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  "Package": "Cardinal",
  "Type": "Package",
  "Title": "A mass spectrometry imaging toolbox for statistical analysis",
  "Version": "3.15.0",
  "Date": "2015-1-12",
  "Authors@R": "person(\"Kylie Ariel\", \"Bemis\",\nemail = \"k.bemis@northeastern.edu\",\nrole = c(\"aut\", \"cre\"))",
  "Description": "Implements statistical & computational tools for analyzing\nmass spectrometry imaging datasets, including methods for\nefficient pre-processing, spatial segmentation, and\nclassification.",
  "License": "Artistic-2.0 | file LICENSE",
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  "biocViews": "Software, Infrastructure, Proteomics, Lipidomics,\nMassSpectrometry, ImagingMassSpectrometry, ImmunoOncology,\nNormalization, Clustering, Classification, Regression",
  "URL": "http://www.cardinalmsi.org",
  "BugReports": "https://github.com/kuwisdelu/Cardinal/issues",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:40:31 UTC",
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  "Author": "Kylie Ariel Bemis [aut, cre]",
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    "aggregate",
    "as_facets",
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    "contrastTest",
    "convertMSImagingArrays2Experiment",
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    "coord",
    "coord<-",
    "coordNames",
    "coordNames<-",
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    "cpal",
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    "crossValidate",
    "domain",
    "domain<-",
    "dpal",
    "dpals",
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    "estimateDomain",
    "estimateReferenceMz",
    "estimateReferencePeaks",
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    "experimentData<-",
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    "featureData<-",
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    "findNeighbors",
    "fitted",
    "flash",
    "getCardinalBPPARAM",
    "getCardinalChunksize",
    "getCardinalLogger",
    "getCardinalNChunks",
    "getCardinalNumBlocks",
    "getCardinalParallel",
    "getCardinalSerialize",
    "getCardinalVerbose",
    "iData",
    "iData<-",
    "image",
    "image3D",
    "intensity",
    "intensity<-",
    "is3D",
    "isCentroided",
    "keys",
    "keys<-",
    "logLik",
    "makeFactor",
    "MassDataFrame",
    "meansTest",
    "modelData",
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    "MSImagingArrays",
    "MSImagingExperiment",
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    "mzAlign",
    "mzBin",
    "mzFilter",
    "NMF",
    "normalize",
    "nrun",
    "OPLS",
    "PCA",
    "pData",
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    "peakAlign",
    "peakBin",
    "peakFilter",
    "peakPick",
    "peakProcess",
    "pixelApply",
    "pixelData",
    "pixelData<-",
    "pixelNames",
    "pixelNames<-",
    "pixels",
    "plot",
    "PLS",
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    "predict",
    "presetImageDef",
    "process",
    "rbind",
    "readAnalyze",
    "readImzML",
    "readMSIData",
    "recalibrate",
    "reduceBaseline",
    "reset",
    "residuals",
    "resultData",
    "resultData<-",
    "resultNames",
    "resultNames<-",
    "ResultsList",
    "rowMeans",
    "rownames",
    "rownames<-",
    "rowStats",
    "rowSums",
    "run",
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    "runNames",
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    "saveCardinalLog",
    "segmentationTest",
    "selectROI",
    "setCardinalBPPARAM",
    "setCardinalChunksize",
    "setCardinalLogger",
    "setCardinalNChunks",
    "setCardinalNumBlocks",
    "setCardinalParallel",
    "setCardinalSerialize",
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    "slice",
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    "spatialDists",
    "spatialFastmap",
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    "spatialShrunkenCentroids",
    "spatialWeights",
    "spectra",
    "spectra<-",
    "SpectraArrays",
    "SpectralImagingArrays",
    "SpectralImagingExperiment",
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    "subsetFeatures",
    "subsetPixels",
    "summarizeFeatures",
    "summarizePixels",
    "topFeatures",
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    "vizi_style",
    "writeAnalyze",
    "writeImzML",
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      "title": "Mass spectrometry imaging tools",
      "topics": [
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        "Cardinal",
        "getCardinalBPPARAM",
        "getCardinalChunksize",
        "getCardinalLogger",
        "getCardinalNChunks",
        "getCardinalParallel",
        "getCardinalSerialize",
        "getCardinalVerbose",
        "saveCardinalLog",
        "setCardinalBPPARAM",
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        "setCardinalLogger",
        "setCardinalNChunks",
        "setCardinalParallel",
        "setCardinalSerialize",
        "setCardinalVerbose",
        "vizi_engine",
        "vizi_par",
        "vizi_style"
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        "bin,MSImagingExperiment-method",
        "bin,SpectralImagingArrays-method",
        "bin,SpectralImagingExperiment-method"
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      "title": "Colocalized features",
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        "colocalized,MSImagingExperiment-method",
        "colocalized,SpatialDGMM-method",
        "colocalized,SpectralImagingExperiment-method",
        "coregister"
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    },
    {
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      "title": "Deprecated and defunct objects in Cardinal",
      "topics": [
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        "class:IAnnotatedDataFrame",
        "class:ImageData",
        "class:iSet",
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        "Hashmat",
        "Hashmat-class",
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        "IAnnotatedDataFrame-class",
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        "iData,ANY-method",
        "iData<-",
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        "pixelApply",
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        "ResultSet",
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      "topics": [
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        "estimateReferenceMz",
        "estimateReferencePeaks"
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      "title": "Find feature indices",
      "topics": [
        "features",
        "features,MSImagingExperiment-method",
        "features,SpectralImagingExperiment-method"
      ]
    },
    {
      "page": "findNeighbors",
      "title": "Find spatial neighbors",
      "topics": [
        "findNeighbors",
        "findNeighbors,ANY-method",
        "findNeighbors,PositionDataFrame-method",
        "findNeighbors,SpectralImagingData-method"
      ]
    },
    {
      "page": "MassDataFrame-class",
      "title": "MassDataFrame: Extended data frame with key columns",
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        "class:MassDataFrame",
        "coerce,DFrame,MassDataFrame-method",
        "MassDataFrame",
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        "mz,MassDataFrame-method",
        "mz<-,MassDataFrame-method",
        "[,MassDataFrame,ANY,ANY,ANY-method"
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      "page": "MeansTest",
      "title": "Linear model-based testing for summarized imaging experiments",
      "topics": [
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        "class:MeansTest",
        "ContrastTest",
        "contrastTest",
        "ContrastTest-class",
        "MeansTest",
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        "meansTest,SpatialDGMM-method",
        "meansTest,SpectralImagingExperiment-method",
        "MeansTest-class",
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        "topFeatures,MeansTest-method"
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    {
      "page": "MSImagingArrays-class",
      "title": "MSImagingArrays: MS imaging data with arbitrary m/z values",
      "topics": [
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        "class:MSImagingArrays",
        "intensity,MSImagingArrays-method",
        "intensity<-,MSImagingArrays-method",
        "MSImagingArrays",
        "MSImagingArrays-class",
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        "mz<-,MSImagingArrays-method",
        "show,MSImagingArrays-method"
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      "page": "MSImagingExperiment-class",
      "title": "MSImagingExperiment: MS imaging data with shared m/z values",
      "topics": [
        "cbind,MSImagingExperiment-method",
        "centroided,MSImagingExperiment_OR_Arrays-method",
        "centroided<-,MSImagingExperiment_OR_Arrays-method",
        "class:MSImagingExperiment",
        "coerce,MSImageSet,MSImagingExperiment-method",
        "experimentData,MSImagingExperiment_OR_Arrays-method",
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        "intensity,MSImagingExperiment-method",
        "intensity<-,MSImagingExperiment-method",
        "isCentroided,MSImagingExperiment_OR_Arrays-method",
        "MSImagingExperiment",
        "MSImagingExperiment-class",
        "mz,missing-method",
        "mz,MSImagingExperiment-method",
        "mz<-,MSImagingExperiment-method",
        "rbind,MSImagingExperiment-method",
        "show,MSImagingExperiment-method"
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    },
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      "page": "normalize",
      "title": "Normalize spectra",
      "topics": [
        "normalize",
        "normalize,MSImagingExperiment_OR_Arrays-method",
        "normalize,SpectralImagingData-method"
      ]
    },
    {
      "page": "peakAlign",
      "title": "Align peaks across spectra",
      "topics": [
        "peakAlign",
        "peakAlign,MSImagingArrays-method",
        "peakAlign,MSImagingExperiment-method",
        "peakAlign,SpectralImagingArrays-method",
        "peakAlign,SpectralImagingExperiment-method"
      ]
    },
    {
      "page": "peakPick",
      "title": "Peak pick spectra",
      "topics": [
        "peakPick",
        "peakPick,MSImagingArrays-method",
        "peakPick,MSImagingExperiment-method",
        "peakPick,SpectralImagingData-method"
      ]
    },
    {
      "page": "peakProcess",
      "title": "Process peaks in mass spectra",
      "topics": [
        "peakProcess",
        "peakProcess,MSImagingExperiment_OR_Arrays-method"
      ]
    },
    {
      "page": "pixels",
      "title": "Find pixel indices",
      "topics": [
        "pixels",
        "pixels,SpectralImagingArrays-method",
        "pixels,SpectralImagingData-method",
        "pixels,SpectralImagingExperiment-method"
      ]
    },
    {
      "page": "plot-image",
      "title": "Plot images from a spectral imaging dataset",
      "topics": [
        "image",
        "image,MSImagingExperiment-method",
        "image,PositionDataFrame-method",
        "image,SpectralImagingExperiment-method",
        "image3D",
        "image3D,MSImagingExperiment-method",
        "plot-image"
      ]
    },
    {
      "page": "plot-spectra",
      "title": "Plot spectra from a spectral imaging dataset",
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        "plot",
        "plot,MSImagingArrays,formula-method",
        "plot,MSImagingArrays,missing-method",
        "plot,MSImagingArrays,numeric-method",
        "plot,MSImagingExperiment,character-method",
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        "plot,SpectralImagingExperiment,character-method",
        "plot,SpectralImagingExperiment,formula-method",
        "plot,SpectralImagingExperiment,missing-method",
        "plot,SpectralImagingExperiment,numeric-method",
        "plot,XDataFrame,character-method",
        "plot,XDataFrame,formula-method",
        "plot,XDataFrame,missing-method",
        "plot-spectra"
      ]
    },
    {
      "page": "PositionDataFrame-class",
      "title": "PositionDataFrame: Extended data frame with key columns",
      "topics": [
        "class:PositionDataFrame",
        "coerce,DFrame,PositionDataFrame-method",
        "coord",
        "coord,PositionDataFrame-method",
        "coord<-",
        "coord<-,PositionDataFrame-method",
        "coordNames",
        "coordNames,PositionDataFrame-method",
        "coordNames<-",
        "coordNames<-,PositionDataFrame-method",
        "is3D",
        "is3D,PositionDataFrame-method",
        "nrun,PositionDataFrame-method",
        "PositionDataFrame",
        "PositionDataFrame-class",
        "run",
        "run,PositionDataFrame-method",
        "run<-",
        "run<-,PositionDataFrame-method",
        "runNames",
        "runNames,PositionDataFrame-method",
        "runNames<-",
        "runNames<-,PositionDataFrame-method",
        "[,PositionDataFrame,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "process",
      "title": "Apply queued processing to spectra",
      "topics": [
        "addProcessing,SpectralImagingData-method",
        "process",
        "process,MSImagingArrays-method",
        "process,MSImagingExperiment-method",
        "process,SpectralImagingArrays-method",
        "process,SpectralImagingExperiment-method",
        "reset"
      ]
    },
    {
      "page": "readMSIData",
      "title": "Read mass spectrometry imaging data files",
      "topics": [
        "coerce,MSImagingArrays,MSImagingExperiment-method",
        "coerce,MSImagingExperiment,MSImagingArrays-method",
        "convertMSImagingArrays2Experiment",
        "convertMSImagingExperiment2Arrays",
        "readAnalyze",
        "readImzML",
        "readMSIData"
      ]
    },
    {
      "page": "recalibrate",
      "title": "Recalibrate spectra",
      "topics": [
        "recalibrate",
        "recalibrate,MSImagingExperiment_OR_Arrays-method",
        "recalibrate,SpectralImagingData-method"
      ]
    },
    {
      "page": "reduceBaseline",
      "title": "Reduce baselines in spectra",
      "topics": [
        "reduceBaseline",
        "reduceBaseline,SpectralImagingData-method"
      ]
    },
    {
      "page": "reexports",
      "title": "Re-exported objects from Cardinal",
      "topics": [
        "as_facets",
        "as_layers",
        "cpal",
        "cpals",
        "dpal",
        "dpals",
        "reexports",
        "SnowfastParam"
      ]
    },
    {
      "page": "ResultsList-class",
      "title": "ResultsList: List of modeling results",
      "topics": [
        "class:ResultsList",
        "fitted,ResultsList-method",
        "image,ResultsList-method",
        "plot,ResultsList,ANY-method",
        "plot,ResultsList,missing-method",
        "predict,ResultsList-method",
        "ResultsList",
        "ResultsList-class",
        "show,ResultsList-method",
        "topFeatures,ResultsList-method"
      ]
    },
    {
      "page": "selectROI",
      "title": "Select regions-of-interest in an image",
      "topics": [
        "makeFactor",
        "selectROI",
        "selectROI,SpectralImagingExperiment-method"
      ]
    },
    {
      "page": "simulateSpectra",
      "title": "Simulate a mass spectrum or MS imaging experiment",
      "topics": [
        "addShape",
        "presetImageDef",
        "simulateImage",
        "simulateSpectra"
      ]
    },
    {
      "page": "sliceImage",
      "title": "Slice an image",
      "topics": [
        "sliceImage"
      ]
    },
    {
      "page": "smooth",
      "title": "Smooth spectra",
      "topics": [
        "smooth",
        "smooth,SpectralImagingData-method",
        "smoothSignal"
      ]
    },
    {
      "page": "SpatialCV",
      "title": "Cross-validation for spectral imaging data",
      "topics": [
        "class:SpatialCV",
        "crossValidate",
        "fitted,SpatialCV-method",
        "image,SpatialCV-method",
        "SpatialCV",
        "SpatialCV-class"
      ]
    },
    {
      "page": "SpatialDGMM",
      "title": "Spatially-aware Dirichlet Gaussian mixture model",
      "topics": [
        "class:SpatialDGMM",
        "image,SpatialDGMM-method",
        "logLik,SpatialDGMM-method",
        "plot,SpatialDGMM,missing-method",
        "SpatialDGMM",
        "spatialDGMM",
        "spatialDGMM,ANY-method",
        "spatialDGMM,SpectralImagingExperiment-method",
        "SpatialDGMM-class"
      ]
    },
    {
      "page": "spatialDists",
      "title": "Calculate spatially-smoothed distances",
      "topics": [
        "spatialDists",
        "spatialDists,ANY-method",
        "spatialDists,PositionDataFrame-method",
        "spatialDists,SpectralImagingExperiment-method"
      ]
    },
    {
      "page": "SpatialFastmap",
      "title": "Spatially-aware FastMap projection",
      "topics": [
        "class:SpatialFastmap",
        "image,SpatialFastmap-method",
        "plot,SpatialFastmap,missing-method",
        "predict,SpatialFastmap-method",
        "SpatialFastmap",
        "spatialFastmap",
        "spatialFastmap,ANY-method",
        "spatialFastmap,SpectralImagingExperiment-method",
        "SpatialFastmap-class"
      ]
    },
    {
      "page": "SpatialKMeans",
      "title": "Spatially-aware K-means clustering",
      "topics": [
        "class:SpatialKMeans",
        "image,SpatialKMeans-method",
        "plot,SpatialKMeans,missing-method",
        "SpatialKMeans",
        "spatialKMeans",
        "spatialKMeans,ANY-method",
        "spatialKMeans,SpectralImagingExperiment-method",
        "SpatialKMeans-class",
        "topFeatures,SpatialKMeans-method"
      ]
    },
    {
      "page": "SpatialNMF",
      "title": "Non-negative matrix factorization",
      "topics": [
        "class:SpatialNMF",
        "image,SpatialNMF-method",
        "NMF",
        "NMF,ANY-method",
        "NMF,SpectralImagingExperiment-method",
        "plot,SpatialNMF,missing-method",
        "predict,SpatialNMF-method",
        "SpatialNMF",
        "SpatialNMF-class"
      ]
    },
    {
      "page": "SpatialPCA",
      "title": "Principal components analysis",
      "topics": [
        "class:SpatialPCA",
        "image,SpatialPCA-method",
        "PCA",
        "PCA,ANY-method",
        "PCA,SpectralImagingExperiment-method",
        "plot,SpatialPCA,missing-method",
        "predict,SpatialPCA-method",
        "SpatialPCA",
        "SpatialPCA-class"
      ]
    },
    {
      "page": "SpatialPLS",
      "title": "Partial least squares (projection to latent structures)",
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        "class:SpatialOPLS",
        "class:SpatialPLS",
        "coef,SpatialOPLS-method",
        "fitted,SpatialOPLS-method",
        "fitted,SpatialPLS-method",
        "image,SpatialOPLS-method",
        "image,SpatialPLS-method",
        "OPLS",
        "OPLS,ANY-method",
        "OPLS,SpectralImagingExperiment-method",
        "plot,SpatialOPLS,missing-method",
        "plot,SpatialPLS,missing-method",
        "PLS",
        "PLS,ANY-method",
        "PLS,SpectralImagingExperiment-method",
        "predict,SpatialOPLS-method",
        "predict,SpatialPLS-method",
        "residuals,SpatialOPLS-method",
        "SpatialOPLS",
        "SpatialOPLS-class",
        "SpatialPLS",
        "SpatialPLS-class",
        "topFeatures,SpatialOPLS-method",
        "topFeatures,SpatialPLS-method"
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      "page": "SpatialResults-class",
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        "class:SpatialResults",
        "coord,SpatialResults-method",
        "coord<-,SpatialResults-method",
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        "logLik,SpatialShrunkenCentroids-method",
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        "predict,SpatialShrunkenCentroids-method",
        "SpatialShrunkenCentroids",
        "spatialShrunkenCentroids",
        "spatialShrunkenCentroids,ANY,ANY-method",
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        "SpatialShrunkenCentroids-class",
        "topFeatures",
        "topFeatures,SpatialShrunkenCentroids-method"
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      "page": "spatialWeights",
      "title": "Calculate spatial weights",
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        "spatialWeights,ANY-method",
        "spatialWeights,PositionDataFrame-method",
        "spatialWeights,SpectralImagingExperiment-method"
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      "page": "SpectraArrays-class",
      "title": "SpectraArrays: List of spectra arrays",
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        "$<-,SpectraArrays-method",
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        "[[,SpectraArrays-method",
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      "page": "SpectralImagingArrays-class",
      "title": "SpectralImagingArrays: Spectral imaging data with arbitrary domain",
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        "cbind,SpectralImagingArrays-method",
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        "[[,SpectralImagingData-method",
        "[[<-,SpectralImagingData-method"
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      "page": "SpectralImagingExperiment-class",
      "title": "SpectralImagingExperiment: Spectral imaging data with shared domain",
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        "class:SpectralImagingExperiment",
        "colnames,SpectralImagingExperiment-method",
        "colnames<-,SpectralImagingExperiment-method",
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        "[<-,SpectralImagingExperiment,ANY,ANY,ANY-method"
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    {
      "page": "spectrapply",
      "title": "Apply functions over spectra",
      "topics": [
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    },
    {
      "page": "subset",
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      "topics": [
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        "subset,SpectralImagingExperiment-method",
        "subsetFeatures",
        "subsetPixels"
      ]
    },
    {
      "page": "summarize",
      "title": "Summarize a spectral imaging dataset",
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        "colStats,SpectralImagingExperiment-method",
        "colSums,SpectralImagingExperiment-method",
        "rowMeans,SpectralImagingExperiment-method",
        "rowStats,SpectralImagingExperiment-method",
        "rowSums,SpectralImagingExperiment-method",
        "summarizeFeatures",
        "summarizePixels"
      ]
    },
    {
      "page": "writeMSIData",
      "title": "Write mass spectrometry imaging data files",
      "topics": [
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        "writeAnalyze,MSImagingExperiment-method",
        "writeAnalyze,SpectralImagingExperiment-method",
        "writeImzML",
        "writeImzML,MSImagingExperiment_OR_Arrays-method",
        "writeMSIData"
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      "page": "XDataFrame-class",
      "title": "XDataFrame: Extended data frame with key columns",
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        "class:XDataFrame",
        "class:XDFrame",
        "classNameForDisplay,XDFrame-method",
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      "source": "Cardinal3-guide.Rmd",
      "filename": "Cardinal3-guide.html",
      "title": "Cardinal 3: User guide for mass spectrometry imaging analysis",
      "author": "Kylie Ariel Bemis",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "Latest: Cardinal 3.6",
        "Previous updates from Cardinal 3",
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        "Installation",
        "Data import",
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        "Common operations on MS imaging datasets",
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        "Backend types",
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      "created": "2024-04-09 03:23:01",
      "modified": "2025-10-09 16:37:48",
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      "title": "Cardinal 3: Statistical methods for mass spectrometry imaging",
      "author": "Kylie Ariel Bemis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Exploratory analysis",
        "Principal components analysis (PCA)",
        "Non-negative matrix factorization (NMF)",
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        "Session information"
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      "modified": "2024-09-08 03:51:42",
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