Cardinal-package	Cardinal-package
$,SpatialResults-method	SpatialResults-class
$,SpectraArrays-method	SpectraArrays-class
$,SpectralImagingData-method	SpectralImagingData-class
$<-,SpectraArrays-method	SpectraArrays-class
$<-,SpectralImagingData-method	SpectralImagingData-class
$<-,XDataFrame-method	XDataFrame-class
addProcessing,SpectralImagingData-method	process
addShape	simulateSpectra
aggregate,SpectralImagingExperiment-method	deprecated
alpha.colors	deprecated
as_facets	reexports
as_layers	reexports
baselineReduction	deprecated
baselineReduction<-	deprecated
bin	bin
bin,MSImagingArrays-method	bin
bin,MSImagingExperiment-method	bin
bin,SpectralImagingArrays-method	bin
bin,SpectralImagingExperiment-method	bin
bw.colors	deprecated
c,MSImagingArrays-method	MSImagingArrays-class
c,SpectraArrays-method	SpectraArrays-class
c,SpectralImagingArrays-method	SpectralImagingArrays-class
Cardinal	Cardinal-package
cbind,MSImagingExperiment-method	MSImagingExperiment-class
cbind,SpectraArrays-method	SpectraArrays-class
cbind,SpectralImagingArrays-method	SpectralImagingArrays-class
cbind,SpectralImagingExperiment-method	SpectralImagingExperiment-class
cbind,XDataFrame-method	XDataFrame-class
centroided,MSImagingExperiment_OR_Arrays-method	MSImagingExperiment-class
centroided<-,MSImagingExperiment_OR_Arrays-method	MSImagingExperiment-class
class:Hashmat	deprecated
class:IAnnotatedDataFrame	deprecated
class:ImageData	deprecated
class:iSet	deprecated
class:MassDataFrame	MassDataFrame-class
class:MeansTest	MeansTest
class:MIAPE-Imaging	deprecated
class:MSImageData	deprecated
class:MSImageProcess	deprecated
class:MSImageSet	deprecated
class:MSImagingArrays	MSImagingArrays-class
class:MSImagingExperiment	MSImagingExperiment-class
class:PositionDataFrame	PositionDataFrame-class
class:ResultSet	deprecated
class:ResultsList	ResultsList-class
class:SImageData	deprecated
class:SImageSet	deprecated
class:SpatialCV	SpatialCV
class:SpatialDGMM	SpatialDGMM
class:SpatialFastmap	SpatialFastmap
class:SpatialKMeans	SpatialKMeans
class:SpatialNMF	SpatialNMF
class:SpatialOPLS	SpatialPLS
class:SpatialPCA	SpatialPCA
class:SpatialPLS	SpatialPLS
class:SpatialResults	SpatialResults-class
class:SpatialShrunkenCentroids	SpatialShrunkenCentroids
class:SpectraArrays	SpectraArrays-class
class:SpectralImagingArrays	SpectralImagingArrays-class
class:SpectralImagingData	SpectralImagingData-class
class:SpectralImagingExperiment	SpectralImagingExperiment-class
class:XDataFrame	XDataFrame-class
class:XDFrame	XDataFrame-class
classNameForDisplay,XDFrame-method	XDataFrame-class
coef,SpatialOPLS-method	SpatialPLS
coerce,DataFrame,XDataFrame-method	XDataFrame-class
coerce,DFrame,MassDataFrame-method	MassDataFrame-class
coerce,DFrame,PositionDataFrame-method	PositionDataFrame-class
coerce,list,SpectraArrays-method	SpectraArrays-class
coerce,MSImageSet,MSImagingExperiment-method	MSImagingExperiment-class
coerce,MSImagingArrays,MSImagingExperiment-method	readMSIData
coerce,MSImagingExperiment,MSImagingArrays-method	readMSIData
coerce,SimpleList,SpectraArrays-method	SpectraArrays-class
coerce,SpectraArrays,list-method	SpectraArrays-class
coerce,SpectraArrays,SimpleList-method	SpectraArrays-class
col.map	deprecated
colMeans,SpectralImagingExperiment-method	summarize
colnames,SpectralImagingExperiment-method	SpectralImagingExperiment-class
colnames<-,SpectralImagingExperiment-method	SpectralImagingExperiment-class
colocalized	colocalized
colocalized,MSImagingExperiment-method	colocalized
colocalized,SpatialDGMM-method	colocalized
colocalized,SpectralImagingExperiment-method	colocalized
color.map	deprecated
colStats,SpectralImagingExperiment-method	summarize
colSums,SpectralImagingExperiment-method	summarize
combine,SpectraArrays,ANY-method	SpectraArrays-class
combine,SpectralImagingArrays,ANY-method	SpectralImagingArrays-class
combine,SpectralImagingExperiment,ANY-method	SpectralImagingExperiment-class
convertMSImagingArrays2Experiment	readMSIData
convertMSImagingExperiment2Arrays	readMSIData
coord	PositionDataFrame-class
coord,PositionDataFrame-method	PositionDataFrame-class
coord,SpatialResults-method	SpatialResults-class
coord,SpectralImagingData-method	SpectralImagingData-class
coord<-	PositionDataFrame-class
coord<-,PositionDataFrame-method	PositionDataFrame-class
coord<-,SpatialResults-method	SpatialResults-class
coord<-,SpectralImagingData-method	SpectralImagingData-class
coordNames	PositionDataFrame-class
coordNames,PositionDataFrame-method	PositionDataFrame-class
coordNames,SpatialResults-method	SpatialResults-class
coordNames,SpectralImagingData-method	SpectralImagingData-class
coordNames<-	PositionDataFrame-class
coordNames<-,PositionDataFrame-method	PositionDataFrame-class
coordNames<-,SpatialResults-method	SpatialResults-class
coordNames<-,SpectralImagingData-method	SpectralImagingData-class
coregister	colocalized
cpal	reexports
cpals	reexports
crossValidate	SpatialCV
cvApply	deprecated
darkmode	deprecated
deprecated	deprecated
dim,SpectraArrays-method	SpectraArrays-class
dim,SpectralImagingArrays-method	SpectralImagingArrays-class
dim,SpectralImagingExperiment-method	SpectralImagingExperiment-class
discrete.colors	deprecated
divergent.colors	deprecated
dpal	reexports
dpals	reexports
dropkeys	XDataFrame-class
dropkeys,XDataFrame-method	XDataFrame-class
estimateDomain	estimateDomain
estimateReferenceMz	estimateDomain
estimateReferencePeaks	estimateDomain
experimentData,MSImagingExperiment_OR_Arrays-method	MSImagingExperiment-class
experimentData<-,MSImagingExperiment_OR_Arrays,ANY-method	MSImagingExperiment-class
fData,SpatialResults-method	SpatialResults-class
fData,SpectralImagingExperiment-method	SpectralImagingExperiment-class
fData<-,SpatialResults,ANY-method	SpatialResults-class
fData<-,SpectralImagingExperiment,ANY-method	SpectralImagingExperiment-class
featureApply	deprecated
featureApply,SpectralImagingExperiment-method	deprecated
featureData,SpatialResults-method	SpatialResults-class
featureData,SpectralImagingExperiment-method	SpectralImagingExperiment-class
featureData<-,SpatialResults,ANY-method	SpatialResults-class
featureData<-,SpectralImagingExperiment,ANY-method	SpectralImagingExperiment-class
featureNames,SpatialResults-method	SpatialResults-class
featureNames,SpectralImagingExperiment-method	SpectralImagingExperiment-class
featureNames<-,SpatialResults-method	SpatialResults-class
featureNames<-,SpectralImagingExperiment-method	SpectralImagingExperiment-class
features	features
features,MSImagingExperiment-method	features
features,SpectralImagingExperiment-method	features
fetch,SpectraArrays-method	SpectraArrays-class
fetch,SpectralImagingData-method	SpectralImagingData-class
findNeighbors	findNeighbors
findNeighbors,ANY-method	findNeighbors
findNeighbors,PositionDataFrame-method	findNeighbors
findNeighbors,SpectralImagingData-method	findNeighbors
fitted,ResultsList-method	ResultsList-class
fitted,SpatialCV-method	SpatialCV
fitted,SpatialOPLS-method	SpatialPLS
fitted,SpatialPLS-method	SpatialPLS
fitted,SpatialResults-method	SpatialResults-class
fitted,SpatialShrunkenCentroids-method	SpatialShrunkenCentroids
flash,SpectraArrays-method	SpectraArrays-class
flash,SpectralImagingData-method	SpectralImagingData-class
getCardinalBPPARAM	Cardinal-package
getCardinalChunksize	Cardinal-package
getCardinalLogger	Cardinal-package
getCardinalNChunks	Cardinal-package
getCardinalNumBlocks	deprecated
getCardinalParallel	Cardinal-package
getCardinalSerialize	Cardinal-package
getCardinalVerbose	Cardinal-package
gradient.colors	deprecated
gridded	deprecated
gridded<-	deprecated
Hashmat	deprecated
Hashmat-class	deprecated
height	deprecated
height<-	deprecated
IAnnotatedDataFrame	deprecated
IAnnotatedDataFrame-class	deprecated
iData	deprecated
iData,ANY-method	deprecated
iData<-	deprecated
iData<-,ANY-method	deprecated
image	plot-image
image,MSImagingExperiment-method	plot-image
image,PositionDataFrame-method	plot-image
image,ResultsList-method	ResultsList-class
image,SpatialCV-method	SpatialCV
image,SpatialDGMM-method	SpatialDGMM
image,SpatialFastmap-method	SpatialFastmap
image,SpatialKMeans-method	SpatialKMeans
image,SpatialNMF-method	SpatialNMF
image,SpatialOPLS-method	SpatialPLS
image,SpatialPCA-method	SpatialPCA
image,SpatialPLS-method	SpatialPLS
image,SpatialResults-method	SpatialResults-class
image,SpatialShrunkenCentroids-method	SpatialShrunkenCentroids
image,SpectralImagingExperiment-method	plot-image
image3D	plot-image
image3D,MSImagingExperiment-method	plot-image
ImageData	deprecated
ImageData-class	deprecated
instrumentVendor	deprecated
intensity,MSImagingArrays-method	MSImagingArrays-class
intensity,MSImagingExperiment-method	MSImagingExperiment-class
intensity.colors	deprecated
intensity<-,MSImagingArrays-method	MSImagingArrays-class
intensity<-,MSImagingExperiment-method	MSImagingExperiment-class
intensityData	deprecated
intensityData<-	deprecated
ionizationType	deprecated
is3D	deprecated
is3D,PositionDataFrame-method	PositionDataFrame-class
is3D,SpectralImagingData-method	SpectralImagingData-class
isCentroided,MSImagingExperiment_OR_Arrays-method	MSImagingExperiment-class
iSet	deprecated
iSet-class	deprecated
jet.colors	deprecated
keys	XDataFrame-class
keys,XDataFrame-method	XDataFrame-class
keys<-	XDataFrame-class
keys<-,XDataFrame-method	XDataFrame-class
length,SpatialResults-method	SpatialResults-class
length,SpectraArrays-method	SpectraArrays-class
length,SpectralImagingArrays-method	SpectralImagingArrays-class
length,SpectralImagingExperiment-method	SpectralImagingExperiment-class
lightmode	deprecated
lineScanDirection	deprecated
logLik,SpatialDGMM-method	SpatialDGMM
logLik,SpatialShrunkenCentroids-method	SpatialShrunkenCentroids
makeFactor	selectROI
massAnalyzerType	deprecated
MassDataFrame	MassDataFrame-class
MassDataFrame-class	MassDataFrame-class
matrixApplication	deprecated
MeansTest	MeansTest
meansTest	MeansTest
meansTest,ANY-method	MeansTest
meansTest,SpatialDGMM-method	MeansTest
meansTest,SpectralImagingExperiment-method	MeansTest
MeansTest-class	MeansTest
MIAPE-Imaging	deprecated
MIAPE-Imaging-class	deprecated
modelData	SpatialResults-class
modelData,SpatialResults-method	SpatialResults-class
modelData<-	SpatialResults-class
modelData<-,SpatialResults-method	SpatialResults-class
msiInfo	deprecated
MSImageData	deprecated
MSImageData-class	deprecated
MSImageProcess	deprecated
MSImageProcess-class	deprecated
MSImageSet	deprecated
MSImageSet-class	deprecated
MSImagingArrays	MSImagingArrays-class
MSImagingArrays-class	MSImagingArrays-class
MSImagingExperiment	MSImagingExperiment-class
MSImagingExperiment-class	MSImagingExperiment-class
mz,MassDataFrame-method	MassDataFrame-class
mz,missing-method	MSImagingExperiment-class
mz,MSImagingArrays-method	MSImagingArrays-class
mz,MSImagingExperiment-method	MSImagingExperiment-class
mz<-,MassDataFrame-method	MassDataFrame-class
mz<-,MSImagingArrays-method	MSImagingArrays-class
mz<-,MSImagingExperiment-method	MSImagingExperiment-class
mzAlign	deprecated
mzAlign,MSImagingExperiment,missing-method	deprecated
mzAlign,MSImagingExperiment,numeric-method	deprecated
mzBin	deprecated
mzBin,MSImagingExperiment,missing-method	deprecated
mzBin,MSImagingExperiment,numeric-method	deprecated
mzData	deprecated
mzData<-	deprecated
mzFilter	deprecated
mzFilter,MSImagingExperiment-method	deprecated
names,SpatialResults-method	SpatialResults-class
names,SpectraArrays-method	SpectraArrays-class
names,SpectralImagingArrays-method	SpectralImagingArrays-class
names,SpectralImagingExperiment-method	SpectralImagingExperiment-class
names<-,SpectraArrays-method	SpectraArrays-class
names<-,SpectralImagingArrays-method	SpectralImagingArrays-class
names<-,SpectralImagingExperiment-method	SpectralImagingExperiment-class
names<-,XDataFrame-method	XDataFrame-class
NMF	SpatialNMF
NMF,ANY-method	SpatialNMF
NMF,SpectralImagingExperiment-method	SpatialNMF
normalization	deprecated
normalization<-	deprecated
normalize	normalize
normalize,MSImagingExperiment_OR_Arrays-method	normalize
normalize,SpectralImagingData-method	normalize
nrun,PositionDataFrame-method	PositionDataFrame-class
nrun,SpatialResults-method	SpatialResults-class
nrun,SpectralImagingData-method	SpectralImagingData-class
OPLS	SpatialPLS
OPLS,ANY-method	SpatialPLS
OPLS,SpectralImagingExperiment-method	SpatialPLS
PCA	SpatialPCA
PCA,ANY-method	SpatialPCA
PCA,SpectralImagingExperiment-method	SpatialPCA
pData,SpatialResults-method	SpatialResults-class
pData,SpectralImagingData-method	SpectralImagingData-class
pData<-,SpatialResults,ANY-method	SpatialResults-class
pData<-,SpectralImagingData,ANY-method	SpectralImagingData-class
peakAlign	peakAlign
peakAlign,MSImagingArrays-method	peakAlign
peakAlign,MSImagingExperiment-method	peakAlign
peakAlign,SpectralImagingArrays-method	peakAlign
peakAlign,SpectralImagingExperiment-method	peakAlign
peakBin	deprecated
peakData	deprecated
peakData<-	deprecated
peakFilter	deprecated
peakFilter,MSImagingExperiment-method	deprecated
peakPick	peakPick
peakPick,MSImagingArrays-method	peakPick
peakPick,MSImagingExperiment-method	peakPick
peakPick,SpectralImagingData-method	peakPick
peakPicking	deprecated
peakPicking<-	deprecated
peakProcess	peakProcess
peakProcess,MSImagingExperiment_OR_Arrays-method	peakProcess
pixelApply	deprecated
pixelApply,SpectralImagingExperiment-method	deprecated
pixelData	SpectralImagingData-class
pixelData,SpatialResults-method	SpatialResults-class
pixelData,SpectralImagingData-method	SpectralImagingData-class
pixelData<-	SpectralImagingData-class
pixelData<-,SpatialResults-method	SpatialResults-class
pixelData<-,SpectralImagingData-method	SpectralImagingData-class
pixelNames	SpectralImagingData-class
pixelNames,SpatialResults-method	SpatialResults-class
pixelNames,SpectralImagingData-method	SpectralImagingData-class
pixelNames<-	SpectralImagingData-class
pixelNames<-,SpatialResults-method	SpatialResults-class
pixelNames<-,SpectralImagingData-method	SpectralImagingData-class
pixels	pixels
pixels,SpectralImagingArrays-method	pixels
pixels,SpectralImagingData-method	pixels
pixels,SpectralImagingExperiment-method	pixels
pixelSize	deprecated
plot	plot-spectra
plot,MeansTest,missing-method	MeansTest
plot,MSImagingArrays,formula-method	plot-spectra
plot,MSImagingArrays,missing-method	plot-spectra
plot,MSImagingArrays,numeric-method	plot-spectra
plot,MSImagingExperiment,character-method	plot-spectra
plot,MSImagingExperiment,formula-method	plot-spectra
plot,MSImagingExperiment,missing-method	plot-spectra
plot,MSImagingExperiment,numeric-method	plot-spectra
plot,ResultsList,ANY-method	ResultsList-class
plot,ResultsList,missing-method	ResultsList-class
plot,SpatialDGMM,missing-method	SpatialDGMM
plot,SpatialFastmap,missing-method	SpatialFastmap
plot,SpatialKMeans,missing-method	SpatialKMeans
plot,SpatialNMF,missing-method	SpatialNMF
plot,SpatialOPLS,missing-method	SpatialPLS
plot,SpatialPCA,missing-method	SpatialPCA
plot,SpatialPLS,missing-method	SpatialPLS
plot,SpatialResults,ANY-method	SpatialResults-class
plot,SpatialShrunkenCentroids,missing-method	SpatialShrunkenCentroids
plot,SpectralImagingArrays,formula-method	plot-spectra
plot,SpectralImagingArrays,missing-method	plot-spectra
plot,SpectralImagingArrays,numeric-method	plot-spectra
plot,SpectralImagingExperiment,character-method	plot-spectra
plot,SpectralImagingExperiment,formula-method	plot-spectra
plot,SpectralImagingExperiment,missing-method	plot-spectra
plot,SpectralImagingExperiment,numeric-method	plot-spectra
plot,XDataFrame,character-method	plot-spectra
plot,XDataFrame,formula-method	plot-spectra
plot,XDataFrame,missing-method	plot-spectra
plot-image	plot-image
plot-spectra	plot-spectra
PLS	SpatialPLS
PLS,ANY-method	SpatialPLS
PLS,SpectralImagingExperiment-method	SpatialPLS
PositionDataFrame	PositionDataFrame-class
PositionDataFrame-class	PositionDataFrame-class
predict,ResultsList-method	ResultsList-class
predict,SpatialFastmap-method	SpatialFastmap
predict,SpatialNMF-method	SpatialNMF
predict,SpatialOPLS-method	SpatialPLS
predict,SpatialPCA-method	SpatialPCA
predict,SpatialPLS-method	SpatialPLS
predict,SpatialShrunkenCentroids-method	SpatialShrunkenCentroids
presetImageDef	simulateSpectra
process	process
process,MSImagingArrays-method	process
process,MSImagingExperiment-method	process
process,SpectralImagingArrays-method	process
process,SpectralImagingExperiment-method	process
processingData,SpectralImagingData-method	SpectralImagingData-class
processingData<-,SpectralImagingData-method	SpectralImagingData-class
rbind,MSImagingExperiment-method	MSImagingExperiment-class
rbind,SpectraArrays-method	SpectraArrays-class
rbind,SpectralImagingArrays-method	SpectralImagingArrays-class
rbind,SpectralImagingExperiment-method	SpectralImagingExperiment-class
rbind,XDataFrame-method	XDataFrame-class
readAnalyze	readMSIData
readImzML	readMSIData
readMSIData	readMSIData
recalibrate	recalibrate
recalibrate,MSImagingExperiment_OR_Arrays-method	recalibrate
recalibrate,SpectralImagingData-method	recalibrate
reduceBaseline	reduceBaseline
reduceBaseline,SpectralImagingData-method	reduceBaseline
reexports	reexports
reset	process
residuals,SpatialOPLS-method	SpatialPLS
resolution	deprecated
resolution<-	deprecated
resultData	deprecated
resultData<-	deprecated
resultNames	deprecated
resultNames<-	deprecated
ResultSet	deprecated
ResultSet-class	deprecated
ResultsList	ResultsList-class
ResultsList-class	ResultsList-class
risk.colors	deprecated
rowMeans,SpectralImagingExperiment-method	summarize
rownames,SpectralImagingExperiment-method	SpectralImagingExperiment-class
rownames<-,SpectralImagingExperiment-method	SpectralImagingExperiment-class
rowStats,SpectralImagingExperiment-method	summarize
rowSums,SpectralImagingExperiment-method	summarize
run	PositionDataFrame-class
run,PositionDataFrame-method	PositionDataFrame-class
run,SpatialResults-method	SpatialResults-class
run,SpectralImagingData-method	SpectralImagingData-class
run<-	PositionDataFrame-class
run<-,PositionDataFrame-method	PositionDataFrame-class
run<-,SpatialResults-method	SpatialResults-class
run<-,SpectralImagingData-method	SpectralImagingData-class
runNames	PositionDataFrame-class
runNames,PositionDataFrame-method	PositionDataFrame-class
runNames,SpatialResults-method	SpatialResults-class
runNames,SpectralImagingData-method	SpectralImagingData-class
runNames<-	PositionDataFrame-class
runNames<-,PositionDataFrame-method	PositionDataFrame-class
runNames<-,SpatialResults-method	SpatialResults-class
runNames<-,SpectralImagingData-method	SpectralImagingData-class
saveCardinalLog	Cardinal-package
scanDirection	deprecated
scanPattern	deprecated
scanPolarity	deprecated
scanType	deprecated
segmentationTest	MeansTest
selectROI	selectROI
selectROI,SpectralImagingExperiment-method	selectROI
setCardinalBPPARAM	Cardinal-package
setCardinalChunksize	Cardinal-package
setCardinalLogger	Cardinal-package
setCardinalNChunks	Cardinal-package
setCardinalNumBlocks	deprecated
setCardinalParallel	Cardinal-package
setCardinalSerialize	Cardinal-package
setCardinalVerbose	Cardinal-package
show,MSImagingArrays-method	MSImagingArrays-class
show,MSImagingExperiment-method	MSImagingExperiment-class
show,ResultsList-method	ResultsList-class
show,SpatialResults-method	SpatialResults-class
show,SpectraArrays-method	SpectraArrays-class
show,SpectralImagingArrays-method	SpectralImagingArrays-class
show,SpectralImagingData-method	SpectralImagingData-class
show,SpectralImagingExperiment-method	SpectralImagingExperiment-class
show,XDataFrame-method	XDataFrame-class
SImageData	deprecated
SImageData-class	deprecated
SImageSet	deprecated
SImageSet-class	deprecated
simulateImage	simulateSpectra
simulateSpectra	simulateSpectra
simulateSpectrum	deprecated
slice	deprecated
sliceImage	sliceImage
smooth	smooth
smooth,SpectralImagingData-method	smooth
smoothing	deprecated
smoothing<-	deprecated
smoothSignal	deprecated
smoothSignal,SpectralImagingExperiment-method	deprecated
SnowfastParam	reexports
spatialApply	deprecated
spatialApply,SpectralImagingExperiment-method	deprecated
SpatialCV	SpatialCV
SpatialCV-class	SpatialCV
SpatialDGMM	SpatialDGMM
spatialDGMM	SpatialDGMM
spatialDGMM,ANY-method	SpatialDGMM
spatialDGMM,SpectralImagingExperiment-method	SpatialDGMM
SpatialDGMM-class	SpatialDGMM
spatialDists	spatialDists
spatialDists,ANY-method	spatialDists
spatialDists,PositionDataFrame-method	spatialDists
spatialDists,SpectralImagingExperiment-method	spatialDists
SpatialFastmap	SpatialFastmap
spatialFastmap	SpatialFastmap
spatialFastmap,ANY-method	SpatialFastmap
spatialFastmap,SpectralImagingExperiment-method	SpatialFastmap
SpatialFastmap-class	SpatialFastmap
SpatialKMeans	SpatialKMeans
spatialKMeans	SpatialKMeans
spatialKMeans,ANY-method	SpatialKMeans
spatialKMeans,SpectralImagingExperiment-method	SpatialKMeans
SpatialKMeans-class	SpatialKMeans
SpatialNMF	SpatialNMF
SpatialNMF-class	SpatialNMF
SpatialOPLS	SpatialPLS
SpatialOPLS-class	SpatialPLS
SpatialPCA	SpatialPCA
SpatialPCA-class	SpatialPCA
SpatialPLS	SpatialPLS
SpatialPLS-class	SpatialPLS
SpatialResults	SpatialResults-class
SpatialResults-class	SpatialResults-class
SpatialShrunkenCentroids	SpatialShrunkenCentroids
spatialShrunkenCentroids	SpatialShrunkenCentroids
spatialShrunkenCentroids,ANY,ANY-method	SpatialShrunkenCentroids
spatialShrunkenCentroids,ANY,missing-method	SpatialShrunkenCentroids
spatialShrunkenCentroids,SpectralImagingExperiment,ANY-method	SpatialShrunkenCentroids
spatialShrunkenCentroids,SpectralImagingExperiment,missing-method	SpatialShrunkenCentroids
SpatialShrunkenCentroids-class	SpatialShrunkenCentroids
spatialWeights	spatialWeights
spatialWeights,ANY-method	spatialWeights
spatialWeights,PositionDataFrame-method	spatialWeights
spatialWeights,SpectralImagingExperiment-method	spatialWeights
spectra,SpectralImagingData-method	SpectralImagingData-class
spectra<-,SpectralImagingData-method	SpectralImagingData-class
SpectraArrays	SpectraArrays-class
SpectraArrays-class	SpectraArrays-class
spectraData,SpectralImagingData-method	SpectralImagingData-class
spectraData<-,SpectralImagingData-method	SpectralImagingData-class
SpectralImagingArrays	SpectralImagingArrays-class
SpectralImagingArrays-class	SpectralImagingArrays-class
SpectralImagingData	SpectralImagingData-class
SpectralImagingData-class	SpectralImagingData-class
SpectralImagingExperiment	SpectralImagingExperiment-class
SpectralImagingExperiment-class	SpectralImagingExperiment-class
spectraNames,SpectralImagingData-method	SpectralImagingData-class
spectraNames<-,SpectralImagingData-method	SpectralImagingData-class
spectrapply	spectrapply
spectrapply,SpectralImagingArrays-method	spectrapply
spectrapply,SpectralImagingExperiment-method	spectrapply
spectraVariables,SpectralImagingData-method	SpectralImagingData-class
spectrumRepresentation	deprecated
spectrumRepresentation<-	deprecated
subset,SpectralImagingArrays-method	subset
subset,SpectralImagingExperiment-method	subset
subsetFeatures	subset
subsetPixels	subset
summarizeFeatures	summarize
summarizePixels	summarize
topFeatures	SpatialShrunkenCentroids
topFeatures,MeansTest-method	MeansTest
topFeatures,ResultsList-method	ResultsList-class
topFeatures,SpatialKMeans-method	SpatialKMeans
topFeatures,SpatialOPLS-method	SpatialPLS
topFeatures,SpatialPLS-method	SpatialPLS
topFeatures,SpatialShrunkenCentroids-method	SpatialShrunkenCentroids
vizi_engine	Cardinal-package
vizi_par	Cardinal-package
vizi_style	Cardinal-package
vm_used,SpectraArrays-method	SpectraArrays-class
writeAnalyze	writeMSIData
writeAnalyze,MSImagingExperiment-method	writeMSIData
writeAnalyze,SpectralImagingExperiment-method	writeMSIData
writeImzML	writeMSIData
writeImzML,MSImagingExperiment_OR_Arrays-method	writeMSIData
writeMSIData	writeMSIData
XDataFrame	XDataFrame-class
XDataFrame-class	XDataFrame-class
XDFrame	XDataFrame-class
XDFrame-class	XDataFrame-class
[,MassDataFrame,ANY,ANY,ANY-method	MassDataFrame-class
[,PositionDataFrame,ANY,ANY,ANY-method	PositionDataFrame-class
[,SpectraArrays,ANY,ANY,ANY-method	SpectraArrays-class
[,SpectralImagingArrays,ANY,ANY,ANY-method	SpectralImagingArrays-class
[,SpectralImagingExperiment,ANY,ANY,ANY-method	SpectralImagingExperiment-class
[,XDataFrame,ANY,ANY,ANY-method	XDataFrame-class
[<-,SpectraArrays,ANY,ANY,ANY-method	SpectraArrays-class
[<-,SpectralImagingArrays,ANY,ANY,ANY-method	SpectralImagingArrays-class
[<-,SpectralImagingExperiment,ANY,ANY,ANY-method	SpectralImagingExperiment-class
[<-,XDataFrame,ANY,ANY,ANY-method	XDataFrame-class
[[,SpatialResults-method	SpatialResults-class
[[,SpectraArrays-method	SpectraArrays-class
[[,SpectralImagingData-method	SpectralImagingData-class
[[<-,SpectraArrays-method	SpectraArrays-class
[[<-,SpectralImagingData-method	SpectralImagingData-class
[[<-,XDataFrame-method	XDataFrame-class
