Cardinal-package	Cardinal-package
$,ImagingExperiment-method	ImagingExperiment-class
$,ImagingResult-method	ImagingResult-class
$<-,ImagingExperiment-method	ImagingExperiment-class
$<-,XDataFrame-method	XDataFrame-class
%>%	reexports
addShape	simulateSpectrum
aggregate,MSImagingExperiment-method	aggregate-methods
aggregate,SparseImagingExperiment-method	aggregate-methods
alpha.colors	colors-functions
AnnotatedImage	deprecated
AnnotatedImage-class	deprecated
AnnotatedImageList	deprecated
AnnotatedImageList-class	deprecated
AnnotatedImagingExperiment	deprecated
AnnotatedImagingExperiment-class	deprecated
as.data.frame,XDataFrame-method	XDataFrame-class
as.env,list-method	XDataFrame-class
as.env,XDataFrame-method	XDataFrame-class
as.list,ImageList-method	ImageList-class
as.list,MassDataFrame-method	MassDataFrame-class
as.list,MSImagingInfo-method	MSImagingInfo-class
as.list,PositionDataFrame-method	PositionDataFrame-class
as.matrix,XDataFrame-method	XDataFrame-class
baselineReduction	MSImagingInfo-class
baselineReduction,Vector-method	MSImagingInfo-class
baselineReduction<-	MSImagingInfo-class
baselineReduction<-,Vector-method	MSImagingInfo-class
batchProcess	legacy
batchProcess,MSImageSet-method	legacy
batchProcess-methods	legacy
bw.colors	colors-functions
Cardinal	Cardinal-package
Cardinal-internal	internal
Cardinal-legacy	legacy
Cardinal-reexports	reexports
CardinalLog	Cardinal-package
CardinalVersion	Cardinal-package
cbind,AnnotatedImageList-method	deprecated
cbind,ImageArrayList-method	ImageList-class
cbind,ImagingExperiment-method	ImagingExperiment-class
cbind,MassDataFrame-method	MassDataFrame-class
cbind,MSImagingExperiment-method	MSImagingExperiment-class
cbind,PositionDataFrame-method	PositionDataFrame-class
cbind,SparseImagingExperiment-method	SparseImagingExperiment-class
cbind,SparseImagingResult-method	ImagingResult-class
cbind,XDataFrame-method	XDataFrame-class
centroided	MSImagingExperiment-class
centroided,MSImagingExperiment-method	MSImagingExperiment-class
centroided<-	MSImagingExperiment-class
centroided<-,MSImagingExperiment-method	MSImagingExperiment-class
cividis	reexports
class:AnnotatedImage	deprecated
class:AnnotatedImageList	deprecated
class:AnnotatedImagingExperiment	deprecated
class:Hashmat	legacy
class:IAnnotatedDataFrame	legacy
class:ImageArrayList	ImageList-class
class:ImageData	legacy
class:ImageList	ImageList-class
class:ImagingExperiment	ImagingExperiment-class
class:ImagingResult	ImagingResult-class
class:iSet	legacy
class:MassDataFrame	MassDataFrame-class
class:MeansTest	meansTest-methods
class:MIAPE-Imaging	legacy
class:MSContinuousImagingExperiment	MSContinuousImagingExperiment-class
class:MSContinuousImagingSpectraList	ImageList-class
class:MSImageData	legacy
class:MSImageProcess	legacy
class:MSImageSet	legacy
class:MSImagingExperiment	MSImagingExperiment-class
class:MSImagingInfo	MSImagingInfo-class
class:MSProcessedImagingExperiment	MSProcessedImagingExperiment-class
class:MSProcessedImagingSpectraList	ImageList-class
class:OPLS	PLS-methods
class:PCA	PCA-methods
class:PLS	PLS-methods
class:PositionDataFrame	PositionDataFrame-class
class:ResultSet	legacy
class:SegmentationTest	meansTest-methods
class:SImageData	legacy
class:SImageSet	legacy
class:SimpleImageArrayList	ImageList-class
class:SimpleImageList	ImageList-class
class:SparseImagingExperiment	SparseImagingExperiment-class
class:SparseImagingResult	ImagingResult-class
class:SpatialDGMM	spatialDGMM-methods
class:spatialFastmap	spatialFastmap-methods
class:SpatialKMeans	spatialKMeans-methods
class:SpatialShrunkenCentroids	spatialShrunkenCentroids-methods
class:SummaryDataFrame	internal
class:XDataFrame	XDataFrame-class
col.map	colors-functions
colocalized	colocalized-methods
colocalized,MSImagingExperiment,missing-method	colocalized-methods
colocalized,SparseImagingExperiment,ANY-method	colocalized-methods
colocalized,SpatialDGMM,ANY-method	colocalized-methods
color.map	colors-functions
combine,AnnotatedImageList,ANY-method	deprecated
combine,ImagingExperiment,ANY-method	ImagingExperiment-class
combine,SparseImagingExperiment,ANY-method	SparseImagingExperiment-class
combine,SparseImagingResult,ANY-method	ImagingResult-class
coord	PositionDataFrame-class
coord,AnnotatedImage-method	deprecated
coord,AnnotatedImagingExperiment-method	deprecated
coord,PositionDataFrame-method	PositionDataFrame-class
coord,SparseImagingExperiment-method	SparseImagingExperiment-class
coord-methods	PositionDataFrame-class
coord<-	PositionDataFrame-class
coord<-,AnnotatedImage-method	deprecated
coord<-,PositionDataFrame-method	PositionDataFrame-class
coord<-,SparseImagingExperiment-method	SparseImagingExperiment-class
coordinates	PositionDataFrame-class
coordinates,AnnotatedImage-method	deprecated
coordinates,AnnotatedImagingExperiment-method	deprecated
coordinates,PositionDataFrame-method	PositionDataFrame-class
coordinates,SparseImagingExperiment-method	SparseImagingExperiment-class
coordinates-methods	PositionDataFrame-class
coordinates<-	PositionDataFrame-class
coordinates<-,AnnotatedImage-method	deprecated
coordinates<-,PositionDataFrame-method	PositionDataFrame-class
coordinates<-,SparseImagingExperiment-method	SparseImagingExperiment-class
coordLabels	PositionDataFrame-class
coordLabels,PositionDataFrame-method	PositionDataFrame-class
coordLabels,SparseImagingExperiment-method	SparseImagingExperiment-class
coordLabels-methods	PositionDataFrame-class
coordLabels<-	PositionDataFrame-class
coordLabels<-,PositionDataFrame-method	PositionDataFrame-class
coordLabels<-,SparseImagingExperiment-method	SparseImagingExperiment-class
coordnames	PositionDataFrame-class
coordnames,PositionDataFrame-method	PositionDataFrame-class
coordnames,SparseImagingExperiment-method	SparseImagingExperiment-class
coordnames-methods	PositionDataFrame-class
coordnames<-	PositionDataFrame-class
coordnames<-,PositionDataFrame-method	PositionDataFrame-class
coordnames<-,SparseImagingExperiment-method	SparseImagingExperiment-class
coregister	internal
coregister,SpatialKMeans,missing-method	internal
coregister,SpatialShrunkenCentroids,missing-method	internal
coregister-methods	internal
crossValidate	crossValidate-methods
crossValidate,MSImagingExperiment-method	crossValidate-methods
crossValidate,SparseImagingExperiment-method	crossValidate-methods
crossValidate-methods	crossValidate-methods
cvApply	crossValidate-methods
cvApply,SparseImagingExperiment-method	crossValidate-methods
cvApply-methods	crossValidate-methods
darkmode	colors-functions
Defunct	defunct
Deprecated	deprecated
dim,AnnotatedImageList-method	deprecated
dim,ImageList-method	ImageList-class
dim,ImagingExperiment-method	ImagingExperiment-class
dim,SparseImagingExperiment-method	SparseImagingExperiment-class
dimnames,ImagingExperiment-method	ImagingExperiment-class
dims,AnnotatedImageList-method	deprecated
dims,AnnotatedImagingExperiment-method	deprecated
dims,ImageList-method	ImageList-class
dims,PositionDataFrame-method	PositionDataFrame-class
dims,SparseImagingExperiment-method	SparseImagingExperiment-class
discrete.colors	colors-functions
divergent.colors	colors-functions
domain,MSProcessedImagingSpectraList-method	MSProcessedImagingExperiment-class
domain<-,MSProcessedImagingSpectraList,ANY-method	MSProcessedImagingExperiment-class
domain<-,MSProcessedImagingSpectraList-method	MSProcessedImagingExperiment-class
fData	ImagingExperiment-class
fData,ImagingExperiment-method	ImagingExperiment-class
fData-methods	ImagingExperiment-class
fData<-	ImagingExperiment-class
fData<-,ImagingExperiment,ANY-method	ImagingExperiment-class
featureApply	pixelApply-methods
featureApply,SparseImagingExperiment-method	pixelApply-methods
featureApply-methods	pixelApply-methods
featureData	ImagingExperiment-class
featureData,ImagingExperiment-method	ImagingExperiment-class
featureData-methods	ImagingExperiment-class
featureData<-	ImagingExperiment-class
featureData<-,ImagingExperiment,ANY-method	ImagingExperiment-class
featureData<-,ImagingExperiment-method	ImagingExperiment-class
featureNames	ImagingExperiment-class
featureNames,ImagingExperiment-method	ImagingExperiment-class
featureNames-methods	ImagingExperiment-class
featureNames<-	ImagingExperiment-class
featureNames<-,ImagingExperiment-method	ImagingExperiment-class
features	SparseImagingExperiment-class
features,MSImagingExperiment-method	MSImagingExperiment-class
features,SparseImagingExperiment-method	SparseImagingExperiment-class
features-methods	SparseImagingExperiment-class
findNeighbors	findNeighbors-methods
findNeighbors,IAnnotatedDataFrame-method	findNeighbors-methods
findNeighbors,ImagingExperiment-method	findNeighbors-methods
findNeighbors,iSet-method	findNeighbors-methods
findNeighbors,PositionDataFrame-method	findNeighbors-methods
findNeighbors-methods	findNeighbors-methods
fitted,PLS2-method	PLS-methods
fitted,SpatialShrunkenCentroids2-method	spatialShrunkenCentroids-methods
getCardinalBPPARAM	Cardinal-package
getCardinalDelayProc	Cardinal-package
getCardinalNumBlocks	Cardinal-package
getCardinalVerbose	Cardinal-package
gradient.colors	colors-functions
gridded	PositionDataFrame-class
gridded,PositionDataFrame-method	PositionDataFrame-class
gridded,SparseImagingExperiment-method	SparseImagingExperiment-class
gridded<-	PositionDataFrame-class
gridded<-,PositionDataFrame-method	PositionDataFrame-class
gridded<-,SparseImagingExperiment-method	SparseImagingExperiment-class
Hashmat	legacy
Hashmat-class	legacy
height	deprecated
height,AnnotatedImage-method	deprecated
height,AnnotatedImagingExperiment-method	deprecated
height<-	deprecated
height<-,AnnotatedImage-method	deprecated
IAnnotatedDataFrame	legacy
IAnnotatedDataFrame-class	legacy
iData	ImagingExperiment-class
iData,ImagingExperiment,ANY-method	ImagingExperiment-class
iData,ImagingExperiment,missing-method	ImagingExperiment-class
iData-methods	ImagingExperiment-class
iData<-	ImagingExperiment-class
iData<-,ImagingExperiment,ANY-method	ImagingExperiment-class
iData<-,ImagingExperiment,missing-method	ImagingExperiment-class
iData<-,MSContinuousImagingExperiment,ANY-method	MSContinuousImagingExperiment-class
iData<-,MSContinuousImagingExperiment,missing-method	MSContinuousImagingExperiment-class
iData<-,MSProcessedImagingExperiment,ANY-method	MSProcessedImagingExperiment-class
iData<-,MSProcessedImagingExperiment,missing-method	MSProcessedImagingExperiment-class
image	image-methods
image,AnnotatedImage-method	image-methods
image,AnnotatedImageList-method	image-methods
image,AnnotatedImagingExperiment-method	image-methods
image,formula-method	image-methods
image,MeansTest-method	image-methods
image,MSImagingExperiment-method	image-methods
image,MSImagingSummary-method	image-methods
image,PCA2-method	image-methods
image,PLS2-method	image-methods
image,PositionDataFrame-method	image-methods
image,SegmentationTest-method	image-methods
image,SparseImagingExperiment-method	image-methods
image,SparseImagingResult-method	image-methods
image,SparseImagingSummary-method	image-methods
image,SpatialDGMM-method	image-methods
image,SpatialFastmap2-method	image-methods
image,SpatialKMeans2-method	image-methods
image,SpatialShrunkenCentroids2-method	image-methods
image-methods	image-methods
image3D	image-methods
image3D,MeansTest-method	image-methods
image3D,PCA2-method	image-methods
image3D,PLS2-method	image-methods
image3D,SegmentationTest-method	image-methods
image3D,SparseImagingExperiment-method	image-methods
image3D,SpatialDGMM-method	image-methods
image3D,SpatialFastmap2-method	image-methods
image3D,SpatialKMeans2-method	image-methods
image3D,SpatialShrunkenCentroids2-method	image-methods
ImageArrayList	ImageList-class
ImageArrayList-class	ImageList-class
ImageData	legacy
imageData	ImagingExperiment-class
imageData,ImagingExperiment-method	ImagingExperiment-class
ImageData-class	legacy
imageData-methods	ImagingExperiment-class
imageData<-	ImagingExperiment-class
imageData<-,ImagingExperiment-method	ImagingExperiment-class
imageData<-,MSContinuousImagingExperiment-method	MSContinuousImagingExperiment-class
imageData<-,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
ImageList	ImageList-class
ImageList-class	ImageList-class
ImagingExperiment	ImagingExperiment-class
ImagingExperiment-class	ImagingExperiment-class
ImagingResult	ImagingResult-class
ImagingResult-class	ImagingResult-class
inferno	reexports
initialize,MassDataFrame-method	MassDataFrame-class
initialize,PositionDataFrame-method	PositionDataFrame-class
instrumentModel	MSImagingInfo-class
instrumentModel,Vector-method	MSImagingInfo-class
instrumentVendor	MSImagingInfo-class
instrumentVendor,Vector-method	MSImagingInfo-class
intensity.colors	colors-functions
intensityData	MSProcessedImagingExperiment-class
intensityData,MSImagingInfo-method	MSImagingInfo-class
intensityData,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
intensityData-methods	MSProcessedImagingExperiment-class
intensityData<-	MSProcessedImagingExperiment-class
intensityData<-,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
ionizationType	MSImagingInfo-class
ionizationType,Vector-method	MSImagingInfo-class
is3D	SparseImagingExperiment-class
is3D,PositionDataFrame-method	PositionDataFrame-class
is3D,SparseImagingExperiment-method	SparseImagingExperiment-class
isCentroided	MSImagingExperiment-class
isCentroided,MassDataFrame-method	MassDataFrame-class
isCentroided,MSImagingExperiment-method	MSImagingExperiment-class
isCentroided,MSImagingInfo-method	MSImagingInfo-class
iSet	legacy
iSet-class	legacy
jet.colors	colors-functions
lapply,XDataFrame-method	XDataFrame-class
length,AnnotatedImage-method	deprecated
length,ImageList-method	ImageList-class
length,ImagingExperiment-method	ImagingExperiment-class
length,MSImagingInfo-method	MSImagingInfo-class
length,XDataFrame-method	XDataFrame-class
lightmode	colors-functions
lineScanDirection	MSImagingInfo-class
lineScanDirection,Vector-method	MSImagingInfo-class
logLik,SpatialShrunkenCentroids2-method	spatialShrunkenCentroids-methods
magma	reexports
makeFactor	selectROI-methods
massAnalyzerType	MSImagingInfo-class
massAnalyzerType,Vector-method	MSImagingInfo-class
MassDataFrame	MassDataFrame-class
MassDataFrame-class	MassDataFrame-class
matrixApplication	MSImagingInfo-class
matrixApplication,Vector-method	MSImagingInfo-class
meansTest	meansTest-methods
meansTest,SparseImagingExperiment-method	meansTest-methods
MeansTest-class	meansTest-methods
meansTest-methods	meansTest-methods
MIAPE-Imaging	legacy
MIAPE-Imaging-class	legacy
modelData	ImagingResult-class
modelData,ImagingResult-method	ImagingResult-class
modelData<-	ImagingResult-class
modelData<-,ImagingResult-method	ImagingResult-class
MSContinuousImagingExperiment	MSContinuousImagingExperiment-class
MSContinuousImagingExperiment-class	MSContinuousImagingExperiment-class
MSContinuousImagingSpectraList	ImageList-class
MSContinuousImagingSpectraList-class	ImageList-class
msiInfo	MSImagingInfo-class
msiInfo,MSContinuousImagingExperiment-method	MSImagingInfo-class
msiInfo,MSImagingExperiment-method	MSImagingInfo-class
msiInfo,MSProcessedImagingExperiment-method	MSImagingInfo-class
MSImageData	legacy
MSImageData-class	legacy
MSImageProcess	legacy
MSImageProcess-class	legacy
MSImageSet	legacy
MSImageSet-class	legacy
MSImagingExperiment	MSImagingExperiment-class
MSImagingExperiment-class	MSImagingExperiment-class
MSImagingInfo	MSImagingInfo-class
MSImagingInfo-class	MSImagingInfo-class
MSProcessedImagingExperiment	MSProcessedImagingExperiment-class
MSProcessedImagingExperiment-class	MSProcessedImagingExperiment-class
MSProcessedImagingSpectraList	ImageList-class
MSProcessedImagingSpectraList-class	ImageList-class
mz	mz-methods
mz,MassDataFrame-method	MassDataFrame-class
mz,missing-method	mz-methods
mz,MSImagingExperiment-method	MSImagingExperiment-class
mz-methods	mz-methods
mz<-	mz-methods
mz<-,MassDataFrame-method	MassDataFrame-class
mz<-,MSImagingExperiment-method	MSImagingExperiment-class
mz<-,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
mzAlign	mzAlign-methods
mzAlign,MSImagingExperiment,missing-method	mzAlign-methods
mzAlign,MSImagingExperiment,numeric-method	mzAlign-methods
mzAlign-methods	mzAlign-methods
mzBin	mzBin-methods
mzBin,MSImagingExperiment,missing-method	mzBin-methods
mzBin,MSImagingExperiment,numeric-method	mzBin-methods
mzBin-methods	mzBin-methods
mzData	MSProcessedImagingExperiment-class
mzData,MSImagingInfo-method	MSImagingInfo-class
mzData,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
mzData-methods	MSProcessedImagingExperiment-class
mzData<-	MSProcessedImagingExperiment-class
mzData<-,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
mzFilter	mzFilter-methods
mzFilter,MSImagingExperiment-method	mzFilter-methods
mzFilter-methods	mzFilter-methods
names,ImageList-method	ImageList-class
names,ImagingExperiment-method	ImagingExperiment-class
names,XDataFrame-method	XDataFrame-class
names<-,ImageList-method	ImageList-class
names<-,ImagingExperiment-method	ImagingExperiment-class
normalization	MSImagingInfo-class
normalization,Vector-method	MSImagingInfo-class
normalization<-	MSImagingInfo-class
normalization<-,Vector-method	MSImagingInfo-class
normalize	normalize-methods
normalize,SparseImagingExperiment-method	normalize-methods
normalize-methods	normalize-methods
normalize.reference	normalize-methods
normalize.rms	normalize-methods
normalize.tic	normalize-methods
OPLS	PLS-methods
OPLS,SparseImagingExperiment,ANY-method	PLS-methods
OPLS,SparseImagingExperiment-method	PLS-methods
OPLS-class	PLS-methods
OPLS-methods	PLS-methods
PCA	PCA-methods
PCA,SparseImagingExperiment-method	PCA-methods
PCA-class	PCA-methods
PCA-methods	PCA-methods
pData	ImagingExperiment-class
pData,ImagingExperiment-method	ImagingExperiment-class
pData-methods	ImagingExperiment-class
pData<-	ImagingExperiment-class
pData<-,ImagingExperiment,ANY-method	ImagingExperiment-class
peakAlign	peakAlign-methods
peakAlign,MSImagingExperiment,character-method	peakAlign-methods
peakAlign,MSImagingExperiment,missing-method	peakAlign-methods
peakAlign,MSImagingExperiment,numeric-method	peakAlign-methods
peakAlign-methods	peakAlign-methods
peakAlign.diff	peakAlign-methods
peakAlign.DP	peakAlign-methods
peakBin	peakBin-methods
peakBin,MSImagingExperiment,missing-method	peakBin-methods
peakBin,MSImagingExperiment,numeric-method	peakBin-methods
peakBin-methods	peakBin-methods
peakData	MSImagingExperiment-class
peakData,MSImagingExperiment-method	MSImagingExperiment-class
peakData-methods	MSImagingExperiment-class
peakData<-	MSImagingExperiment-class
peakData<-,MSImagingExperiment-method	MSImagingExperiment-class
peakFilter	mzFilter-methods
peakFilter,MSImagingExperiment-method	mzFilter-methods
peakFilter-methods	mzFilter-methods
peakFilter.freq	mzFilter-methods
peakPick	peakPick-methods
peakPick,MSImagingExperiment-method	peakPick-methods
peakPick-methods	peakPick-methods
peakPick.adaptive	peakPick-methods
peakPick.limpic	peakPick-methods
peakPick.mad	peakPick-methods
peakPick.simple	peakPick-methods
peakPicking	MSImagingInfo-class
peakPicking,Vector-method	MSImagingInfo-class
peakPicking<-	MSImagingInfo-class
peakPicking<-,Vector-method	MSImagingInfo-class
peaks	MSImagingExperiment-class
peaks,MSImagingExperiment-method	MSImagingExperiment-class
peaks-methods	MSImagingExperiment-class
peaks<-	MSImagingExperiment-class
peaks<-,MSImagingExperiment-method	MSImagingExperiment-class
phenoData	ImagingExperiment-class
phenoData,ImagingExperiment-method	ImagingExperiment-class
phenoData-methods	ImagingExperiment-class
phenoData<-	ImagingExperiment-class
phenoData<-,ImagingExperiment,ANY-method	ImagingExperiment-class
pixelApply	pixelApply-methods
pixelApply,SparseImagingExperiment-method	pixelApply-methods
pixelApply-methods	pixelApply-methods
pixelData	ImagingExperiment-class
pixelData,ImagingExperiment-method	ImagingExperiment-class
pixelData,SparseImagingExperiment-method	SparseImagingExperiment-class
pixelData-methods	ImagingExperiment-class
pixelData<-	ImagingExperiment-class
pixelData<-,ImagingExperiment-method	ImagingExperiment-class
pixelData<-,SparseImagingExperiment-method	SparseImagingExperiment-class
pixelNames	ImagingExperiment-class
pixelNames,ImagingExperiment-method	ImagingExperiment-class
pixelNames,SparseImagingExperiment-method	SparseImagingExperiment-class
pixelNames-methods	ImagingExperiment-class
pixelNames<-	ImagingExperiment-class
pixelNames<-,ImagingExperiment-method	ImagingExperiment-class
pixelNames<-,SparseImagingExperiment-method	SparseImagingExperiment-class
pixels	SparseImagingExperiment-class
pixels,MSImagingExperiment-method	MSImagingExperiment-class
pixels,SparseImagingExperiment-method	SparseImagingExperiment-class
pixels-methods	SparseImagingExperiment-class
pixelSize	MSImagingInfo-class
pixelSize,Vector-method	MSImagingInfo-class
plasma	reexports
plot	plot-methods
plot,AnnotatedImage,ANY-method	plot-methods
plot,AnnotatedImageList,ANY-method	plot-methods
plot,AnnotatedImagingExperiment,ANY-method	plot-methods
plot,DataFrame,ANY-method	plot-methods
plot,MassDataFrame,formula-method	plot-methods
plot,MassDataFrame,missing-method	plot-methods
plot,MeansTest,missing-method	plot-methods
plot,MSImagingExperiment,formula-method	plot-methods
plot,MSImagingExperiment,missing-method	plot-methods
plot,MSImagingSummary,missing-method	plot-methods
plot,PCA2,missing-method	plot-methods
plot,PLS2,missing-method	plot-methods
plot,SegmentationTest,missing-method	plot-methods
plot,SparseImagingExperiment,formula-method	plot-methods
plot,SparseImagingExperiment,missing-method	plot-methods
plot,SparseImagingResult,formula-method	plot-methods
plot,SparseImagingResult,missing-method	plot-methods
plot,SparseImagingSummary,formula-method	plot-methods
plot,SparseImagingSummary,missing-method	plot-methods
plot,SpatialDGMM,missing-method	plot-methods
plot,SpatialFastmap2,missing-method	plot-methods
plot,SpatialKMeans2,missing-method	plot-methods
plot,SpatialShrunkenCentroids2,missing-method	plot-methods
plot,XDataFrame,formula-method	plot-methods
plot,XDataFrame,missing-method	plot-methods
plot-methods	plot-methods
PLS	PLS-methods
PLS,SparseImagingExperiment,ANY-method	PLS-methods
PLS,SparseImagingExperiment-method	PLS-methods
PLS-class	PLS-methods
PLS-methods	PLS-methods
PositionDataFrame	PositionDataFrame-class
PositionDataFrame-class	PositionDataFrame-class
predict,PCA2-method	PCA-methods
predict,PLS2-method	PLS-methods
predict,SpatialShrunkenCentroids2-method	spatialShrunkenCentroids-methods
preproc,SparseImagingExperiment-method	SparseImagingExperiment-class
presetImageDef	simulateSpectrum
process	process-methods
process,MSImagingExperiment-method	process-methods
process,SparseImagingExperiment-method	process-methods
process-methods	process-methods
processingData,SparseImagingExperiment-method	SparseImagingExperiment-class
processingData<-,SparseImagingExperiment-method	SparseImagingExperiment-class
pull,MSImagingExperiment-method	MSImagingExperiment-class
pull,SparseImagingExperiment-method	SparseImagingExperiment-class
range,AnnotatedImage-method	deprecated
rbind,AnnotatedImageList-method	deprecated
rbind,ImageArrayList-method	ImageList-class
rbind,ImagingExperiment-method	ImagingExperiment-class
rbind,MassDataFrame-method	MassDataFrame-class
rbind,MSImagingExperiment-method	MSImagingExperiment-class
rbind,PositionDataFrame-method	PositionDataFrame-class
rbind,SparseImagingExperiment-method	SparseImagingExperiment-class
rbind,SparseImagingResult-method	ImagingResult-class
rbind,XDataFrame-method	XDataFrame-class
readAnalyze	readMSIData
readImzML	readMSIData
readMSIData	readMSIData
reduceBaseline	reduceBaseline-methods
reduceBaseline,SparseImagingExperiment-method	reduceBaseline-methods
reduceBaseline-methods	reduceBaseline-methods
reduceBaseline.locmin	reduceBaseline-methods
reduceBaseline.median	reduceBaseline-methods
resolution	PositionDataFrame-class
resolution,AnnotatedImage-method	deprecated
resolution,AnnotatedImagingExperiment-method	deprecated
resolution,MassDataFrame-method	MassDataFrame-class
resolution,MSImagingExperiment-method	MSImagingExperiment-class
resolution,PositionDataFrame-method	PositionDataFrame-class
resolution,SparseImagingExperiment-method	SparseImagingExperiment-class
resolution<-	PositionDataFrame-class
resolution<-,AnnotatedImage-method	deprecated
resolution<-,MassDataFrame-method	MassDataFrame-class
resolution<-,MSImagingExperiment-method	MSImagingExperiment-class
resolution<-,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
resolution<-,PositionDataFrame-method	PositionDataFrame-class
resolution<-,SparseImagingExperiment-method	SparseImagingExperiment-class
resultData	ImagingResult-class
resultData,ImagingResult,ANY-method	ImagingResult-class
resultData,ImagingResult,missing-method	ImagingResult-class
resultData<-	ImagingResult-class
resultData<-,ImagingResult,ANY-method	ImagingResult-class
resultData<-,ImagingResult,missing-method	ImagingResult-class
resultNames	ImagingResult-class
resultNames,ImagingResult-method	ImagingResult-class
resultNames<-	ImagingResult-class
ResultSet	legacy
ResultSet-class	legacy
risk.colors	colors-functions
run	PositionDataFrame-class
run,PositionDataFrame-method	PositionDataFrame-class
run,SparseImagingExperiment-method	SparseImagingExperiment-class
run<-	PositionDataFrame-class
run<-,PositionDataFrame-method	PositionDataFrame-class
run<-,SparseImagingExperiment-method	SparseImagingExperiment-class
runNames	PositionDataFrame-class
runNames,PositionDataFrame-method	PositionDataFrame-class
runNames,SparseImagingExperiment-method	SparseImagingExperiment-class
runNames<-	PositionDataFrame-class
runNames<-,PositionDataFrame-method	PositionDataFrame-class
runNames<-,SparseImagingExperiment-method	SparseImagingExperiment-class
sampleNames	ImagingExperiment-class
sampleNames,ImagingExperiment-method	ImagingExperiment-class
sampleNames-methods	ImagingExperiment-class
sampleNames<-	ImagingExperiment-class
sampleNames<-,ImagingExperiment,ANY-method	ImagingExperiment-class
sampler,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
sampler,MSProcessedImagingSpectraList-method	MSProcessedImagingExperiment-class
sampler<-,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
sampler<-,MSProcessedImagingSpectraList-method	MSProcessedImagingExperiment-class
scanDirection	MSImagingInfo-class
scanDirection,Vector-method	MSImagingInfo-class
scanPattern	MSImagingInfo-class
scanPattern,Vector-method	MSImagingInfo-class
scanPolarity	MSImagingInfo-class
scanPolarity,Vector-method	MSImagingInfo-class
scans,MSImagingInfo-method	MSImagingInfo-class
scanType	MSImagingInfo-class
scanType,Vector-method	MSImagingInfo-class
segmentationTest	meansTest-methods
segmentationTest,SparseImagingExperiment-method	meansTest-methods
segmentationTest,SpatialDGMM-method	meansTest-methods
SegmentationTest-class	meansTest-methods
segmentationTest-methods	meansTest-methods
selectROI	selectROI-methods
selectROI,SparseImagingExperiment-method	selectROI-methods
selectROI-methods	selectROI-methods
setCardinalBPPARAM	Cardinal-package
setCardinalDelayProc	Cardinal-package
setCardinalNumBlocks	Cardinal-package
setCardinalVerbose	Cardinal-package
setup.layout	plot-methods
show,AnnotatedImageList-method	deprecated
show,AnnotatedImagingExperiment-method	deprecated
show,ImagingExperiment-method	ImagingExperiment-class
show,ImagingResult-method	ImagingResult-class
show,MSImagingExperiment-method	MSImagingExperiment-class
show,SimpleImageList-method	ImageList-class
show,SparseImagingExperiment-method	SparseImagingExperiment-class
show,SparseImagingResult-method	ImagingResult-class
show,SummaryDataFrame-method	internal
show,XDataFrame-method	XDataFrame-class
showNames	XDataFrame-class
showNames,MassDataFrame-method	MassDataFrame-class
showNames,PositionDataFrame-method	PositionDataFrame-class
showNames,XDataFrame-method	XDataFrame-class
SImageData	legacy
SImageData-class	legacy
SImageSet	legacy
SImageSet-class	legacy
SimpleImageArrayList-class	ImageList-class
SimpleImageList-class	ImageList-class
simulateImage	simulateSpectrum
simulateSpectrum	simulateSpectrum
slice	slice-methods
slice,SparseImagingExperiment-method	slice-methods
smooth	smoothSignal-methods
smooth,SparseImagingExperiment-method	smoothSignal-methods
smooth-methods	smoothSignal-methods
smoothing	MSImagingInfo-class
smoothing,Vector-method	MSImagingInfo-class
smoothing<-	MSImagingInfo-class
smoothing<-,Vector-method	MSImagingInfo-class
smoothSignal	smoothSignal-methods
smoothSignal,SparseImagingExperiment-method	smoothSignal-methods
smoothSignal-methods	smoothSignal-methods
smoothSignal.gaussian	smoothSignal-methods
smoothSignal.ma	smoothSignal-methods
smoothSignal.sgolay	smoothSignal-methods
sort,XDataFrame-method	XDataFrame-class
SparseImagingExperiment	SparseImagingExperiment-class
SparseImagingExperiment-class	SparseImagingExperiment-class
SparseImagingResult	ImagingResult-class
SparseImagingResult-class	ImagingResult-class
spatialApply	deprecated
spatialApply,SparseImagingExperiment-method	deprecated
spatialApply-methods	deprecated
spatialDGMM	spatialDGMM-methods
spatialDGMM,SparseImagingExperiment-method	spatialDGMM-methods
SpatialDGMM-class	spatialDGMM-methods
spatialDGMM-methods	spatialDGMM-methods
spatialFastmap	spatialFastmap-methods
spatialFastmap,SparseImagingExperiment-method	spatialFastmap-methods
spatialFastmap-class	spatialFastmap-methods
spatialFastmap-methods	spatialFastmap-methods
spatialKMeans	spatialKMeans-methods
spatialKMeans,SparseImagingExperiment-method	spatialKMeans-methods
SpatialKMeans-class	spatialKMeans-methods
spatialKMeans-methods	spatialKMeans-methods
spatialShrunkenCentroids	spatialShrunkenCentroids-methods
spatialShrunkenCentroids,SparseImagingExperiment,ANY-method	spatialShrunkenCentroids-methods
spatialShrunkenCentroids,SparseImagingExperiment,missing-method	spatialShrunkenCentroids-methods
SpatialShrunkenCentroids-class	spatialShrunkenCentroids-methods
spatialShrunkenCentroids-methods	spatialShrunkenCentroids-methods
spatialWeights	findNeighbors-methods
spatialWeights,IAnnotatedDataFrame-method	findNeighbors-methods
spatialWeights,ImagingExperiment-method	findNeighbors-methods
spatialWeights,iSet-method	findNeighbors-methods
spatialWeights,PositionDataFrame-method	findNeighbors-methods
spatialWeights-methods	findNeighbors-methods
spectra	MSImagingExperiment-class
spectra,MSImagingExperiment-method	MSImagingExperiment-class
spectra-methods	MSImagingExperiment-class
spectra<-	MSImagingExperiment-class
spectra<-,MSImagingExperiment-method	MSImagingExperiment-class
spectraData	MSImagingExperiment-class
spectraData,MSImagingExperiment-method	MSImagingExperiment-class
spectraData-methods	MSImagingExperiment-class
spectraData<-	MSImagingExperiment-class
spectraData<-,MSImagingExperiment-method	MSImagingExperiment-class
spectrumRepresentation	MSImagingInfo-class
spectrumRepresentation,Vector-method	MSImagingInfo-class
spectrumRepresentation<-	MSImagingInfo-class
spectrumRepresentation<-,Vector-method	MSImagingInfo-class
subset,SparseImagingExperiment-method	subset-methods
subsetFeatures	subset-methods
subsetPixels	subset-methods
summarizeFeatures	aggregate-methods
summarizePixels	aggregate-methods
summary,CrossValidated2-method	crossValidate-methods
summary,MeansTest-method	meansTest-methods
summary,PCA2-method	PCA-methods
summary,PLS2-method	PLS-methods
summary,SegmentationTest-method	meansTest-methods
summary,SpatialDGMM-method	spatialDGMM-methods
summary,SpatialFastmap2-method	spatialFastmap-methods
summary,SpatialKMeans2-method	spatialKMeans-methods
summary,SpatialShrunkenCentroids2-method	spatialShrunkenCentroids-methods
summary,SummaryDataFrame-method	internal
SummaryDataFrame	internal
SummaryDataFrame-class	internal
tolerance,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
tolerance,MSProcessedImagingSpectraList-method	MSProcessedImagingExperiment-class
tolerance<-,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
tolerance<-,MSProcessedImagingSpectraList-method	MSProcessedImagingExperiment-class
topFeatures	topFeatures-methods
topFeatures,CrossValidated-method	topFeatures-methods
topFeatures,MeansTest-method	topFeatures-methods
topFeatures,OPLS-method	topFeatures-methods
topFeatures,PCA-method	topFeatures-methods
topFeatures,PLS-method	topFeatures-methods
topFeatures,ResultSet-method	topFeatures-methods
topFeatures,SegmentationTest-method	topFeatures-methods
topFeatures,SpatialKMeans-method	topFeatures-methods
topFeatures,SpatialKMeans2-method	topFeatures-methods
topFeatures,SpatialShrunkenCentroids-method	topFeatures-methods
topFeatures,SpatialShrunkenCentroids2-method	topFeatures-methods
topFeatures-methods	topFeatures-methods
viridis	reexports
width,AnnotatedImage-method	deprecated
width,AnnotatedImagingExperiment-method	deprecated
width<-,AnnotatedImage-method	deprecated
writeAnalyze	writeMSIData
writeAnalyze,MSImageSet-method	writeMSIData
writeImzML	writeMSIData
writeImzML,MSImageSet-method	writeMSIData
writeMSIData	writeMSIData
writeMSIData,MSImageSet,character-method	writeMSIData
XDataFrame	XDataFrame-class
XDataFrame-class	XDataFrame-class
[,AnnotatedImageList,ANY,ANY,ANY-method	deprecated
[,ImageArrayList,ANY,ANY,ANY-method	ImageList-class
[,ImageArrayList-method	ImageList-class
[,ImagingExperiment,ANY,ANY,ANY-method	ImagingExperiment-class
[,MassDataFrame,ANY,ANY,ANY-method	MassDataFrame-class
[,MSContinuousImagingSpectraList,ANY,ANY,ANY-method	MSContinuousImagingExperiment-class
[,MSProcessedImagingSpectraList,ANY,ANY,ANY-method	MSProcessedImagingExperiment-class
[,PositionDataFrame,ANY,ANY,ANY-method	PositionDataFrame-class
[,SparseImagingExperiment,ANY,ANY,ANY-method	SparseImagingExperiment-class
[,SparseImagingResult,ANY,ANY,ANY-method	ImagingResult-class
[,XDataFrame,ANY,ANY,ANY-method	XDataFrame-class
[<-,ImageArrayList,ANY,ANY,ANY-method	ImageList-class
[<-,ImagingExperiment,ANY,ANY,ANY-method	ImagingExperiment-class
[<-,SparseImagingExperiment,ANY,ANY,ANY-method	SparseImagingExperiment-class
[[,ImageList,ANY,ANY-method	ImageList-class
[[,ImageList-method	ImageList-class
[[,ImagingExperiment,ANY,ANY-method	ImagingExperiment-class
[[,ImagingExperiment-method	ImagingExperiment-class
[[,ImagingResult,ANY,ANY-method	ImagingResult-class
[[,ImagingResult-method	ImagingResult-class
[[,SparseImagingResult,ANY,ANY-method	ImagingResult-class
[[,SparseImagingResult-method	ImagingResult-class
[[<-,ImageList,ANY,ANY-method	ImageList-class
[[<-,ImageList-method	ImageList-class
[[<-,ImagingExperiment,ANY,ANY-method	ImagingExperiment-class
[[<-,ImagingExperiment-method	ImagingExperiment-class
[[<-,ImagingResult,ANY,ANY-method	ImagingResult-class
[[<-,ImagingResult-method	ImagingResult-class
[[<-,MSContinuousImagingSpectraList,ANY,ANY-method	MSContinuousImagingExperiment-class
[[<-,MSContinuousImagingSpectraList-method	ImageList-class
[[<-,MSProcessedImagingSpectraList,ANY,ANY-method	MSProcessedImagingExperiment-class
[[<-,MSProcessedImagingSpectraList-method	ImageList-class
[[<-,SparseImagingResult,ANY,ANY-method	ImagingResult-class
[[<-,SparseImagingResult-method	ImagingResult-class
[[<-,XDataFrame,ANY,ANY-method	XDataFrame-class
[[<-,XDataFrame-method	XDataFrame-class
