{
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  "Package": "GCIMS",
  "Type": "Package",
  "Title": "Pre-processing for GC-IMS data",
  "Version": "0.1.1",
  "Encoding": "UTF-8",
  "Date": "2024-04-29",
  "Authors@R": "c(\nperson(\ngiven = \"Sergio\",\nfamily = \"Oller Moreno\",\nemail = \"soller@ibecbarcelona.eu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8994-1549\")\n),\nperson(\ngiven = \"Celia\",\nfamily = \"Mallafré Muro\",\nemail = \"cmallafre@ibecbarcelona.eu\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0001-8247-1719\")\n),\nperson(\ngiven = \"Luis\",\nfamily = \"Fernandez\",\nemail = \"lfernandez@ibecbarcelona.eu\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0001-9790-6287\")\n),\nperson(\ngiven = \"Eduardo\",\nfamily = \"Caballero Saldivar\",\nemail = \"ecaballero@ibecbarcelona.eu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-9698-0749\")\n),\nperson(\ngiven = \"Arnau\",\nfamily = \"Blanco Borrego\",\nemail = \"blancoarnau@gmail.com\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-5287-7491\")\n),\nperson(\ngiven = \"Antonio\",\nfamily = \"Pardo Matínez\",\nemail = \"a.pardo@ub.edu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-4369-544X\")\n),\nperson(\ngiven = \"Santiago\",\nfamily = \"Marco Colás\",\nemail = \"smarco@ibecbarcelona.eu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-2663-2965\")\n),\nperson(\ngiven = \"Institute for Bioengineering of Catalonia\",\nrole = \"cph\"\n)\n)",
  "Description": "A package for the analysis of ion mobility spectrometry\n(IMS) measurements, as well as samples from multicapillary\ncolumns coupled with IMS (MCC-IMS) and gas chromatography\ncoupled to ion mobility spectrometry (GC-IMS). The package\nprovides a complete workflow for the analysis, importing the\ndata, preprocessing the spectra as well as classification and\nregression techniques for the modelling of the spectra. The\npackage also includes visualization helpers, to represent\ntopographic plots, extracted and total ion chromatograms and\nIMS spectra.",
  "License": "MIT + file LICENSE",
  "biocViews": "Software, Preprocessing, Visualization, Classification,\nCheminformatics, Metabolomics, DataImport",
  "RoxygenNote": "7.3.1",
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  "Roxygen": "list(markdown = TRUE)",
  "Remotes": [
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  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://zeehio.r-universe.dev",
  "Date/Publication": "2025-05-03 14:11:22 UTC",
  "RemoteUrl": "https://github.com/sipss/GCIMS",
  "RemoteRef": "HEAD",
  "RemoteSha": "bf3825eb751e4320e3b60a1ddc0e6a03e5f8ffa5",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 19:32:38 UTC",
    "User": "root"
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  "Author": "Sergio Oller Moreno [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-8994-1549>),\nCelia Mallafré Muro [aut] (ORCID:\n<https://orcid.org/0000-0001-8247-1719>),\nLuis Fernandez [aut] (ORCID: <https://orcid.org/0000-0001-9790-6287>),\nEduardo Caballero Saldivar [aut] (ORCID:\n<https://orcid.org/0000-0002-9698-0749>),\nArnau Blanco Borrego [aut] (ORCID:\n<https://orcid.org/0000-0002-5287-7491>),\nAntonio Pardo Matínez [aut] (ORCID:\n<https://orcid.org/0000-0003-4369-544X>),\nSantiago Marco Colás [aut] (ORCID:\n<https://orcid.org/0000-0003-2663-2965>),\nInstitute for Bioengineering of Catalonia [cph]",
  "Maintainer": "Sergio Oller Moreno <soller@ibecbarcelona.eu>",
  "MD5sum": "5e3c5ff57a4c43a13d40e31701032b6a",
  "_user": "zeehio",
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  "_created": "2026-05-29T19:32:38.000Z",
  "_published": "2026-05-31T06:00:55.325Z",
  "_distro": "noble",
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  "_selfowned": true,
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  "_updates": [],
  "_tags": [],
  "_topics": [
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    "preprocessing",
    "visualization",
    "classification",
    "cheminformatics",
    "metabolomics",
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  "_exports": [
    "add_peaklist_rect",
    "align",
    "alignDt",
    "alignPlots",
    "alignRt_ip",
    "alignRt_pow",
    "alignRt_ptw",
    "baseline",
    "baseline<-",
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    "create_annotations_table",
    "cubic_root_trans",
    "decimate",
    "DelayedOperation",
    "description",
    "description<-",
    "download_three_ketones_dataset",
    "dtime",
    "estimateBaseline",
    "filterDt",
    "filterRt",
    "findPeaks",
    "GCIMSChromatogram",
    "GCIMSDataset",
    "GCIMSDataset_fromList",
    "GCIMSSample",
    "GCIMSSpectrum",
    "getChromatogram",
    "getRIC",
    "getSample",
    "getSpectrum",
    "getTIS",
    "imputePeakTable",
    "integratePeaks",
    "intensity",
    "intensity<-",
    "omit_times",
    "overlay_peaklist",
    "pData",
    "pData<-",
    "peaks",
    "peaks<-",
    "peakTable",
    "plot",
    "plot_interactive",
    "plotRaw",
    "plotRIC",
    "plotTIS",
    "prealign",
    "read_mea",
    "realize",
    "rtime",
    "sampleNames",
    "sampleNames<-",
    "show_progress_bar",
    "smooth",
    "updateObject"
  ],
  "_help": [
    {
      "page": "add_peaklist_rect",
      "title": "Add peak list rectangles to a raw plot",
      "topics": [
        "add_peaklist_rect"
      ]
    },
    {
      "page": "align-GCIMSDataset-method",
      "title": "Align a GCIMS dataset",
      "topics": [
        "align,GCIMSDataset-method"
      ]
    },
    {
      "page": "align-GCIMSSample-method",
      "title": "Align a GCIMSSample object, in retention time",
      "topics": [
        "align,GCIMSSample-method"
      ]
    },
    {
      "page": "alignDt",
      "title": "Align a GCIMSSample in drift time with a multiplicative correction",
      "topics": [
        "alignDt"
      ]
    },
    {
      "page": "alignPlots",
      "title": "Plots to interpret alignment results",
      "topics": [
        "alignPlots"
      ]
    },
    {
      "page": "alignRt_ip",
      "title": "Align a GCIMSSample in retention time with a multiplicative correction",
      "topics": [
        "alignRt_ip"
      ]
    },
    {
      "page": "alignRt_pow",
      "title": "Align a GCIMSSample in retention time with parametric optimized warping",
      "topics": [
        "alignRt_pow"
      ]
    },
    {
      "page": "alignRt_ptw",
      "title": "Align a GCIMSSample in retention time using parametric time warping",
      "topics": [
        "alignRt_ptw"
      ]
    },
    {
      "page": "as.data.frame.GCIMSSample",
      "title": "Turn the intensity matrix into a data frame",
      "topics": [
        "as.data.frame.GCIMSSample"
      ]
    },
    {
      "page": "clusterPeaks",
      "title": "Group peaks in clusters",
      "topics": [
        "clusterPeaks"
      ]
    },
    {
      "page": "create_annotations_table",
      "title": "Create a table for defining dataset annotations",
      "topics": [
        "create_annotations_table"
      ]
    },
    {
      "page": "cubic_root_trans",
      "title": "Cubic root transformation",
      "topics": [
        "cubic_root_trans"
      ]
    },
    {
      "page": "decimate-GCIMSDataset-method",
      "title": "Decimate a GCIMS dataset keeping 1 out of n points",
      "topics": [
        "decimate,GCIMSDataset-method"
      ]
    },
    {
      "page": "decimate-GCIMSSample-method",
      "title": "Decimates a GCIMS sample",
      "topics": [
        "decimate,GCIMSSample-method"
      ]
    },
    {
      "page": "DelayedOperation",
      "title": "Create a DelayedOperation object",
      "topics": [
        "DelayedOperation"
      ]
    },
    {
      "page": "DelayedOperation-class",
      "title": "Delayed Operation class",
      "topics": [
        "DelayedOperation-class"
      ]
    },
    {
      "page": "download_three_ketones_dataset",
      "title": "Download three samples (6-ketone mixture)",
      "topics": [
        "download_three_ketones_dataset"
      ]
    },
    {
      "page": "dtime-GCIMSChromatogram-method",
      "title": "Get the drift time of the chromatogram",
      "concept": [
        "GCIMSChromatogram"
      ],
      "topics": [
        "dtime,GCIMSChromatogram-method"
      ]
    },
    {
      "page": "dtime-GCIMSDataset-method",
      "title": "Get A reference drift time vector for the dataset",
      "topics": [
        "dtime,GCIMSDataset-method"
      ]
    },
    {
      "page": "estimateBaseline-GCIMSChromatogram-method",
      "title": "Estimate the baseline of a GCIMS Chromatogram using a connect local minima algorithm",
      "concept": [
        "GCIMSChromatogram"
      ],
      "topics": [
        "baseline,GCIMSChromatogram-method",
        "baseline<-,GCIMSChromatogram-method",
        "estimateBaseline,GCIMSChromatogram-method"
      ]
    },
    {
      "page": "estimateBaseline-GCIMSDataset-method",
      "title": "Estimate the baseline of a GCIMS Sample using a connect local minima algorithm",
      "topics": [
        "estimateBaseline,GCIMSDataset-method"
      ]
    },
    {
      "page": "estimateBaseline-GCIMSSample-method",
      "title": "Estimate the baseline of a GCIMS Sample using a connect local minima algorithm",
      "topics": [
        "baseline,GCIMSSample-method",
        "baseline<-,GCIMSSample-method",
        "estimateBaseline,GCIMSSample-method"
      ]
    },
    {
      "page": "estimateBaseline-GCIMSSpectrum-method",
      "title": "Estimate the baseline of a GCIMS Spectrum using a connect local minima algorithm",
      "topics": [
        "baseline,GCIMSSpectrum-method",
        "baseline<-,GCIMSSpectrum-method",
        "estimateBaseline,GCIMSSpectrum-method"
      ]
    },
    {
      "page": "filterDt-GCIMSDataset-method",
      "title": "Filter GCIMSDataset samples by drift time",
      "topics": [
        "filterDt,GCIMSDataset-method"
      ]
    },
    {
      "page": "filterDt-GCIMSSample-method",
      "title": "Filter GCIMSSample samples by drift time",
      "topics": [
        "filterDt,GCIMSSample-method"
      ]
    },
    {
      "page": "filterRt-GCIMSDataset-method",
      "title": "Filter GCIMSDataset samples by retention time",
      "topics": [
        "filterRt,GCIMSDataset-method"
      ]
    },
    {
      "page": "filterRt-GCIMSSample-method",
      "title": "Filter GCIMSSample samples by retention time",
      "topics": [
        "filterRt,GCIMSSample-method"
      ]
    },
    {
      "page": "findPeaks",
      "title": "Find Peaks in an object",
      "topics": [
        "findPeaks"
      ]
    },
    {
      "page": "findPeaks-GCIMSChromatogram-method",
      "title": "Peak detection for a GCIMSChromatogram",
      "concept": [
        "GCIMSChromatogram"
      ],
      "topics": [
        "findPeaks,GCIMSChromatogram-method"
      ]
    },
    {
      "page": "findPeaks-GCIMSDataset-method",
      "title": "Peak detection on the GCIMS dataset",
      "topics": [
        "findPeaks,GCIMSDataset-method"
      ]
    },
    {
      "page": "findPeaks-GCIMSSample-method",
      "title": "Peak detection for a GCIMSSample",
      "topics": [
        "findPeaks,GCIMSSample-method"
      ]
    },
    {
      "page": "findPeaks-GCIMSSpectrum-method",
      "title": "Peak detection for a GCIMSSpectrum",
      "concept": [
        "GCIMSSpectrum"
      ],
      "topics": [
        "findPeaks,GCIMSSpectrum-method"
      ]
    },
    {
      "page": "GCIMS-generics",
      "title": "GCIMS Generics",
      "topics": [
        "align",
        "baseline",
        "baseline<-",
        "decimate",
        "dtime",
        "estimateBaseline",
        "filterDt",
        "GCIMS-generics",
        "getRIC",
        "getTIS",
        "integratePeaks",
        "plotRIC",
        "plotTIS",
        "prealign"
      ]
    },
    {
      "page": "GCIMSChromatogram",
      "title": "Create a GCIMSChromatogram object",
      "concept": [
        "GCIMSChromatogram"
      ],
      "topics": [
        "GCIMSChromatogram"
      ]
    },
    {
      "page": "GCIMSChromatogram-class",
      "title": "GCIMSChromatogram class",
      "concept": [
        "GCIMSChromatogram"
      ],
      "topics": [
        "as.data.frame.GCIMSChromatogram",
        "description,GCIMSChromatogram-method",
        "description<-,GCIMSChromatogram,ANY-method",
        "GCIMSChromatogram-class",
        "peaks,GCIMSChromatogram-method",
        "peaks<-,GCIMSChromatogram-method",
        "plot,GCIMSChromatogram,ANY-method"
      ]
    },
    {
      "page": "GCIMSDataset",
      "title": "GCIMSDataset",
      "topics": [
        "GCIMSDataset",
        "GCIMSDataset-class"
      ]
    },
    {
      "page": "GCIMSDataset_fromList",
      "title": "GCIMSDataset_fromList",
      "topics": [
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      "page": "GCIMSSample",
      "title": "Create a GCIMSSample object",
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      "page": "GCIMSSample-class",
      "title": "GCIMSSample class",
      "topics": [
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      "page": "GCIMSSample-methods",
      "title": "Methods for the GCIMSSample class",
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    },
    {
      "page": "getChromatogram",
      "title": "Get the extracted ion chromatogram",
      "topics": [
        "getChromatogram"
      ]
    },
    {
      "page": "getRIC-GCIMSDataset-method",
      "title": "Get Reverse Ion Chromatogram",
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    },
    {
      "page": "getRIC-GCIMSSample-method",
      "title": "Get the reverse ion chromatogram",
      "topics": [
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    },
    {
      "page": "getSpectrum",
      "title": "Get IMS spectrum from a sample",
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    },
    {
      "page": "getTIS-GCIMSDataset-method",
      "title": "Get Total Ion Spectra matrix",
      "topics": [
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      "page": "getTIS-GCIMSSample-method",
      "title": "Get the total ion spectrum",
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    {
      "page": "imputePeakTable",
      "title": "Impute a Peak table",
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      "concept": [
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      "page": "omit_times",
      "title": "Omit ROIs present in certain retention and drift times",
      "topics": [
        "omit_times"
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    },
    {
      "page": "overlay_peaklist",
      "title": "Overlay a peak list to a plot",
      "topics": [
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    },
    {
      "page": "pData-GCIMSDataset-method",
      "title": "Get/Set the phenotype data",
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      "page": "peakTable",
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    {
      "page": "plot_interactive",
      "title": "Make a plot interactive",
      "topics": [
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      "page": "plot-GCIMSSample-ANY-method",
      "title": "Topographical plot of a GCIMSSample object",
      "topics": [
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      "page": "plotRIC-GCIMSDataset-method",
      "title": "Plot Reverse Ion Chromatograms",
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      "page": "prealign-GCIMSSample-method",
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