AnnotatedImage-class    AnnotatedImage: Optical images with annotations
AnnotatedImagingExperiment-class
                        AnnotatedImagingExperiment: Mass spectrometry
                        imaging experiments
Cardinal-defunct        Defunct functions and methods in Cardinal
Cardinal-deprecated     Deprecated functions and methods in Cardinal
Cardinal-package        Mass spectrometry imaging tools
Cardinal-reexports      Objects exported from other packages
Hashmat-class           Hashmat: Sparse matrix class using lists as
                        hash tables
IAnnotatedDataFrame-class
                        IAnnotatedDataFrame: Class containing measured
                        variables and their metadata for imaging
                        experiments
ImageData-class         ImageData: Class containing arrays of imaging
                        data
ImageList-class         ImageList: Abstract image data list
ImagingExperiment-class
                        ImagingExperiment: Abstract class for imaging
                        experiments
ImagingResult-class     ImagingResult: Results of statistical analysis
                        of imaging experiments
MIAPE-Imaging-class     MIAPE-Imaging: Class for storing mass
                        spectrometry imaging experiment information
MSContinuousImagingExperiment-class
                        MSContinuousImagingExperiment: "Continuous"
                        mass spectrometry imaging experiments
MSImageData-class       MSImageData: Class containing mass spectrometry
                        image data
MSImageProcess-class    MSImageProcess: Class containing mass spectral
                        preprocessing information
MSImageSet-class        MSImageSet: Class to contain mass spectrometry
                        imaging experiment data
MSImagingExperiment-class
                        MSImagingExperiment: Mass spectrometry imaging
                        experiments
MSImagingInfo-class     MSImagingInfo: Mass spectrometry imaging
                        metadata for imzML conversion
MSProcessedImagingExperiment-class
                        MSProcessedImagingExperiment: "Processed" mass
                        spectrometry imaging experiments
MassDataFrame-class     MassDataFrame: data frame with mass-to-charge
                        ratio metadata
PCA-methods             Principal components analysis
PLS-methods             Partial least squares
PositionDataFrame-class
                        PositionDataFrame: data frame with spatial
                        position metadata
ResultSet-class         ResultSet: Class to contain analysis results
                        for imaging experiments
SImageData-class        SImageData: Class containing sparse image data
SImageSet-class         SIMageSet: Class to contain pixel-sparse
                        imaging data
SparseImagingExperiment-class
                        SparseImagingExperiment: Pixel-sparse imaging
                        experiments
SummaryDataFrame-class
                        SummaryDataFrame: object summaries
XDataFrame-class        XDataFrame: DataFrame with eXtra metadata
                        columns
batchProcess-methods    Batch Pre-Processing on an Imaging Dataset
colocalized             Colocalized features
coregister-methods      Coregister images
cvApply-methods         Apply cross-validation to imaging analyses
filter                  Data transformation and summarization
findNeighbors-methods   Find spatial neighbors and spatial weightst
iSet-class              iSet: Class to contain high-throughput imaging
                        experiment data and metadata
image-methods           Plot an image of the pixel data of an imaging
                        dataset
intensity.colors        Color palettes for imaging
meansTest-methods       Linear model-based testing for summarized
                        imaging experiments
mz-methods              Manipulate mass-to-charge-ratio values
mzAlign-methods         Mass align an imaging dataset
mzBin-methods           Mass bin an imaging dataset
mzFilter-methods        Filter the features of an imaging dataset by
                        intensity
normalize-methods       Normalize an imaging dataset
peakAlign-methods       Peak align an imaging dataset
peakBin-methods         Peak bin an imaging dataset
peakPick-methods        Peak pick an imaging dataset
pixelApply-methods      Apply functions over imaging datasets
plot-methods            Plot a signal from the feature data of an
                        imaging dataset
process-methods         Delayed Processing of Imaging Datasets
readMSIData             Read mass spectrometry imaging data files
reduceBaseline-methods
                        Reduce the baseline for an imaging dataset
reduceDimension-methods
                        Reduce the dimension of an imaging dataset
selectROI-methods       Select regions-of-interest of an imaging
                        dataset
simulateSpectrum        Simulate a mass spectrum or MS imaging
                        experiment
slice                   Slice an image
smoothSignal-methods    Smooth the signals of a imaging dataset
spatialDGMM-methods     Spatially-aware Dirichlet Gaussian mixture
                        model
spatialFastmap-methods
                        Spatially-aware FastMap projection
spatialKMeans-methods   Spatially-aware k-means clustering
spatialShrunkenCentroids-methods
                        Spatially-aware shrunken centroid clustering
                        and classification
standardizeRuns-methods
                        Standardize between runs in an imaging dataset
topFeatures-methods     Top-ranked features from imaging analysis
                        results
writeMSIData            Write mass spectrometry imaging data files
