Cardinal-package	Cardinal-package
$,ImagingExperiment-method	ImagingExperiment-class
$,iSet-method	iSet-class
$,ResultImagingExperiment-method	ResultImagingExperiment-class
$,ResultSet-method	ResultSet-class
$<-,ImagingExperiment-method	ImagingExperiment-class
$<-,iSet-method	iSet-class
$<-,XDataFrame-method	XDataFrame-class
%>%	reexports
abstract,MIAPE-Imaging-method	MIAPE-Imaging-class
addShape	simulateSpectrum
alpha.colors	colors-functions
annotatedDataFrameFrom,ImageData-method	ImageData-class
arrange,DataFrame-method	dplyr-methods
arrange,SummaryDataFrame-method	dplyr-methods
arrange,XDataFrame-method	dplyr-methods
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	MSImageProcess-class
baselineReduction,MSImageProcess-method	MSImageProcess-class
baselineReduction,Vector-method	MSImagingInfo-class
baselineReduction<-	MSImageProcess-class
baselineReduction<-,MSImageProcess-method	MSImageProcess-class
baselineReduction<-,Vector-method	MSImagingInfo-class
batchProcess	batchProcess-methods
batchProcess,MSImageSet-method	batchProcess-methods
batchProcess-methods	batchProcess-methods
Binmat	deprecated
Binmat-class	deprecated
bw.colors	colors-functions
Cardinal	Cardinal-package
Cardinal-defunct	defunct
Cardinal-deprecated	deprecated
Cardinal-reexports	reexports
cbind,Hashmat-method	Hashmat-class
cbind,ImageArrayList-method	ImageList-class
cbind,MassDataFrame-method	MassDataFrame-class
cbind,MSImagingExperiment-method	MSImagingExperiment-class
cbind,PositionDataFrame-method	PositionDataFrame-class
cbind,SparseImagingExperiment-method	SparseImagingExperiment-class
cbind,SparseResultImagingExperiment-method	ResultImagingExperiment-class
cbind,XDataFrame-method	XDataFrame-class
centroided	MSImageProcess-class
centroided,MSImageProcess-method	MSImageProcess-class
centroided,MSImageSet-method	MSImageSet-class
centroided,MSImagingExperiment-method	MSImagingExperiment-class
centroided<-	MSImageProcess-class
centroided<-,MSImageProcess-method	MSImageProcess-class
centroided<-,MSImageSet-method	MSImageSet-class
centroided<-,MSImagingExperiment-method	MSImagingExperiment-class
cividis	reexports
class:Binmat	deprecated
class:Hashmat	Hashmat-class
class:IAnnotatedDataFrame	IAnnotatedDataFrame-class
class:ImageArrayList	ImageList-class
class:ImageData	ImageData-class
class:ImageList	ImageList-class
class:ImagingExperiment	ImagingExperiment-class
class:iSet	iSet-class
class:MassDataFrame	MassDataFrame-class
class:MeansTest	meansTest-methods
class:MIAPE-Imaging	MIAPE-Imaging-class
class:MSContinuousImagingExperiment	MSContinuousImagingExperiment-class
class:MSContinuousImagingSpectraList	ImageList-class
class:MSImageData	MSImageData-class
class:MSImageProcess	MSImageProcess-class
class:MSImageSet	MSImageSet-class
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:ResultImagingExperiment	ResultImagingExperiment-class
class:ResultSet	ResultSet-class
class:SegmentationTest	meansTest-methods
class:SImageData	SImageData-class
class:SImageSet	SImageSet-class
class:SimpleImageArrayList	ImageList-class
class:SimpleImageList	ImageList-class
class:SparseImagingExperiment	SparseImagingExperiment-class
class:SparseResultImagingExperiment	ResultImagingExperiment-class
class:SpatialDGMM	spatialDGMM-methods
class:spatialFastmap	spatialFastmap-methods
class:SpatialKMeans	spatialKMeans-methods
class:SpatialShrunkenCentroids	spatialShrunkenCentroids-methods
class:SummaryDataFrame	SummaryDataFrame-class
class:XDataFrame	XDataFrame-class
col.map	colors-functions
collect,MSImagingExperiment-method	MSImagingExperiment-class
collect,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
collect,SparseImagingExperiment-method	SparseImagingExperiment-class
colnames,Hashmat-method	Hashmat-class
colnames<-,Hashmat-method	Hashmat-class
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,array,array-method	ImageData-class
combine,Hashmat,Hashmat-method	Hashmat-class
combine,IAnnotatedDataFrame,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
combine,ImageData,ImageData-method	ImageData-class
combine,iSet,iSet-method	iSet-class
combine,MIAPE-Imaging,MIAPE-Imaging-method	MIAPE-Imaging-class
combine,MSImageProcess,MSImageProcess-method	MSImageProcess-class
combine,MSImageSet,MSImageSet-method	MSImageSet-class
combine,SImageData,SImageData-method	SImageData-class
combine,SImageSet,SImageSet-method	SImageSet-class
combine,SparseImagingExperiment,ANY-method	SparseImagingExperiment-class
combine,SparseResultImagingExperiment,ANY-method	ResultImagingExperiment-class
combine,vector,vector-method	ImageData-class
combiner,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
combiner,MSProcessedImagingSpectraList-method	MSProcessedImagingExperiment-class
combiner<-,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
combiner<-,MSProcessedImagingSpectraList-method	MSProcessedImagingExperiment-class
coord	PositionDataFrame-class
coord,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
coord,iSet-method	iSet-class
coord,PositionDataFrame-method	PositionDataFrame-class
coord,SImageData-method	SImageData-class
coord,SparseImagingExperiment-method	SparseImagingExperiment-class
coord-methods	PositionDataFrame-class
coord<-	PositionDataFrame-class
coord<-,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
coord<-,iSet-method	iSet-class
coord<-,PositionDataFrame-method	PositionDataFrame-class
coord<-,SImageData-method	SImageData-class
coord<-,SImageSet-method	SImageSet-class
coord<-,SparseImagingExperiment-method	SparseImagingExperiment-class
coordinates	PositionDataFrame-class
coordinates,PositionDataFrame-method	PositionDataFrame-class
coordinates,SparseImagingExperiment-method	SparseImagingExperiment-class
coordinates-methods	PositionDataFrame-class
coordinates<-	PositionDataFrame-class
coordinates<-,PositionDataFrame-method	PositionDataFrame-class
coordinates<-,SparseImagingExperiment-method	SparseImagingExperiment-class
coordLabels	PositionDataFrame-class
coordLabels,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
coordLabels,iSet-method	iSet-class
coordLabels,PositionDataFrame-method	PositionDataFrame-class
coordLabels,SparseImagingExperiment-method	SparseImagingExperiment-class
coordLabels-methods	PositionDataFrame-class
coordLabels<-	PositionDataFrame-class
coordLabels<-,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
coordLabels<-,iSet-method	iSet-class
coordLabels<-,PositionDataFrame-method	PositionDataFrame-class
coordLabels<-,SImageSet-method	SImageSet-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,ANY-method	PositionDataFrame-class
coordnames<-,SparseImagingExperiment,ANY-method	SparseImagingExperiment-class
coregister	coregister-methods
coregister,SpatialKMeans,missing-method	coregister-methods
coregister,SpatialShrunkenCentroids,missing-method	coregister-methods
coregister-methods	coregister-methods
crossValidate	cvApply-methods
crossValidate,MSImagingExperiment-method	cvApply-methods
crossValidate,SparseImagingExperiment-method	cvApply-methods
crossValidate-methods	cvApply-methods
cvApply	cvApply-methods
cvApply,SImageSet-method	cvApply-methods
cvApply,SparseImagingExperiment-method	cvApply-methods
cvApply-methods	cvApply-methods
darkmode	colors-functions
dim,Hashmat-method	Hashmat-class
dim,ImageData-method	ImageData-class
dim,ImageList-method	ImageList-class
dim,ImagingExperiment-method	ImagingExperiment-class
dim,iSet-method	iSet-class
dim,SImageData-method	SImageData-class
dim<-,Hashmat-method	Hashmat-class
dimnames,Hashmat-method	Hashmat-class
dimnames,ImagingExperiment-method	ImagingExperiment-class
dimnames<-,Hashmat,ANY-method	Hashmat-class
dimnames<-,Hashmat-method	Hashmat-class
dims,ImageData-method	ImageData-class
dims,ImageList-method	ImageList-class
dims,iSet-method	iSet-class
dims,PositionDataFrame-method	PositionDataFrame-class
dims,SImageData-method	SImageData-class
dims,SparseImagingExperiment-method	SparseImagingExperiment-class
discrete.colors	colors-functions
divergent.colors	colors-functions
embeddingMethod	MIAPE-Imaging-class
embeddingMethod,MIAPE-Imaging-method	MIAPE-Imaging-class
embeddingMethod<-	MIAPE-Imaging-class
embeddingMethod<-,MIAPE-Imaging-method	MIAPE-Imaging-class
experimentData,iSet-method	iSet-class
experimentData<-,iSet,ANY-method	iSet-class
expinfo,MIAPE-Imaging-method	MIAPE-Imaging-class
fData	ImagingExperiment-class
fData,ImagingExperiment-method	ImagingExperiment-class
fData,iSet-method	iSet-class
fData-methods	ImagingExperiment-class
fData<-	ImagingExperiment-class
fData<-,ImagingExperiment,ANY-method	ImagingExperiment-class
fData<-,ImagingExperiment-method	ImagingExperiment-class
fData<-,iSet,ANY-method	iSet-class
fData<-,iSet-method	iSet-class
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	iSet-class
featureData-methods	ImagingExperiment-class
featureData<-	ImagingExperiment-class
featureData<-,ImagingExperiment,ANY-method	ImagingExperiment-class
featureData<-,ImagingExperiment-method	ImagingExperiment-class
featureData<-,iSet,ANY-method	iSet-class
featureData<-,iSet-method	iSet-class
featureNames	ImagingExperiment-class
featureNames,ImagingExperiment-method	ImagingExperiment-class
featureNames,iSet-method	iSet-class
featureNames,SImageData-method	SImageData-class
featureNames-methods	ImagingExperiment-class
featureNames<-	ImagingExperiment-class
featureNames<-,ImagingExperiment-method	ImagingExperiment-class
featureNames<-,iSet-method	iSet-class
featureNames<-,SImageData-method	SImageData-class
featureNames<-,SImageSet-method	SImageSet-class
features	ImagingExperiment-class
features,ImagingExperiment-method	ImagingExperiment-class
features,iSet-method	iSet-class
features,MSImageSet-method	MSImageSet-class
features,MSImagingExperiment-method	MSImagingExperiment-class
features-methods	ImagingExperiment-class
files	MSImageProcess-class
files,MSImageProcess-method	MSImageProcess-class
files<-	MSImageProcess-class
files<-,MSImageProcess-method	MSImageProcess-class
filter	dplyr-methods
filter,DataFrame-method	dplyr-methods
filter,ImagingExperiment-method	dplyr-methods
filter,SummaryDataFrame-method	dplyr-methods
filter,XDataFrame-method	dplyr-methods
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	iSet-class
fvarLabels<-,iSet-method	iSet-class
fvarMetadata,iSet-method	iSet-class
fvarMetadata<-,iSet,ANY-method	iSet-class
fvarMetadata<-,iSet-method	iSet-class
generateImage	generateSpectrum
generateSpectrum	generateSpectrum
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	reexports
groups,XDataFrame-method	XDataFrame-class
group_by	reexports
group_by,DataFrame-method	dplyr-methods
group_by,XDataFrame-method	dplyr-methods
Hashmat	Hashmat-class
Hashmat-class	Hashmat-class
IAnnotatedDataFrame	IAnnotatedDataFrame-class
IAnnotatedDataFrame-class	IAnnotatedDataFrame-class
iData	ImagingExperiment-class
iData,ImagingExperiment,ANY-method	ImagingExperiment-class
iData,ImagingExperiment,missing-method	ImagingExperiment-class
iData,iSet-method	iSet-class
iData,SImageData,ANY-method	SImageData-class
iData,SImageSet,ANY-method	SImageSet-class
iData-methods	ImagingExperiment-class
iData<-	ImagingExperiment-class
iData<-,ImagingExperiment,ANY-method	ImagingExperiment-class
iData<-,ImagingExperiment,missing-method	ImagingExperiment-class
iData<-,iSet-method	iSet-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
iData<-,SImageData,ANY-method	SImageData-class
iData<-,SImageSet,ANY-method	SImageSet-class
image	image-methods
image,CrossValidated-method	image-methods
image,formula-method	image-methods
image,MSImageSet-method	image-methods
image,MSImagingExperiment-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,SparseResultImagingExperiment-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,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	ImageData-class
imageData	ImagingExperiment-class
imageData,ImagingExperiment-method	ImagingExperiment-class
imageData,iSet-method	iSet-class
imageData,MSImagingInfo-method	MSImagingInfo-class
ImageData-class	ImageData-class
imageData-methods	ImagingExperiment-class
imageData<-	ImagingExperiment-class
imageData<-,ImagingExperiment-method	ImagingExperiment-class
imageData<-,iSet-method	iSet-class
imageData<-,MSContinuousImagingExperiment-method	MSContinuousImagingExperiment-class
imageData<-,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
ImageList	ImageList-class
ImageList-class	ImageList-class
imageShape	MIAPE-Imaging-class
imageShape,MIAPE-Imaging-method	MIAPE-Imaging-class
imageShape<-	MIAPE-Imaging-class
imageShape<-,MIAPE-Imaging-method	MIAPE-Imaging-class
ImagingExperiment	ImagingExperiment-class
ImagingExperiment-class	ImagingExperiment-class
inferno	reexports
initialize,Hashmat-method	Hashmat-class
initialize,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
initialize,ImageData-method	ImageData-class
initialize,iSet-method	iSet-class
initialize,MassDataFrame-method	MassDataFrame-class
initialize,MSImageData-method	MSImageData-class
initialize,MSImageProcess-method	MSImageProcess-class
initialize,MSImageSet-method	MSImageSet-class
initialize,PositionDataFrame-method	PositionDataFrame-class
initialize,SImageData-method	SImageData-class
initialize,SImageSet-method	SImageSet-class
inSituChemistry	MIAPE-Imaging-class
inSituChemistry,MIAPE-Imaging-method	MIAPE-Imaging-class
inSituChemistry<-	MIAPE-Imaging-class
inSituChemistry<-,MIAPE-Imaging-method	MIAPE-Imaging-class
instrumentModel	MIAPE-Imaging-class
instrumentModel,MIAPE-Imaging-method	MIAPE-Imaging-class
instrumentModel,Vector-method	MSImagingInfo-class
instrumentModel<-	MIAPE-Imaging-class
instrumentModel<-,MIAPE-Imaging-method	MIAPE-Imaging-class
instrumentModel<-,Vector-method	MSImagingInfo-class
instrumentVendor	MIAPE-Imaging-class
instrumentVendor,MIAPE-Imaging-method	MIAPE-Imaging-class
instrumentVendor,Vector-method	MSImagingInfo-class
instrumentVendor<-	MIAPE-Imaging-class
instrumentVendor<-,MIAPE-Imaging-method	MIAPE-Imaging-class
instrumentVendor<-,Vector-method	MSImagingInfo-class
intensity.colors	colors-functions
ionizationType	MIAPE-Imaging-class
ionizationType,MIAPE-Imaging-method	MIAPE-Imaging-class
ionizationType,Vector-method	MSImagingInfo-class
ionizationType<-	MIAPE-Imaging-class
ionizationType<-,MIAPE-Imaging-method	MIAPE-Imaging-class
ionizationType<-,Vector-method	MSImagingInfo-class
iSet	iSet-class
iSet-class	iSet-class
jet.colors	colors-functions
keys	Hashmat-class
keys,Hashmat-method	Hashmat-class
keys,MSProcessedImagingSpectraList-method	MSProcessedImagingExperiment-class
keys<-	Hashmat-class
keys<-,Hashmat,character-method	Hashmat-class
keys<-,Hashmat,list-method	Hashmat-class
keys<-,Hashmat-method	Hashmat-class
keys<-,MSProcessedImagingSpectraList,ANY-method	MSProcessedImagingExperiment-class
lapply,XDataFrame-method	XDataFrame-class
length,ImageList-method	ImageList-class
length,ImagingExperiment-method	ImagingExperiment-class
length,iSet-method	iSet-class
length,MSImagingInfo-method	MSImagingInfo-class
length,ResultSet-method	ResultSet-class
length,XDataFrame-method	XDataFrame-class
lightmode	colors-functions
lineScanDirection	MIAPE-Imaging-class
lineScanDirection,MIAPE-Imaging-method	MIAPE-Imaging-class
lineScanDirection,Vector-method	MSImagingInfo-class
lineScanDirection<-	MIAPE-Imaging-class
lineScanDirection<-,MIAPE-Imaging-method	MIAPE-Imaging-class
lineScanDirection<-,Vector-method	MSImagingInfo-class
logLik,SpatialShrunkenCentroids-method	spatialShrunkenCentroids-methods
logLik,SpatialShrunkenCentroids2-method	spatialShrunkenCentroids-methods
magma	reexports
makeFactor	selectROI-methods
massAnalyzerType	MIAPE-Imaging-class
massAnalyzerType,MIAPE-Imaging-method	MIAPE-Imaging-class
massAnalyzerType,Vector-method	MSImagingInfo-class
massAnalyzerType<-	MIAPE-Imaging-class
massAnalyzerType<-,MIAPE-Imaging-method	MIAPE-Imaging-class
massAnalyzerType<-,Vector-method	MSImagingInfo-class
MassDataFrame	MassDataFrame-class
MassDataFrame-class	MassDataFrame-class
matrixApplication	MIAPE-Imaging-class
matrixApplication,MIAPE-Imaging-method	MIAPE-Imaging-class
matrixApplication,Vector-method	MSImagingInfo-class
matrixApplication<-	MIAPE-Imaging-class
matrixApplication<-,MIAPE-Imaging-method	MIAPE-Imaging-class
matrixApplication<-,Vector-method	MSImagingInfo-class
meansTest	meansTest-methods
meansTest,SparseImagingExperiment-method	meansTest-methods
MeansTest-class	meansTest-methods
meansTest-methods	meansTest-methods
MIAPE-Imaging	MIAPE-Imaging-class
MIAPE-Imaging-class	MIAPE-Imaging-class
modelData	ResultImagingExperiment-class
modelData,ResultImagingExperiment-method	ResultImagingExperiment-class
modelData,ResultSet-method	ResultSet-class
modelData<-	ResultImagingExperiment-class
modelData<-,ResultImagingExperiment-method	ResultImagingExperiment-class
modelData<-,ResultSet-method	ResultSet-class
MSContinuousImagingExperiment	MSContinuousImagingExperiment-class
MSContinuousImagingExperiment-class	MSContinuousImagingExperiment-class
MSContinuousImagingSpectraList	ImageList-class
MSContinuousImagingSpectraList-class	ImageList-class
msiInfo	MSImagingInfo-class
msiInfo,MIAPE-Imaging-method	MIAPE-Imaging-class
msiInfo,MSContinuousImagingExperiment-method	MSImagingInfo-class
msiInfo,MSImageSet-method	MSImagingInfo-class
msiInfo,MSImagingExperiment-method	MSImagingInfo-class
msiInfo,MSProcessedImagingExperiment-method	MSImagingInfo-class
MSImageData	MSImageData-class
MSImageData-class	MSImageData-class
MSImageProcess	MSImageProcess-class
MSImageProcess-class	MSImageProcess-class
MSImageSet	MSImageSet-class
MSImageSet-class	MSImageSet-class
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	dplyr-methods
mutate,DataFrame-method	dplyr-methods
mutate,ImagingExperiment-method	dplyr-methods
mutate,SummaryDataFrame-method	dplyr-methods
mutate,XDataFrame-method	dplyr-methods
mz	mz-methods
mz,MassDataFrame-method	MassDataFrame-class
mz,missing-method	mz-methods
mz,MSImageSet-method	MSImageSet-class
mz,MSImagingExperiment-method	MSImagingExperiment-class
mz-methods	mz-methods
mz<-	mz-methods
mz<-,MassDataFrame-method	MassDataFrame-class
mz<-,MSImageSet-method	MSImageSet-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,MSImageData-method	MSImageData-class
mzData,MSImagingInfo-method	MSImagingInfo-class
mzData,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
mzData,SImageData-method	SImageData-class
mzData-methods	MSProcessedImagingExperiment-class
mzData<-	MSProcessedImagingExperiment-class
mzData<-,MSImageData-method	MSImageData-class
mzData<-,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
mzData<-,SImageData-method	SImageData-class
mzFilter	peakFilter-methods
mzFilter,MSImagingExperiment-method	peakFilter-methods
mzFilter-methods	peakFilter-methods
names,ImageData-method	ImageData-class
names,ImageList-method	ImageList-class
names,ResultSet-method	ResultSet-class
names,XDataFrame-method	XDataFrame-class
names<-,ImageData-method	ImageData-class
names<-,ImageList-method	ImageList-class
normalization	MSImageProcess-class
normalization,MSImageProcess-method	MSImageProcess-class
normalization,Vector-method	MSImagingInfo-class
normalization<-	MSImageProcess-class
normalization<-,MSImageProcess-method	MSImageProcess-class
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	MIAPE-Imaging-class
notes<-,MIAPE-Imaging,character-method	MIAPE-Imaging-class
notes<-,MIAPE-Imaging,list-method	MIAPE-Imaging-class
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	MIAPE-Imaging-class
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	Hashmat-class
pData,ImagingExperiment-method	ImagingExperiment-class
pData,iSet-method	iSet-class
pData-methods	ImagingExperiment-class
pData<-	ImagingExperiment-class
pData<-,Hashmat,ANY-method	Hashmat-class
pData<-,Hashmat-method	Hashmat-class
pData<-,ImagingExperiment,ANY-method	ImagingExperiment-class
pData<-,ImagingExperiment-method	ImagingExperiment-class
pData<-,iSet,ANY-method	iSet-class
pData<-,iSet-method	iSet-class
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	MSProcessedImagingExperiment-class
peakData,MSImageData-method	MSImageData-class
peakData,MSImagingInfo-method	MSImagingInfo-class
peakData,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
peakData,SImageData-method	SImageData-class
peakData-methods	MSProcessedImagingExperiment-class
peakData<-	MSProcessedImagingExperiment-class
peakData<-,MSImageData-method	MSImageData-class
peakData<-,MSProcessedImagingExperiment-method	MSProcessedImagingExperiment-class
peakData<-,SImageData-method	SImageData-class
peakFilter	peakFilter-methods
peakFilter,MSImageSet-method	peakFilter-methods
peakFilter,MSImagingExperiment-method	peakFilter-methods
peakFilter-methods	peakFilter-methods
peakFilter.freq	peakFilter-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	MSImageProcess-class
peakPicking,MSImageProcess-method	MSImageProcess-class
peakPicking,Vector-method	MSImagingInfo-class
peakPicking<-	MSImageProcess-class
peakPicking<-,MSImageProcess-method	MSImageProcess-class
peakPicking<-,Vector-method	MSImagingInfo-class
peaks	MSImagingExperiment-class
peaks,MSImageSet-method	MSImageSet-class
peaks,MSImagingExperiment-method	MSImagingExperiment-class
peaks-methods	MSImagingExperiment-class
peaks<-	MSImagingExperiment-class
peaks<-,MSImageSet-method	MSImageSet-class
peaks<-,MSImagingExperiment-method	MSImagingExperiment-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	iSet-class
pixelData-methods	ImagingExperiment-class
pixelData<-	ImagingExperiment-class
pixelData<-,ImagingExperiment-method	ImagingExperiment-class
pixelData<-,iSet-method	iSet-class
pixelNames	ImagingExperiment-class
pixelNames,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
pixelNames,ImagingExperiment-method	ImagingExperiment-class
pixelNames,iSet-method	iSet-class
pixelNames,SImageData-method	SImageData-class
pixelNames-methods	ImagingExperiment-class
pixelNames<-	ImagingExperiment-class
pixelNames<-,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
pixelNames<-,ImagingExperiment-method	ImagingExperiment-class
pixelNames<-,iSet-method	iSet-class
pixelNames<-,SImageData-method	SImageData-class
pixelNames<-,SImageSet-method	SImageSet-class
pixels	ImagingExperiment-class
pixels,ImagingExperiment-method	ImagingExperiment-class
pixels,iSet-method	iSet-class
pixels,MSImageSet-method	MSImageSet-class
pixels,MSImagingExperiment-method	MSImagingExperiment-class
pixels-methods	ImagingExperiment-class
pixelSize	MIAPE-Imaging-class
pixelSize,MIAPE-Imaging-method	MIAPE-Imaging-class
pixelSize,Vector-method	MSImagingInfo-class
pixelSize<-	MIAPE-Imaging-class
pixelSize<-,MIAPE-Imaging-method	MIAPE-Imaging-class
pixelSize<-,Vector-method	MSImagingInfo-class
plasma	reexports
plot	plot-methods
plot,CrossValidated,missing-method	plot-methods
plot,DataFrame,ANY-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,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,SImageSet,formula-method	plot-methods
plot,SImageSet,missing-method	plot-methods
plot,SparseImagingExperiment,formula-method	plot-methods
plot,SparseImagingExperiment,missing-method	plot-methods
plot,SparseResultImagingExperiment,formula-method	plot-methods
plot,SparseResultImagingExperiment,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	cvApply-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	SImageData-class
positionArray,SImageData-method	SImageData-class
positionArray<-	SImageData-class
positionArray<-,SImageData-method	SImageData-class
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	MIAPE-Imaging-class
preproc,SparseImagingExperiment-method	SparseImagingExperiment-class
preproc<-,MIAPE-Imaging-method	MIAPE-Imaging-class
presetImageDef	simulateSpectrum
print.summary.CrossValidated	cvApply-methods
print.summary.iSet	iSet-class
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,SparseImagingExperiment-method	process-methods
process-methods	process-methods
processingData	MSImageSet-class
processingData,MSImageSet-method	MSImageSet-class
processingData,SparseImagingExperiment-method	SparseImagingExperiment-class
processingData-methods	MSImageSet-class
processingData<-	MSImageSet-class
processingData<-,MSImageSet-method	MSImageSet-class
processingData<-,SparseImagingExperiment-method	SparseImagingExperiment-class
prochistory	MSImageProcess-class
prochistory,MSImageProcess-method	MSImageProcess-class
prochistory<-	MSImageProcess-class
prochistory<-,MSImageProcess,character-method	MSImageProcess-class
prochistory<-,MSImageProcess,list-method	MSImageProcess-class
prochistory<-,MSImageProcess-method	MSImageProcess-class
protocolData,iSet-method	iSet-class
protocolData<-,iSet,ANY-method	iSet-class
pubMedIds,MIAPE-Imaging-method	MIAPE-Imaging-class
pubMedIds<-,MIAPE-Imaging,ANY-method	MIAPE-Imaging-class
rbind,Hashmat-method	Hashmat-class
rbind,ImageArrayList-method	ImageList-class
rbind,MassDataFrame-method	MassDataFrame-class
rbind,MSImagingExperiment-method	MSImagingExperiment-class
rbind,PositionDataFrame-method	PositionDataFrame-class
rbind,SparseImagingExperiment-method	SparseImagingExperiment-class
rbind,SparseResultImagingExperiment-method	ResultImagingExperiment-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	reduceDimension-methods
reduceDimension,MSImageSet,missing-method	reduceDimension-methods
reduceDimension,MSImageSet,MSImageSet-method	reduceDimension-methods
reduceDimension,MSImageSet,numeric-method	reduceDimension-methods
reduceDimension-methods	reduceDimension-methods
reduceDimension.bin	reduceDimension-methods
reduceDimension.peaks	reduceDimension-methods
reduceDimension.resample	reduceDimension-methods
regeneratePositions	SImageData-class
regeneratePositions,SImageData-method	SImageData-class
regeneratePositions,SImageSet-method	SImageSet-class
resolution	PositionDataFrame-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<-,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	ResultImagingExperiment-class
resultData,ResultImagingExperiment,ANY-method	ResultImagingExperiment-class
resultData,ResultImagingExperiment,missing-method	ResultImagingExperiment-class
resultData,ResultSet,ANY-method	ResultSet-class
resultData,ResultSet-method	ResultSet-class
resultData<-	ResultImagingExperiment-class
resultData<-,ResultImagingExperiment,ANY-method	ResultImagingExperiment-class
resultData<-,ResultImagingExperiment,missing-method	ResultImagingExperiment-class
resultData<-,ResultSet,missing-method	ResultSet-class
resultData<-,ResultSet-method	ResultSet-class
ResultImagingExperiment	ResultImagingExperiment-class
ResultImagingExperiment-class	ResultImagingExperiment-class
resultNames	ResultImagingExperiment-class
resultNames,ResultImagingExperiment-method	ResultImagingExperiment-class
resultNames<-	ResultImagingExperiment-class
ResultSet	ResultSet-class
ResultSet-class	ResultSet-class
risk.colors	colors-functions
rownames,Hashmat-method	Hashmat-class
rownames<-,Hashmat-method	Hashmat-class
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,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
sampleNames,iSet-method	iSet-class
sampleNames<-,IAnnotatedDataFrame,ANY-method	IAnnotatedDataFrame-class
sampleNames<-,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
sampleNames<-,iSet,ANY-method	iSet-class
sampleNames<-,iSet-method	iSet-class
samples,MIAPE-Imaging-method	MIAPE-Imaging-class
scanDirection	MIAPE-Imaging-class
scanDirection,MIAPE-Imaging-method	MIAPE-Imaging-class
scanDirection,Vector-method	MSImagingInfo-class
scanDirection<-	MIAPE-Imaging-class
scanDirection<-,MIAPE-Imaging-method	MIAPE-Imaging-class
scanDirection<-,Vector-method	MSImagingInfo-class
scanPattern	MIAPE-Imaging-class
scanPattern,MIAPE-Imaging-method	MIAPE-Imaging-class
scanPattern,Vector-method	MSImagingInfo-class
scanPattern<-	MIAPE-Imaging-class
scanPattern<-,MIAPE-Imaging-method	MIAPE-Imaging-class
scanPattern<-,Vector-method	MSImagingInfo-class
scanPolarity	MIAPE-Imaging-class
scanPolarity,MIAPE-Imaging-method	MIAPE-Imaging-class
scanPolarity,Vector-method	MSImagingInfo-class
scanPolarity<-	MIAPE-Imaging-class
scanPolarity<-,MIAPE-Imaging-method	MIAPE-Imaging-class
scanPolarity<-,Vector-method	MSImagingInfo-class
scans,MSImagingInfo-method	MSImagingInfo-class
scanType	MIAPE-Imaging-class
scanType,MIAPE-Imaging-method	MIAPE-Imaging-class
scanType,Vector-method	MSImagingInfo-class
scanType<-	MIAPE-Imaging-class
scanType<-,MIAPE-Imaging-method	MIAPE-Imaging-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
select	dplyr-methods
select,DataFrame-method	dplyr-methods
select,ImagingExperiment-method	dplyr-methods
select,SImageSet-method	defunct
select,SummaryDataFrame-method	dplyr-methods
select,XDataFrame-method	dplyr-methods
selectROI	selectROI-methods
selectROI,SImageSet-method	selectROI-methods
selectROI,SparseImagingExperiment-method	selectROI-methods
selectROI-methods	selectROI-methods
show,Hashmat-method	Hashmat-class
show,ImageData-method	ImageData-class
show,ImagingExperiment-method	ImagingExperiment-class
show,MIAPE-Imaging-method	MIAPE-Imaging-class
show,MSImageProcess-method	MSImageProcess-class
show,MSImagingExperiment-method	MSImagingExperiment-class
show,ResultImagingExperiment-method	ResultImagingExperiment-class
show,ResultSet-method	ResultSet-class
show,SimpleImageList-method	ImageList-class
show,SparseImagingExperiment-method	SparseImagingExperiment-class
show,SparseResultImagingExperiment-method	ResultImagingExperiment-class
show,SummaryDataFrame-method	SummaryDataFrame-class
show,XDataFrame-method	XDataFrame-class
showNames	XDataFrame-class
showNames,MassDataFrame-method	MassDataFrame-class
showNames,PositionDataFrame-method	PositionDataFrame-class
showNames,XDataFrame-method	XDataFrame-class
SImageData	SImageData-class
SImageData-class	SImageData-class
SImageSet	SImageSet-class
SImageSet-class	SImageSet-class
SimpleImageArrayList-class	ImageList-class
SimpleImageList-class	ImageList-class
simulateImage	simulateSpectrum
simulateSpectrum	simulateSpectrum
slice	slice-methods
slice,SparseImagingExperiment-method	slice-methods
smoothing	MSImageProcess-class
smoothing,MSImageProcess-method	MSImageProcess-class
smoothing,Vector-method	MSImagingInfo-class
smoothing<-	MSImageProcess-class
smoothing<-,MSImageProcess-method	MSImageProcess-class
smoothing<-,Vector-method	MSImagingInfo-class
smoothSignal	smoothSignal-methods.R
smoothSignal,MSImageSet-method	smoothSignal-methods.R
smoothSignal,SparseImagingExperiment-method	smoothSignal-methods.R
smoothSignal-methods	smoothSignal-methods.R
smoothSignal.gaussian	smoothSignal-methods.R
smoothSignal.ma	smoothSignal-methods.R
smoothSignal.sgolay	smoothSignal-methods.R
softwareName	MIAPE-Imaging-class
softwareName,MIAPE-Imaging-method	MIAPE-Imaging-class
softwareName<-	MIAPE-Imaging-class
softwareName<-,MIAPE-Imaging-method	MIAPE-Imaging-class
softwareVersion	MIAPE-Imaging-class
softwareVersion,MIAPE-Imaging-method	MIAPE-Imaging-class
softwareVersion<-	MIAPE-Imaging-class
softwareVersion<-,MIAPE-Imaging-method	MIAPE-Imaging-class
SparseImagingExperiment	SparseImagingExperiment-class
SparseImagingExperiment-class	SparseImagingExperiment-class
SparseResultImagingExperiment	ResultImagingExperiment-class
SparseResultImagingExperiment-class	ResultImagingExperiment-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	MIAPE-Imaging-class
specimenOrigin,MIAPE-Imaging-method	MIAPE-Imaging-class
specimenOrigin<-	MIAPE-Imaging-class
specimenOrigin<-,MIAPE-Imaging-method	MIAPE-Imaging-class
specimenType	MIAPE-Imaging-class
specimenType,MIAPE-Imaging-method	MIAPE-Imaging-class
specimenType<-	MIAPE-Imaging-class
specimenType<-,MIAPE-Imaging-method	MIAPE-Imaging-class
spectra	MSImagingExperiment-class
spectra,MSImageSet-method	MSImageSet-class
spectra,MSImagingExperiment-method	MSImagingExperiment-class
spectra-methods	MSImagingExperiment-class
spectra<-	MSImagingExperiment-class
spectra<-,MSImageSet-method	MSImageSet-class
spectra<-,MSImagingExperiment-method	MSImagingExperiment-class
spectrumRepresentation	MSImageProcess-class
spectrumRepresentation,MSImageProcess-method	MSImageProcess-class
spectrumRepresentation,Vector-method	MSImagingInfo-class
spectrumRepresentation<-	MSImageProcess-class
spectrumRepresentation<-,MSImageProcess-method	MSImageProcess-class
spectrumRepresentation<-,Vector-method	MSImagingInfo-class
stainingMethod	MIAPE-Imaging-class
stainingMethod,MIAPE-Imaging-method	MIAPE-Imaging-class
stainingMethod<-	MIAPE-Imaging-class
stainingMethod<-,MIAPE-Imaging-method	MIAPE-Imaging-class
standardizeRuns	standardizeRuns-methods
standardizeRuns,MSImageSet-method	standardizeRuns-methods
standardizeRuns-methods	standardizeRuns-methods
standardizeRuns.sum	standardizeRuns-methods
standardizeSamples	defunct
storageMode,ImageData-method	ImageData-class
storageMode,iSet-method	iSet-class
storageMode<-,ImageData,character-method	ImageData-class
storageMode<-,iSet,ANY-method	iSet-class
storageMode<-,iSet,character-method	iSet-class
summarize	dplyr-methods
summarize,DataFrame-method	dplyr-methods
summarize,SparseImagingExperiment-method	dplyr-methods
summarize,SummaryDataFrame-method	dplyr-methods
summarize,XDataFrame-method	dplyr-methods
summary,CrossValidated-method	cvApply-methods
summary,CrossValidated2-method	cvApply-methods
summary,iSet-method	iSet-class
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	SummaryDataFrame-class
SummaryDataFrame	SummaryDataFrame-class
SummaryDataFrame-class	SummaryDataFrame-class
tissueThickness	MIAPE-Imaging-class
tissueThickness,MIAPE-Imaging-method	MIAPE-Imaging-class
tissueThickness<-	MIAPE-Imaging-class
tissueThickness<-,MIAPE-Imaging-method	MIAPE-Imaging-class
tissueWash	MIAPE-Imaging-class
tissueWash,MIAPE-Imaging-method	MIAPE-Imaging-class
tissueWash<-	MIAPE-Imaging-class
tissueWash<-,MIAPE-Imaging-method	MIAPE-Imaging-class
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,SpatialShrunkenCentroids-method	topFeatures-methods
topFeatures,SpatialShrunkenCentroids2-method	topFeatures-methods
topFeatures-methods	topFeatures-methods
topLabels	deprecated
topLabels,ANY-method	deprecated
ungroup	reexports
ungroup,XDataFrame-method	dplyr-methods
varLabels,iSet-method	iSet-class
varLabels<-,iSet-method	iSet-class
varMetadata,iSet-method	iSet-class
varMetadata<-,iSet,ANY-method	iSet-class
varMetadata<-,iSet-method	iSet-class
viridis	reexports
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
[,Hashmat,ANY,ANY,ANY-method	Hashmat-class
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