot Retention Time Index Deviation",
      "topics": [
        "plotAllRIdev",
        "plotRIdev"
      ]
    },
    {
      "page": "plotSpectra",
      "title": "Plot a Spectra Comparison",
      "topics": [
        "plotAllSpectra",
        "plotSpectra"
      ]
    },
    {
      "page": "Profile",
      "title": "Average the correlating masses for each metabolite",
      "topics": [
        "Profile"
      ]
    },
    {
      "page": "ProfileCleanUp",
      "title": "Reduce redundancy of the profile",
      "topics": [
        "ProfileCleanUp"
      ]
    },
    {
      "page": "quantMatrix",
      "title": "Create an intensity matrix using quantification masses",
      "topics": [
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      ]
    },
    {
      "page": "ri_data_extract",
      "title": "Extract peak data from a RI file",
      "topics": [
        "ri_data_extract"
      ]
    },
    {
      "page": "ri_plot_peak",
      "title": "Plot peak RI across samples - low level interface",
      "topics": [
        "ri_plot_peak"
      ]
    },
    {
      "page": "ri2rt",
      "title": "Retention Time Index to Retention Time conversion",
      "topics": [
        "ri2rt"
      ]
    },
    {
      "page": "RIcorrect",
      "title": "Peak picking from CDF files and RI correction",
      "topics": [
        "RIcorrect"
      ]
    },
    {
      "page": "riMatrix",
      "title": "Retention Time Index Matrix",
      "topics": [
        "riMatrix"
      ]
    },
    {
      "page": "rt2ri",
      "title": "Retention Time to Retention Time Index conversion",
      "topics": [
        "rt2ri"
      ]
    },
    {
      "page": "sampleRI",
      "title": "Sample specific RI detection",
      "topics": [
        "sampleRI"
      ]
    },
    {
      "page": "TargetSearch-defunct",
      "title": "Defunct functions in package 'TargetSearch'",
      "topics": [
        "fixRIcorrection",
        "fixRIcorrection-defunct",
        "TargetSearch-defunct",
        "TargetSearchGUI"
      ]
    },
    {
      "page": "TargetSearch-deprecated",
      "title": "Deprecated functions in package 'TargetSearch'",
      "topics": [
        "TargetSearch-deprecated"
      ]
    },
    {
      "page": "file",
      "title": "Convert RI files from text to binary format and vice versa",
      "topics": [
        "bin2text",
        "text2bin"
      ]
    },
    {
      "page": "TSExample",
      "title": "Example GC-MS data for TargetSearch Package",
      "topics": [
        "corRI",
        "metabProfile",
        "peakData",
        "refLibrary",
        "RImatrix",
        "sampleDescription",
        "TSExample"
      ]
    },
    {
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