Cardinal-package	Cardinal-package
$,ImagingExperiment-method	ImagingExperiment-class
$,ImagingResult-method	ImagingResult-class
$,iSet-method	legacy
$,ResultSet-method	legacy
$<-,ImagingExperiment-method	ImagingExperiment-class
$<-,iSet-method	legacy
$<-,XDataFrame-method	XDataFrame-class
%>%	reexports
abstract,MIAPE-Imaging-method	legacy
addShape	simulateSpectrum
aggregate,MSImagingExperiment-method	aggregate-methods
aggregate,SparseImagingExperiment-method	aggregate-methods
alpha.colors	colors-functions
annotatedDataFrameFrom,ImageData-method	legacy
AnnotatedImage	AnnotatedImage-class
AnnotatedImage-class	AnnotatedImage-class
AnnotatedImageList	AnnotatedImagingExperiment-class
AnnotatedImageList-class	AnnotatedImagingExperiment-class
AnnotatedImagingExperiment	AnnotatedImagingExperiment-class
AnnotatedImagingExperiment-class	AnnotatedImagingExperiment-class
arrange	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,MSImageProcess-method	legacy
baselineReduction,Vector-method	MSImagingInfo-class
baselineReduction<-	MSImagingInfo-class
baselineReduction<-,MSImageProcess-method	legacy
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	AnnotatedImagingExperiment-class
cbind,Hashmat-method	legacy
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,MSImageProcess-method	legacy
centroided,MSImageSet-method	legacy
centroided,MSImagingExperiment-method	MSImagingExperiment-class
centroided<-	MSImagingExperiment-class
centroided<-,MSImageProcess-method	legacy
centroided<-,MSImageSet-method	legacy
centroided<-,MSImagingExperiment-method	MSImagingExperiment-class
cividis	reexports
class:AnnotatedImage	AnnotatedImage-class
class:AnnotatedImageList	AnnotatedImagingExperiment-class
class:AnnotatedImagingExperiment	AnnotatedImagingExperiment-class
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
collect	deprecated
collect.MSImagingExperiment	deprecated
collect.MSProcessedImagingExperiment	deprecated
collect.SparseImagingExperiment	deprecated
colnames,Hashmat-method	legacy
colnames<-,Hashmat-method	legacy
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	AnnotatedImagingExperiment-class
combine,array,array-method	legacy
combine,Hashmat,Hashmat-method	legacy
combine,IAnnotatedDataFrame,IAnnotatedDataFrame-method	legacy
combine,ImageData,ImageData-method	legacy
combine,ImagingExperiment,ANY-method	ImagingExperiment-class
combine,iSet,iSet-method	legacy
combine,MIAPE-Imaging,MIAPE-Imaging-method	legacy
combine,MSImageProcess,MSImageProcess-method	legacy
combine,MSImageSet,MSImageSet-method	legacy
combine,SImageData,SImageData-method	legacy
combine,SImageSet,SImageSet-method	legacy
combine,SparseImagingExperiment,ANY-method	SparseImagingExperiment-class
combine,SparseImagingResult,ANY-method	ImagingResult-class
combine,vector,vector-method	legacy
combiner,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
combiner,MSProcessedImagingSpectraList-method	MSProcessedImagingExperiment-class
combiner<-,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
combiner<-,MSProcessedImagingSpectraList-method	MSProcessedImagingExperiment-class
coord	PositionDataFrame-class
coord,AnnotatedImage-method	AnnotatedImage-class
coord,AnnotatedImagingExperiment-method	AnnotatedImagingExperiment-class
coord,IAnnotatedDataFrame-method	legacy
coord,iSet-method	legacy
coord,PositionDataFrame-method	PositionDataFrame-class
coord,SImageData-method	legacy
coord,SparseImagingExperiment-method	SparseImagingExperiment-class
coord-methods	PositionDataFrame-class
coord<-	PositionDataFrame-class
coord<-,AnnotatedImage-method	AnnotatedImage-class
coord<-,IAnnotatedDataFrame-method	legacy
coord<-,iSet-method	legacy
coord<-,PositionDataFrame-method	PositionDataFrame-class
coord<-,SImageData-method	legacy
coord<-,SImageSet-method	legacy
coord<-,SparseImagingExperiment-method	SparseImagingExperiment-class
coordinates	PositionDataFrame-class
coordinates,AnnotatedImage-method	AnnotatedImage-class
coordinates,AnnotatedImagingExperiment-method	AnnotatedImagingExperiment-class
coordinates,PositionDataFrame-method	PositionDataFrame-class
coordinates,SparseImagingExperiment-method	SparseImagingExperiment-class
coordinates-methods	PositionDataFrame-class
coordinates<-	PositionDataFrame-class
coordinates<-,AnnotatedImage-method	AnnotatedImage-class
coordinates<-,PositionDataFrame-method	PositionDataFrame-class
coordinates<-,SparseImagingExperiment-method	SparseImagingExperiment-class
coordLabels	PositionDataFrame-class
coordLabels,IAnnotatedDataFrame-method	legacy
coordLabels,iSet-method	legacy
coordLabels,PositionDataFrame-method	PositionDataFrame-class
coordLabels,SparseImagingExperiment-method	SparseImagingExperiment-class
coordLabels-methods	PositionDataFrame-class
coordLabels<-	PositionDataFrame-class
coordLabels<-,IAnnotatedDataFrame-method	legacy
coordLabels<-,iSet-method	legacy
coordLabels<-,PositionDataFrame-method	PositionDataFrame-class
coordLabels<-,SImageSet-method	legacy
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,ANY-method	PositionDataFrame-class
coordnames<-,SparseImagingExperiment,ANY-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,SImageSet-method	crossValidate-methods
cvApply,SparseImagingExperiment-method	crossValidate-methods
cvApply-methods	crossValidate-methods
darkmode	colors-functions
Defunct	defunct
Deprecated	deprecated
dim,AnnotatedImageList-method	AnnotatedImagingExperiment-class
dim,Hashmat-method	legacy
dim,ImageData-method	legacy
dim,ImageList-method	ImageList-class
dim,ImagingExperiment-method	ImagingExperiment-class
dim,iSet-method	legacy
dim,SImageData-method	legacy
dim,SparseImagingExperiment-method	SparseImagingExperiment-class
dim<-,Hashmat-method	legacy
dimnames,Hashmat-method	legacy
dimnames,ImagingExperiment-method	ImagingExperiment-class
dimnames<-,Hashmat,ANY-method	legacy
dimnames<-,Hashmat-method	legacy
dims,AnnotatedImageList-method	AnnotatedImagingExperiment-class
dims,AnnotatedImagingExperiment-method	AnnotatedImagingExperiment-class
dims,ImageData-method	legacy
dims,ImageList-method	ImageList-class
dims,iSet-method	legacy
dims,PositionDataFrame-method	PositionDataFrame-class
dims,SImageData-method	legacy
dims,SparseImagingExperiment-method	SparseImagingExperiment-class
discrete.colors	colors-functions
divergent.colors	colors-functions
embeddingMethod	legacy
embeddingMethod,MIAPE-Imaging-method	legacy
experimentData,iSet-method	legacy
experimentData<-,iSet,ANY-method	legacy
expinfo,MIAPE-Imaging-method	legacy
fData	ImagingExperiment-class
fData,ImagingExperiment-method	ImagingExperiment-class
fData,iSet-method	legacy
fData-methods	ImagingExperiment-class
fData<-	ImagingExperiment-class
fData<-,ImagingExperiment,ANY-method	ImagingExperiment-class
fData<-,iSet,ANY-method	legacy
fData<-,iSet-method	legacy
featureApply	pixelApply-methods
featureApply,SImageSet-method	pixelApply-methods
featureApply,SparseImagingExperiment-method	pixelApply-methods
featureApply-methods	pixelApply-methods
featureData	ImagingExperiment-class
featureData,ImagingExperiment-method	ImagingExperiment-class
featureData,iSet-method	legacy
featureData-methods	ImagingExperiment-class
featureData<-	ImagingExperiment-class
featureData<-,ImagingExperiment,ANY-method	ImagingExperiment-class
featureData<-,ImagingExperiment-method	ImagingExperiment-class
featureData<-,iSet,ANY-method	legacy
featureData<-,iSet-method	legacy
featureNames	ImagingExperiment-class
featureNames,ImagingExperiment-method	ImagingExperiment-class
featureNames,iSet-method	legacy
featureNames,SImageData-method	legacy
featureNames-methods	ImagingExperiment-class
featureNames<-	ImagingExperiment-class
featureNames<-,ImagingExperiment-method	ImagingExperiment-class
featureNames<-,iSet-method	legacy
featureNames<-,SImageData-method	legacy
featureNames<-,SImageSet-method	legacy
features	SparseImagingExperiment-class
features,iSet-method	legacy
features,MSImageSet-method	legacy
features,MSImagingExperiment-method	MSImagingExperiment-class
features,SparseImagingExperiment-method	SparseImagingExperiment-class
features-methods	SparseImagingExperiment-class
filter	deprecated
filter.SparseImagingExperiment	deprecated
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
fvarLabels,iSet-method	legacy
fvarLabels<-,iSet-method	legacy
fvarMetadata,iSet-method	legacy
fvarMetadata<-,iSet,ANY-method	legacy
fvarMetadata<-,iSet-method	legacy
generateImage	defunct
generateSpectrum	defunct
getCardinalBPPARAM	Cardinal-package
getCardinalDelayProc	Cardinal-package
getCardinalNumBlocks	Cardinal-package
getCardinalVerbose	Cardinal-package
gradient.colors	colors-functions
gridded,PositionDataFrame-method	PositionDataFrame-class
gridded,SparseImagingExperiment-method	SparseImagingExperiment-class
gridded<-,PositionDataFrame,ANY-method	PositionDataFrame-class
gridded<-,SparseImagingExperiment,ANY-method	SparseImagingExperiment-class
groups	deprecated
group_by	deprecated
Hashmat	legacy
Hashmat-class	legacy
height	AnnotatedImage-class
height,AnnotatedImage-method	AnnotatedImage-class
height,AnnotatedImagingExperiment-method	AnnotatedImagingExperiment-class
height<-	AnnotatedImage-class
height<-,AnnotatedImage-method	AnnotatedImage-class
IAnnotatedDataFrame	legacy
IAnnotatedDataFrame-class	legacy
iData	ImagingExperiment-class
iData,ImagingExperiment,ANY-method	ImagingExperiment-class
iData,ImagingExperiment,missing-method	ImagingExperiment-class
iData,iSet-method	legacy
iData,SImageData,ANY-method	legacy
iData,SImageSet,ANY-method	legacy
iData-methods	ImagingExperiment-class
iData<-	ImagingExperiment-class
iData<-,ImagingExperiment,ANY-method	ImagingExperiment-class
iData<-,ImagingExperiment,missing-method	ImagingExperiment-class
iData<-,iSet-method	legacy
iData<-,MSContinuousImagingExperiment,ANY-method	MSContinuousImagingExperiment-class
iData<-,MSContinuousImagingExperiment,missing-method	MSContinuousImagingExperiment-class
iData<-,MSProcessedImagingExperiment,ANY-method	MSProcessedImagingExperiment-class
iData<-,MSProcessedImagingExperiment,missing-method	MSProcessedImagingExperiment-class
iData<-,SImageData,ANY-method	legacy
iData<-,SImageSet,ANY-method	legacy
image	image-methods
image,AnnotatedImage-method	image-methods
image,AnnotatedImageList-method	image-methods
image,AnnotatedImagingExperiment-method	image-methods
image,CrossValidated-method	image-methods
image,formula-method	image-methods
image,MeansTest-method	image-methods
image,MSImageSet-method	image-methods
image,MSImagingExperiment-method	image-methods
image,MSImagingSummary-method	image-methods
image,OPLS-method	image-methods
image,PCA-method	image-methods
image,PCA2-method	image-methods
image,PLS-method	image-methods
image,PLS2-method	image-methods
image,PositionDataFrame-method	image-methods
image,ResultSet-method	image-methods
image,SegmentationTest-method	image-methods
image,SImageSet-method	image-methods
image,SparseImagingExperiment-method	image-methods
image,SparseImagingResult-method	image-methods
image,SparseImagingSummary-method	image-methods
image,SpatialDGMM-method	image-methods
image,SpatialFastmap-method	image-methods
image,SpatialFastmap2-method	image-methods
image,SpatialKMeans-method	image-methods
image,SpatialKMeans2-method	image-methods
image,SpatialShrunkenCentroids-method	image-methods
image,SpatialShrunkenCentroids2-method	image-methods
image-methods	image-methods
image3D	image-methods
image3D,CrossValidated-method	image-methods
image3D,MeansTest-method	image-methods
image3D,MSImageSet-method	image-methods
image3D,OPLS-method	image-methods
image3D,PCA-method	image-methods
image3D,PCA2-method	image-methods
image3D,PLS-method	image-methods
image3D,PLS2-method	image-methods
image3D,ResultSet-method	image-methods
image3D,SegmentationTest-method	image-methods
image3D,SImageSet-method	image-methods
image3D,SparseImagingExperiment-method	image-methods
image3D,SpatialDGMM-method	image-methods
image3D,SpatialFastmap-method	image-methods
image3D,SpatialFastmap2-method	image-methods
image3D,SpatialKMeans-method	image-methods
image3D,SpatialKMeans2-method	image-methods
image3D,SpatialShrunkenCentroids-method	image-methods
image3D,SpatialShrunkenCentroids2-method	image-methods
image3D-methods	image-methods
ImageArrayList	ImageList-class
ImageArrayList-class	ImageList-class
ImageData	legacy
imageData	ImagingExperiment-class
imageData,ImagingExperiment-method	ImagingExperiment-class
imageData,iSet-method	legacy
ImageData-class	legacy
imageData-methods	ImagingExperiment-class
imageData<-	ImagingExperiment-class
imageData<-,ImagingExperiment-method	ImagingExperiment-class
imageData<-,iSet-method	legacy
imageData<-,MSContinuousImagingExperiment-method	MSContinuousImagingExperiment-class
imageData<-,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
ImageList	ImageList-class
ImageList-class	ImageList-class
imageShape	legacy
imageShape,MIAPE-Imaging-method	legacy
ImagingExperiment	ImagingExperiment-class
ImagingExperiment-class	ImagingExperiment-class
ImagingResult	ImagingResult-class
ImagingResult-class	ImagingResult-class
inferno	reexports
initialize,Hashmat-method	legacy
initialize,IAnnotatedDataFrame-method	legacy
initialize,ImageData-method	legacy
initialize,iSet-method	legacy
initialize,MassDataFrame-method	MassDataFrame-class
initialize,MSImageData-method	legacy
initialize,MSImageProcess-method	legacy
initialize,MSImageSet-method	legacy
initialize,PositionDataFrame-method	PositionDataFrame-class
initialize,SImageData-method	legacy
initialize,SImageSet-method	legacy
inSituChemistry	legacy
inSituChemistry,MIAPE-Imaging-method	legacy
instrumentModel	MSImagingInfo-class
instrumentModel,MIAPE-Imaging-method	legacy
instrumentModel,Vector-method	MSImagingInfo-class
instrumentVendor	MSImagingInfo-class
instrumentVendor,MIAPE-Imaging-method	legacy
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,MIAPE-Imaging-method	legacy
ionizationType,Vector-method	MSImagingInfo-class
is3D	SparseImagingExperiment-class
is3D,IAnnotatedDataFrame-method	legacy
is3D,PositionDataFrame-method	PositionDataFrame-class
is3D,SImageSet-method	legacy
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
keys	legacy
keys,Hashmat-method	legacy
keys,MSProcessedImagingSpectraList-method	MSProcessedImagingExperiment-class
keys<-	legacy
keys<-,Hashmat,character-method	legacy
keys<-,Hashmat,list-method	legacy
keys<-,Hashmat-method	legacy
keys<-,MSProcessedImagingSpectraList,ANY-method	MSProcessedImagingExperiment-class
lapply,XDataFrame-method	XDataFrame-class
length,AnnotatedImage-method	AnnotatedImage-class
length,ImageList-method	ImageList-class
length,ImagingExperiment-method	ImagingExperiment-class
length,iSet-method	legacy
length,MSImagingInfo-method	MSImagingInfo-class
length,ResultSet-method	legacy
length,XDataFrame-method	XDataFrame-class
lightmode	colors-functions
lineScanDirection	MSImagingInfo-class
lineScanDirection,MIAPE-Imaging-method	legacy
lineScanDirection,Vector-method	MSImagingInfo-class
logLik,SpatialShrunkenCentroids-method	spatialShrunkenCentroids-methods
logLik,SpatialShrunkenCentroids2-method	spatialShrunkenCentroids-methods
magma	reexports
makeFactor	selectROI-methods
massAnalyzerType	MSImagingInfo-class
massAnalyzerType,MIAPE-Imaging-method	legacy
massAnalyzerType,Vector-method	MSImagingInfo-class
MassDataFrame	MassDataFrame-class
MassDataFrame-class	MassDataFrame-class
matrixApplication	MSImagingInfo-class
matrixApplication,MIAPE-Imaging-method	legacy
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,ResultSet-method	legacy
modelData<-	ImagingResult-class
modelData<-,ImagingResult-method	ImagingResult-class
modelData<-,ResultSet-method	legacy
MSContinuousImagingExperiment	MSContinuousImagingExperiment-class
MSContinuousImagingExperiment-class	MSContinuousImagingExperiment-class
MSContinuousImagingSpectraList	ImageList-class
MSContinuousImagingSpectraList-class	ImageList-class
msiInfo	MSImagingInfo-class
msiInfo,MIAPE-Imaging-method	legacy
msiInfo,MSContinuousImagingExperiment-method	MSImagingInfo-class
msiInfo,MSImageSet-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
mutate	deprecated
mutate.SparseImagingExperiment	deprecated
mz	mz-methods
mz,MassDataFrame-method	MassDataFrame-class
mz,missing-method	mz-methods
mz,MSImageSet-method	legacy
mz,MSImagingExperiment-method	MSImagingExperiment-class
mz-methods	mz-methods
mz<-	mz-methods
mz<-,MassDataFrame-method	MassDataFrame-class
mz<-,MSImageSet-method	legacy
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,MSImageData-method	legacy
mzData,MSImagingInfo-method	MSImagingInfo-class
mzData,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
mzData,SImageData-method	legacy
mzData-methods	MSProcessedImagingExperiment-class
mzData<-	MSProcessedImagingExperiment-class
mzData<-,MSImageData-method	legacy
mzData<-,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
mzData<-,SImageData-method	legacy
mzFilter	mzFilter-methods
mzFilter,MSImagingExperiment-method	mzFilter-methods
mzFilter-methods	mzFilter-methods
names,ImageData-method	legacy
names,ImageList-method	ImageList-class
names,ImagingExperiment-method	ImagingExperiment-class
names,ResultSet-method	legacy
names,XDataFrame-method	XDataFrame-class
names<-,ImageData-method	legacy
names<-,ImageList-method	ImageList-class
names<-,ImagingExperiment-method	ImagingExperiment-class
normalization	MSImagingInfo-class
normalization,MSImageProcess-method	legacy
normalization,Vector-method	MSImagingInfo-class
normalization<-	MSImagingInfo-class
normalization<-,MSImageProcess-method	legacy
normalization<-,Vector-method	MSImagingInfo-class
normalize	normalize-methods
normalize,MSImageSet-method	normalize-methods
normalize,SparseImagingExperiment-method	normalize-methods
normalize-methods	normalize-methods
normalize.reference	normalize-methods
normalize.rms	normalize-methods
normalize.tic	normalize-methods
notes,MIAPE-Imaging-method	legacy
notes<-,MIAPE-Imaging,character-method	legacy
notes<-,MIAPE-Imaging,list-method	legacy
OPLS	PLS-methods
OPLS,SImageSet,ANY-method	PLS-methods
OPLS,SImageSet,matrix-method	PLS-methods
OPLS,SparseImagingExperiment,ANY-method	PLS-methods
OPLS-class	PLS-methods
OPLS-methods	PLS-methods
otherInfo,MIAPE-Imaging-method	legacy
PCA	PCA-methods
PCA,SImageSet-method	PCA-methods
PCA,SparseImagingExperiment-method	PCA-methods
PCA-class	PCA-methods
PCA-methods	PCA-methods
pData	ImagingExperiment-class
pData,Hashmat-method	legacy
pData,ImagingExperiment-method	ImagingExperiment-class
pData,iSet-method	legacy
pData-methods	ImagingExperiment-class
pData<-	ImagingExperiment-class
pData<-,Hashmat,ANY-method	legacy
pData<-,Hashmat-method	legacy
pData<-,ImagingExperiment,ANY-method	ImagingExperiment-class
pData<-,iSet,ANY-method	legacy
pData<-,iSet-method	legacy
peakAlign	peakAlign-methods
peakAlign,MSImageSet,missing-method	peakAlign-methods
peakAlign,MSImageSet,MSImageSet-method	peakAlign-methods
peakAlign,MSImageSet,numeric-method	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,MSImageData-method	legacy
peakData,MSImagingExperiment-method	MSImagingExperiment-class
peakData,SImageData-method	legacy
peakData-methods	MSImagingExperiment-class
peakData<-	MSImagingExperiment-class
peakData<-,MSImageData-method	legacy
peakData<-,MSImagingExperiment-method	MSImagingExperiment-class
peakData<-,SImageData-method	legacy
peakFilter	mzFilter-methods
peakFilter,MSImageSet-method	mzFilter-methods
peakFilter,MSImagingExperiment-method	mzFilter-methods
peakFilter-methods	mzFilter-methods
peakFilter.freq	mzFilter-methods
peakPick	peakPick-methods
peakPick,MSImageSet-method	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,MSImageProcess-method	legacy
peakPicking,Vector-method	MSImagingInfo-class
peakPicking<-	MSImagingInfo-class
peakPicking<-,MSImageProcess-method	legacy
peakPicking<-,Vector-method	MSImagingInfo-class
peaks	MSImagingExperiment-class
peaks,MSImageSet-method	legacy
peaks,MSImagingExperiment-method	MSImagingExperiment-class
peaks-methods	MSImagingExperiment-class
peaks<-	MSImagingExperiment-class
peaks<-,MSImageSet-method	legacy
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,SImageSet-method	pixelApply-methods
pixelApply,SparseImagingExperiment-method	pixelApply-methods
pixelApply-methods	pixelApply-methods
pixelData	ImagingExperiment-class
pixelData,ImagingExperiment-method	ImagingExperiment-class
pixelData,iSet-method	legacy
pixelData,SparseImagingExperiment-method	SparseImagingExperiment-class
pixelData-methods	ImagingExperiment-class
pixelData<-	ImagingExperiment-class
pixelData<-,ImagingExperiment-method	ImagingExperiment-class
pixelData<-,iSet-method	legacy
pixelData<-,SparseImagingExperiment-method	SparseImagingExperiment-class
pixelNames	ImagingExperiment-class
pixelNames,IAnnotatedDataFrame-method	legacy
pixelNames,ImagingExperiment-method	ImagingExperiment-class
pixelNames,iSet-method	legacy
pixelNames,SImageData-method	legacy
pixelNames,SparseImagingExperiment-method	SparseImagingExperiment-class
pixelNames-methods	ImagingExperiment-class
pixelNames<-	ImagingExperiment-class
pixelNames<-,IAnnotatedDataFrame-method	legacy
pixelNames<-,ImagingExperiment-method	ImagingExperiment-class
pixelNames<-,iSet-method	legacy
pixelNames<-,SImageData-method	legacy
pixelNames<-,SImageSet-method	legacy
pixelNames<-,SparseImagingExperiment-method	SparseImagingExperiment-class
pixels	SparseImagingExperiment-class
pixels,iSet-method	legacy
pixels,MSImageSet-method	legacy
pixels,MSImagingExperiment-method	MSImagingExperiment-class
pixels,SparseImagingExperiment-method	SparseImagingExperiment-class
pixels-methods	SparseImagingExperiment-class
pixelSize	MSImagingInfo-class
pixelSize,MIAPE-Imaging-method	legacy
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,CrossValidated,missing-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,MSImageSet,formula-method	plot-methods
plot,MSImageSet,missing-method	plot-methods
plot,MSImagingExperiment,formula-method	plot-methods
plot,MSImagingExperiment,missing-method	plot-methods
plot,MSImagingSummary,missing-method	plot-methods
plot,OPLS,missing-method	plot-methods
plot,PCA,missing-method	plot-methods
plot,PCA2,missing-method	plot-methods
plot,PLS,missing-method	plot-methods
plot,PLS2,missing-method	plot-methods
plot,ResultSet,formula-method	plot-methods
plot,ResultSet,missing-method	plot-methods
plot,SegmentationTest,missing-method	plot-methods
plot,SImageSet,formula-method	plot-methods
plot,SImageSet,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,SpatialFastmap,missing-method	plot-methods
plot,SpatialFastmap2,missing-method	plot-methods
plot,SpatialKMeans,missing-method	plot-methods
plot,SpatialKMeans2,missing-method	plot-methods
plot,SpatialShrunkenCentroids,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
plot.summary.CrossValidated	crossValidate-methods
plot.summary.OPLS	PLS-methods
plot.summary.PCA	PCA-methods
plot.summary.PLS	PLS-methods
plot.summary.SpatialFastmap	spatialFastmap-methods
plot.summary.SpatialKMeans	spatialKMeans-methods
plot.summary.SpatialShrunkenCentroids	spatialShrunkenCentroids-methods
PLS	PLS-methods
PLS,SImageSet,ANY-method	PLS-methods
PLS,SImageSet,matrix-method	PLS-methods
PLS,SparseImagingExperiment,ANY-method	PLS-methods
PLS-class	PLS-methods
PLS-methods	PLS-methods
positionArray	legacy
positionArray,SImageData-method	legacy
positionArray<-	legacy
positionArray<-,SImageData-method	legacy
PositionDataFrame	PositionDataFrame-class
PositionDataFrame-class	PositionDataFrame-class
predict,OPLS-method	PLS-methods
predict,PCA-method	PCA-methods
predict,PCA2-method	PCA-methods
predict,PLS-method	PLS-methods
predict,PLS2-method	PLS-methods
predict,SpatialShrunkenCentroids-method	spatialShrunkenCentroids-methods
predict,SpatialShrunkenCentroids2-method	spatialShrunkenCentroids-methods
preproc,MIAPE-Imaging-method	legacy
preproc,SparseImagingExperiment-method	SparseImagingExperiment-class
preproc<-,MIAPE-Imaging-method	legacy
presetImageDef	simulateSpectrum
print.summary.CrossValidated	crossValidate-methods
print.summary.iSet	legacy
print.summary.OPLS	PLS-methods
print.summary.PCA	PCA-methods
print.summary.PLS	PLS-methods
print.summary.SpatialFastmap	spatialFastmap-methods
print.summary.SpatialKMeans	spatialKMeans-methods
print.summary.SpatialShrunkenCentroids	spatialShrunkenCentroids-methods
process	process-methods
process,MSImagingExperiment-method	process-methods
process,SparseImagingExperiment-method	process-methods
process-methods	process-methods
processingData	legacy
processingData,MSImageSet-method	legacy
processingData,SparseImagingExperiment-method	SparseImagingExperiment-class
processingData-methods	legacy
processingData<-	legacy
processingData<-,MSImageSet-method	legacy
processingData<-,SparseImagingExperiment-method	SparseImagingExperiment-class
protocolData,iSet-method	legacy
protocolData<-,iSet,ANY-method	legacy
pubMedIds,MIAPE-Imaging-method	legacy
pubMedIds<-,MIAPE-Imaging,ANY-method	legacy
pull,MSImagingExperiment-method	MSImagingExperiment-class
pull,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
pull,SparseImagingExperiment-method	SparseImagingExperiment-class
range,AnnotatedImage-method	AnnotatedImage-class
rbind,AnnotatedImageList-method	AnnotatedImagingExperiment-class
rbind,Hashmat-method	legacy
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,MSImageSet-method	reduceBaseline-methods
reduceBaseline,SparseImagingExperiment-method	reduceBaseline-methods
reduceBaseline-methods	reduceBaseline-methods
reduceBaseline.locmin	reduceBaseline-methods
reduceBaseline.median	reduceBaseline-methods
reduceDimension	legacy
reduceDimension,MSImageSet,missing-method	legacy
reduceDimension,MSImageSet,MSImageSet-method	legacy
reduceDimension,MSImageSet,numeric-method	legacy
reduceDimension-methods	legacy
reduceDimension.bin	legacy
reduceDimension.peaks	legacy
reduceDimension.resample	legacy
regeneratePositions	legacy
regeneratePositions,SImageData-method	legacy
regeneratePositions,SImageSet-method	legacy
resolution	PositionDataFrame-class
resolution,AnnotatedImage-method	AnnotatedImage-class
resolution,AnnotatedImagingExperiment-method	AnnotatedImagingExperiment-class
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	AnnotatedImage-class
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,ResultSet,ANY-method	legacy
resultData,ResultSet-method	legacy
resultData<-	ImagingResult-class
resultData<-,ImagingResult,ANY-method	ImagingResult-class
resultData<-,ImagingResult,missing-method	ImagingResult-class
resultData<-,ResultSet,missing-method	legacy
resultData<-,ResultSet-method	legacy
resultNames	ImagingResult-class
resultNames,ImagingResult-method	ImagingResult-class
resultNames<-	ImagingResult-class
ResultSet	legacy
ResultSet-class	legacy
risk.colors	colors-functions
rownames,Hashmat-method	legacy
rownames<-,Hashmat-method	legacy
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,IAnnotatedDataFrame-method	legacy
sampleNames,ImagingExperiment-method	ImagingExperiment-class
sampleNames,iSet-method	legacy
sampleNames-methods	ImagingExperiment-class
sampleNames<-	ImagingExperiment-class
sampleNames<-,IAnnotatedDataFrame,ANY-method	legacy
sampleNames<-,IAnnotatedDataFrame-method	legacy
sampleNames<-,ImagingExperiment,ANY-method	ImagingExperiment-class
sampleNames<-,iSet,ANY-method	legacy
sampleNames<-,iSet-method	legacy
samples,MIAPE-Imaging-method	legacy
scanDirection	MSImagingInfo-class
scanDirection,MIAPE-Imaging-method	legacy
scanDirection,Vector-method	MSImagingInfo-class
scanPattern	MSImagingInfo-class
scanPattern,MIAPE-Imaging-method	legacy
scanPattern,Vector-method	MSImagingInfo-class
scanPolarity	MSImagingInfo-class
scanPolarity,MIAPE-Imaging-method	legacy
scanPolarity,Vector-method	MSImagingInfo-class
scans,MSImagingInfo-method	MSImagingInfo-class
scanType	MSImagingInfo-class
scanType,MIAPE-Imaging-method	legacy
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
select	deprecated
select.SparseImagingExperiment	deprecated
selectROI	selectROI-methods
selectROI,SImageSet-method	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	AnnotatedImagingExperiment-class
show,AnnotatedImagingExperiment-method	AnnotatedImagingExperiment-class
show,Hashmat-method	legacy
show,IAnnotatedDataFrame-method	legacy
show,ImageData-method	legacy
show,ImagingExperiment-method	ImagingExperiment-class
show,ImagingResult-method	ImagingResult-class
show,iSet-method	legacy
show,MIAPE-Imaging-method	legacy
show,MSImageProcess-method	legacy
show,MSImageSet-method	legacy
show,MSImagingExperiment-method	MSImagingExperiment-class
show,ResultSet-method	legacy
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
slice.SparseImagingExperiment	deprecated
smooth	smoothSignal-methods
smooth,SparseImagingExperiment-method	smoothSignal-methods
smooth-methods	smoothSignal-methods
smoothing	MSImagingInfo-class
smoothing,MSImageProcess-method	legacy
smoothing,Vector-method	MSImagingInfo-class
smoothing<-	MSImagingInfo-class
smoothing<-,MSImageProcess-method	legacy
smoothing<-,Vector-method	MSImagingInfo-class
smoothSignal	smoothSignal-methods
smoothSignal,MSImageSet-method	smoothSignal-methods
smoothSignal,SparseImagingExperiment-method	smoothSignal-methods
smoothSignal-methods	smoothSignal-methods
smoothSignal.gaussian	smoothSignal-methods
smoothSignal.ma	smoothSignal-methods
smoothSignal.sgolay	smoothSignal-methods
softwareName	legacy
softwareName,MIAPE-Imaging-method	legacy
softwareVersion	legacy
softwareVersion,MIAPE-Imaging-method	legacy
sort,XDataFrame-method	XDataFrame-class
SparseImagingExperiment	SparseImagingExperiment-class
SparseImagingExperiment-class	SparseImagingExperiment-class
SparseImagingResult	ImagingResult-class
SparseImagingResult-class	ImagingResult-class
spatialApply	pixelApply-methods
spatialApply,SparseImagingExperiment-method	pixelApply-methods
spatialApply-methods	pixelApply-methods
spatialDGMM	spatialDGMM-methods
spatialDGMM,SparseImagingExperiment-method	spatialDGMM-methods
SpatialDGMM-class	spatialDGMM-methods
spatialDGMM-methods	spatialDGMM-methods
spatialFastmap	spatialFastmap-methods
spatialFastmap,SImageSet-method	spatialFastmap-methods
spatialFastmap,SparseImagingExperiment-method	spatialFastmap-methods
spatialFastmap-class	spatialFastmap-methods
spatialFastmap-methods	spatialFastmap-methods
spatialKMeans	spatialKMeans-methods
spatialKMeans,SImageSet-method	spatialKMeans-methods
spatialKMeans,SparseImagingExperiment-method	spatialKMeans-methods
SpatialKMeans-class	spatialKMeans-methods
spatialKMeans-methods	spatialKMeans-methods
spatialShrunkenCentroids	spatialShrunkenCentroids-methods
spatialShrunkenCentroids,SImageSet,character-method	spatialShrunkenCentroids-methods
spatialShrunkenCentroids,SImageSet,factor-method	spatialShrunkenCentroids-methods
spatialShrunkenCentroids,SImageSet,missing-method	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
specimenOrigin	legacy
specimenOrigin,MIAPE-Imaging-method	legacy
specimenType	legacy
specimenType,MIAPE-Imaging-method	legacy
spectra	MSImagingExperiment-class
spectra,MSImageSet-method	legacy
spectra,MSImagingExperiment-method	MSImagingExperiment-class
spectra-methods	MSImagingExperiment-class
spectra<-	MSImagingExperiment-class
spectra<-,MSImageSet-method	legacy
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,MSImageProcess-method	legacy
spectrumRepresentation,Vector-method	MSImagingInfo-class
spectrumRepresentation<-	MSImagingInfo-class
spectrumRepresentation<-,MSImageProcess-method	legacy
spectrumRepresentation<-,Vector-method	MSImagingInfo-class
stainingMethod	legacy
stainingMethod,MIAPE-Imaging-method	legacy
standardizeRuns	legacy
standardizeRuns,MSImageSet-method	legacy
standardizeRuns-methods	legacy
standardizeRuns.sum	legacy
storageMode,ImageData-method	legacy
storageMode,iSet-method	legacy
storageMode<-,ImageData,character-method	legacy
storageMode<-,iSet,ANY-method	legacy
storageMode<-,iSet,character-method	legacy
subset,SparseImagingExperiment-method	subset-methods
subsetFeatures	subset-methods
subsetPixels	subset-methods
summarise	deprecated
summarise.MSImagingExperiment	deprecated
summarise.SparseImagingExperiment	deprecated
summarize	deprecated
summarizeFeatures	aggregate-methods
summarizePixels	aggregate-methods
summary,CrossValidated-method	crossValidate-methods
summary,CrossValidated2-method	crossValidate-methods
summary,iSet-method	legacy
summary,MeansTest-method	meansTest-methods
summary,OPLS-method	PLS-methods
summary,PCA-method	PCA-methods
summary,PCA2-method	PCA-methods
summary,PLS-method	PLS-methods
summary,PLS2-method	PLS-methods
summary,SegmentationTest-method	meansTest-methods
summary,SpatialDGMM-method	spatialDGMM-methods
summary,SpatialFastmap-method	spatialFastmap-methods
summary,SpatialFastmap2-method	spatialFastmap-methods
summary,SpatialKMeans-method	spatialKMeans-methods
summary,SpatialKMeans2-method	spatialKMeans-methods
summary,SpatialShrunkenCentroids-method	spatialShrunkenCentroids-methods
summary,SpatialShrunkenCentroids2-method	spatialShrunkenCentroids-methods
summary,SummaryDataFrame-method	internal
SummaryDataFrame	internal
SummaryDataFrame-class	internal
tissueThickness	legacy
tissueThickness,MIAPE-Imaging-method	legacy
tissueWash	legacy
tissueWash,MIAPE-Imaging-method	legacy
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
ungroup	deprecated
varLabels,iSet-method	legacy
varLabels<-,iSet-method	legacy
varMetadata,iSet-method	legacy
varMetadata<-,iSet,ANY-method	legacy
varMetadata<-,iSet-method	legacy
viridis	reexports
width,AnnotatedImage-method	AnnotatedImage-class
width,AnnotatedImagingExperiment-method	AnnotatedImagingExperiment-class
width<-,AnnotatedImage-method	AnnotatedImage-class
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	AnnotatedImagingExperiment-class
[,Hashmat,ANY,ANY,ANY-method	legacy
[,Hashmat,ANY,ANY,NULL-method	legacy
[,Hashmat-method	legacy
[,IAnnotatedDataFrame,ANY,ANY,ANY-method	legacy
[,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
[,ResultSet,ANY,ANY,ANY-method	legacy
[,ResultSet-method	legacy
[,SImageData,ANY,ANY,ANY-method	legacy
[,SImageData,ANY,ANY,NULL-method	legacy
[,SImageData-method	legacy
[,SImageSet,ANY,ANY,ANY-method	legacy
[,SImageSet-method	legacy
[,SparseImagingExperiment,ANY,ANY,ANY-method	SparseImagingExperiment-class
[,SparseImagingResult,ANY,ANY,ANY-method	ImagingResult-class
[,XDataFrame,ANY,ANY,ANY-method	XDataFrame-class
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