Cardinal: A mass spectrometry imaging toolbox for statistical analysis

Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.

AuthorKylie A. Bemis <k.bemis@northeastern.edu>
Date of publicationNone
MaintainerKylie A. Bemis <k.bemis@northeastern.edu>
LicenseArtistic-2.0
Version1.6.0
http://www.cardinalmsi.org

View on Bioconductor

Man pages

batchProcess-methods: Batch Pre-Processing on an Imaging Dataset

Binmat-class: On-Disk Matrix Class Using On-Demand Disk Reads

Cardinal-package: Mass spectrometry imaging tools

colors-functions: Color Palettes for Imaging

coord-methods: Retrieve Pixel Coordinates from iSets

coregister-methods: Coregister Images

cvApply-methods: Apply Cross-Validated Analysis to Imaging Datasets

generateImage: Generate a Simulated Image

generateSpectrum: Generate a Simulated Spectrum

Hashmat-class: Sparse Matrix Class Using Lists as Hash Tables

IAnnotatedDataFrame-class: Class Containing Measured Variables and Their Meta-Data...

ImageData-class: Class Containing Arrays of Imaging Data

imageData-methods: Retrieve Image Data from iSets

image-methods: Plot the Pixel-Space of an Imaging Dataset

iSet-class: Class to Contain High-Throughput Imaging Experiment Data and...

MIAPE-Imaging-class: Class for Storing Mass Spectrometry Imaging Experiment...

MSImageData-class: Class Containing Mass Spectrometry Image Data

MSImageProcess-class: Class Containing Mass Spectral Pre-Processing Information

MSImageSet-class: Class to Contain Mass Spectrometry Imaging Experiment Data

mz-methods: Retrieve m/z-values from MSImageSets

normalize-methods: Normalize an Imaging Dataset

OPLS-methods: Orthogonal Partial Least Squares

PCA-methods: Principal Components Analysis

peakAlign-methods: Peak Align an Imaging Dataset

peakFilter-methods: Peak Filter an Imaging Dataset

peakPick-methods: Peak Pick an Imaging Dataset

pixelApply-methods: Apply Functions over Imaging Datasets

pixelData-methods: Retrieve Information on Pixels in iSet-derived Classes

pixelNames-methods: Retrieve Pixel Names from iSets

pixels-methods: Retrieve Pixel or Feature Indices Based on Metadata

plot-methods: Plot the Feature-Space of an Imaging Dataset

PLS-methods: Partial Least Squares

processingData-methods: Retrieve Pre-Processing Information from MSImageSets

readMSIData: Read Mass Spectrometry Imaging Data Files

reduceBaseline-methods: Reduce the Baseline for an Imaging Dataset

reduceDimension-methods: Reduce the Dimension of an Imaging Dataset

ResultSet-class: Class to Contain Analysis Results for Imaging Experiments

select-methods: Select Regions of an Imaging Dataset

SImageData-class: Class Containing Sparse Image Data

SImageSet-class: Class to Contain Pixel-Sparse Imaging Data

spatialKMeans-methods: Spatially-Aware K-Means Clustering

spatialShrunkenCentroids-methods: Spatially-Aware Shrunken Centroid Clustering and...

standardizeSamples-methods: Standardize the Samples in an Imaging Dataset

topLabels-methods: Retrieve Top-Ranked Labels from Analysis Results

Functions

abstract,MIAPE-Imaging-method Man page
alpha.colors Man page
annotatedDataFrameFrom,ImageData-method Man page
baselineReduction Man page
baselineReduction<- Man page
baselineReduction<-,MSImageProcess-method Man page
baselineReduction,MSImageProcess-method Man page
batchProcess Man page
batchProcess-methods Man page
batchProcess,MSImageSet-method Man page
Binmat Man page
[,Binmat,ANY,ANY,ANY-method Man page
Binmat-class Man page
[,Binmat-method Man page
Cardinal Man page
Cardinal-package Man page
cbind,Binmat-method Man page
cbind,Hashmat-method Man page
centroided Man page
centroided<- Man page
centroided<-,MSImageProcess-method Man page
centroided,MSImageProcess-method Man page
centroided<-,MSImageSet-method Man page
centroided,MSImageSet-method Man page
class:Binmat Man page
class:Hashmat Man page
class:IAnnotatedDataFrame Man page
class:ImageData Man page
class:iSet Man page
class:MIAPE-Imaging Man page
class:MSImageData Man page
class:MSImageProcess Man page
class:MSImageSet Man page
class:OPLS Man page
class:PCA Man page
class:PLS Man page
class:ResultSet Man page
class:SImageData Man page
class:SImageSet Man page
class:SpatialKMeans Man page
class:SpatialShrunkenCentroids Man page
colnames<-,Binmat-method Man page
colnames,Binmat-method Man page
colnames<-,Hashmat-method Man page
colnames,Hashmat-method Man page
combine,array,array-method Man page
combine,Hashmat,Hashmat-method Man page
combine,IAnnotatedDataFrame,IAnnotatedDataFrame-method Man page
combine,ImageData,ImageData-method Man page
combine,iSet,iSet-method Man page
combine,MIAPE-Imaging,MIAPE-Imaging-method Man page
combine,MSImageProcess,MSImageProcess-method Man page
combine,MSImageSet,MSImageSet-method Man page
combine,SImageData,SImageData-method Man page
combine,SImageSet,SImageSet-method Man page
coord Man page
coord<- Man page
coord<-,IAnnotatedDataFrame-method Man page
coord,IAnnotatedDataFrame-method Man page
coordinates Man page
coordinates<- Man page
coordinates-methods Man page
coord<-,iSet-method Man page
coord,iSet-method Man page
coordLabels Man page
coordLabels<- Man page
coordLabels<-,IAnnotatedDataFrame-method Man page
coordLabels,IAnnotatedDataFrame-method Man page
coordLabels<-,iSet-method Man page
coordLabels,iSet-method Man page
coordLabels-methods Man page
coordLabels<-,SImageSet-method Man page
coord-methods Man page
coord<-,SImageData-method Man page
coord,SImageData-method Man page
coord<-,SImageSet-method Man page
coregister Man page
coregister-methods Man page
coregister,SpatialKMeans,missing-method Man page
coregister,SpatialShrunkenCentroids,missing-method Man page
cvApply Man page
cvApply-methods Man page
cvApply,SImageSet-method Man page
dim<-,Binmat-method Man page
dim,Binmat-method Man page
dim<-,Hashmat-method Man page
dim,Hashmat-method Man page
dim,ImageData-method Man page
dim,iSet-method Man page
dimnames<-,Binmat,ANY-method Man page
dimnames<-,Binmat-method Man page
dimnames,Binmat-method Man page
dimnames<-,Hashmat,ANY-method Man page
dimnames<-,Hashmat-method Man page
dimnames,Hashmat-method Man page
dims,ImageData-method Man page
dim,SImageData-method Man page
dims,iSet-method Man page
dims,SImageData-method Man page
embeddingMethod Man page
embeddingMethod<- Man page
embeddingMethod<-,MIAPE-Imaging-method Man page
embeddingMethod,MIAPE-Imaging-method Man page
experimentData<-,iSet-method Man page
experimentData,iSet-method Man page
expinfo,MIAPE-Imaging-method Man page
fData<-,iSet,ANY-method Man page
fData<-,iSet-method Man page
fData,iSet-method Man page
featureApply Man page
featureApply-methods Man page
featureApply,SImageSet-method Man page
featureData<-,iSet,ANY-method Man page
featureData<-,iSet-method Man page
featureData,iSet-method Man page
featureNames<-,iSet-method Man page
featureNames,iSet-method Man page
featureNames<-,SImageData-method Man page
featureNames,SImageData-method Man page
featureNames<-,SImageSet-method Man page
features Man page
features,iSet-method Man page
features-methods Man page
features,MSImageSet-method Man page
files Man page
files<- Man page
files<-,MSImageProcess-method Man page
files,MSImageProcess-method Man page
fvarLabels<-,iSet-method Man page
fvarLabels,iSet-method Man page
fvarMetadata<-,iSet,ANY-method Man page
fvarMetadata<-,iSet-method Man page
fvarMetadata,iSet-method Man page
generateImage Man page
generateSpectrum Man page
gradient.colors Man page
Hashmat Man page
[<-,Hashmat,ANY,ANY,ANY-method Man page
[,Hashmat,ANY,ANY,ANY-method Man page
Hashmat-class Man page
[<-,Hashmat-method Man page
[,Hashmat-method Man page
IAnnotatedDataFrame Man page
[,IAnnotatedDataFrame,ANY,ANY,ANY-method Man page
IAnnotatedDataFrame-class Man page
iData Man page
iData<- Man page
iData<-,iSet-method Man page
iData,iSet-method Man page
iData-methods Man page
iData<-,SImageData-method Man page
iData,SImageData-method Man page
iData<-,SImageSet-method Man page
iData,SImageSet-method Man page
image Man page
image3D Man page
image3D-methods Man page
image3D,SImageSet-method Man page
image,CrossValidated-method Man page
imageData Man page
imageData<- Man page
ImageData Man page
[[<-,ImageData,character,missing-method Man page
[[,ImageData,character,missing-method Man page
ImageData-class Man page
imageData<-,iSet-method Man page
imageData,iSet-method Man page
[[<-,ImageData-method Man page
[[,ImageData-method Man page
imageData-methods Man page
image-methods Man page
image,MSImageSet-method Man page
image,OPLS-method Man page
image,PCA-method Man page
image,PLS-method Man page
image,ResultSet-method Man page
imageShape Man page
imageShape<- Man page
imageShape<-,MIAPE-Imaging-method Man page
imageShape,MIAPE-Imaging-method Man page
image,SImageSet-method Man page
image,SpatialKMeans-method Man page
image,SpatialShrunkenCentroids-method Man page
initialize,Binmat-method Man page
initialize,Hashmat-method Man page
initialize,IAnnotatedDataFrame-method Man page
initialize,ImageData-method Man page
initialize,iSet-method Man page
initialize,MSImageData-method Man page
initialize,MSImageProcess-method Man page
initialize,MSImageSet-method Man page
initialize,SImageData-method Man page
initialize,SImageSet-method Man page
inSituChemistry Man page
inSituChemistry<- Man page
inSituChemistry<-,MIAPE-Imaging-method Man page
inSituChemistry,MIAPE-Imaging-method Man page
instrumentModel Man page
instrumentModel<- Man page
instrumentModel<-,MIAPE-Imaging-method Man page
instrumentModel,MIAPE-Imaging-method Man page
instrumentVendor Man page
instrumentVendor<- Man page
instrumentVendor<-,MIAPE-Imaging-method Man page
instrumentVendor,MIAPE-Imaging-method Man page
intensity.colors Man page
ionizationType Man page
ionizationType<- Man page
ionizationType<-,MIAPE-Imaging-method Man page
ionizationType,MIAPE-Imaging-method Man page
iSet Man page
[[<-,iSet,ANY,ANY-method Man page
[[,iSet,ANY,ANY-method Man page
iSet-class Man page
[[<-,iSet-method Man page
[[,iSet-method Man page
$<-,iSet-method Man page
$,iSet-method Man page
keys Man page
keys<- Man page
keys<-,Hashmat,character-method Man page
keys<-,Hashmat,list-method Man page
keys<-,Hashmat-method Man page
keys,Hashmat-method Man page
length,ResultSet-method Man page
lineScanDirection Man page
lineScanDirection<- Man page
lineScanDirection<-,MIAPE-Imaging-method Man page
lineScanDirection,MIAPE-Imaging-method Man page
logLik,SpatialShrunkenCentroids-method Man page
massAnalyzerType Man page
massAnalyzerType<- Man page
massAnalyzerType<-,MIAPE-Imaging-method Man page
massAnalyzerType,MIAPE-Imaging-method Man page
matrixApplication Man page
matrixApplication<- Man page
matrixApplication<-,MIAPE-Imaging-method Man page
matrixApplication,MIAPE-Imaging-method Man page
MIAPE-Imaging Man page
MIAPE-Imaging-class Man page
modelData Man page
modelData<- Man page
modelData<-,ResultSet-method Man page
modelData,ResultSet-method Man page
msiInfo Man page
msiInfo,MIAPE-Imaging-method Man page
MSImageData Man page
MSImageData-class Man page
MSImageProcess Man page
MSImageProcess-class Man page
MSImageSet Man page
MSImageSet-class Man page
mz Man page
mz<- Man page
mzData Man page
mzData<- Man page
mzData-methods Man page
mzData<-,MSImageData-method Man page
mzData,MSImageData-method Man page
mzData<-,SImageData-method Man page
mzData,SImageData-method Man page
mz-methods Man page
mz<-,MSImageSet-method Man page
mz,MSImageSet-method Man page
names<-,ImageData-method Man page
names,ImageData-method Man page
names,ResultSet-method Man page
normalization Man page
normalization<- Man page
normalization<-,MSImageProcess-method Man page
normalization,MSImageProcess-method Man page
normalize Man page
normalize-methods Man page
normalize,MSImageSet-method Man page
normalize.tic Man page
notes<-,MIAPE-Imaging-method Man page
notes,MIAPE-Imaging-method Man page
OPLS Man page
OPLS-class Man page
OPLS-methods Man page
OPLS,SImageSet,character-method Man page
OPLS,SImageSet,factor-method Man page
OPLS,SImageSet,matrix-method Man page
OPLS,SImageSet,numeric-method Man page
otherInfo,MIAPE-Imaging-method Man page
PCA Man page
PCA-class Man page
PCA-methods Man page
PCA,SImageSet-method Man page
pData Man page
pData<- Man page
pData<-,Hashmat,ANY-method Man page
pData<-,Hashmat-method Man page
pData,Hashmat-method Man page
pData<-,iSet,ANY-method Man page
pData<-,iSet-method Man page
pData,iSet-method Man page
pData-methods Man page
peakAlign Man page
peakAlign.diff Man page
peakAlign.DP Man page
peakAlign-methods Man page
peakAlign,MSImageSet,missing-method Man page
peakAlign,MSImageSet,MSImageSet-method Man page
peakAlign,MSImageSet,numeric-method Man page
peakData Man page
peakData<- Man page
peakData-methods Man page
peakData<-,MSImageData-method Man page
peakData,MSImageData-method Man page
peakData<-,SImageData-method Man page
peakData,SImageData-method Man page
peakFilter Man page
peakFilter.freq Man page
peakFilter-methods Man page
peakFilter,MSImageSet-method Man page
peakPick Man page
peakPick.adaptive Man page
peakPicking Man page
peakPicking<- Man page
peakPicking<-,MSImageProcess-method Man page
peakPicking,MSImageProcess-method Man page
peakPick.limpic Man page
peakPick-methods Man page
peakPick,MSImageSet-method Man page
peakPick.simple Man page
peaks Man page
peaks<- Man page
peaks-methods Man page
peaks<-,MSImageSet-method Man page
peaks,MSImageSet-method Man page
pixelApply Man page
pixelApply-methods Man page
pixelApply,SImageSet-method Man page
pixelData Man page
pixelData<- Man page
pixelData<-,iSet-method Man page
pixelData,iSet-method Man page
pixelData-methods Man page
pixelNames Man page
pixelNames<- Man page
pixelNames<-,IAnnotatedDataFrame-method Man page
pixelNames,IAnnotatedDataFrame-method Man page
pixelNames<-,iSet-method Man page
pixelNames,iSet-method Man page
pixelNames-methods Man page
pixelNames<-,SImageData-method Man page
pixelNames,SImageData-method Man page
pixelNames<-,SImageSet-method Man page
pixels Man page
pixels,iSet-method Man page
pixelSize Man page
pixelSize<- Man page
pixelSize<-,MIAPE-Imaging-method Man page
pixelSize,MIAPE-Imaging-method Man page
pixels-methods Man page
pixels,MSImageSet-method Man page
plot Man page
plot,CrossValidated,missing-method Man page
plot-methods Man page
plot,MSImageSet,formula-method Man page
plot,MSImageSet,missing-method Man page
plot,OPLS,missing-method Man page
plot,PCA,missing-method Man page
plot,PLS,missing-method Man page
plot,ResultSet,formula-method Man page
plot,ResultSet,missing-method Man page
plot,SImageSet,formula-method Man page
plot,SImageSet,missing-method Man page
plot,SpatialKMeans,missing-method Man page
plot,SpatialShrunkenCentroids,missing-method Man page
plot.summary.CrossValidated Man page
plot.summary.OPLS Man page
plot.summary.PCA Man page
plot.summary.PLS Man page
plot.summary.SpatialKMeans Man page
plot.summary.SpatialShrunkenCentroids Man page
PLS Man page
PLS-class Man page
PLS-methods Man page
PLS,SImageSet,character-method Man page
PLS,SImageSet,factor-method Man page
PLS,SImageSet,matrix-method Man page
PLS,SImageSet,numeric-method Man page
positionArray Man page
positionArray<- Man page
positionArray<-,SImageData-method Man page
positionArray,SImageData-method Man page
predict,OPLS-method Man page
predict,PCA-method Man page
predict,PCA-method Man page
predict,PLS-method Man page
predict,SpatialShrunkenCentroids-method Man page
print.summary.CrossValidated Man page
print.summary.iSet Man page
print.summary.OPLS Man page
print.summary.PCA Man page
print.summary.PLS Man page
print.summary.SpatialKMeans Man page
print.summary.SpatialShrunkenCentroids Man page
processingData Man page
processingData<- Man page
processingData-methods Man page
processingData<-,MSImageSet-method Man page
processingData,MSImageSet-method Man page
prochistory Man page
prochistory<- Man page
prochistory<-,MSImageProcess,character-method Man page
prochistory<-,MSImageProcess,list-method Man page
prochistory<-,MSImageProcess-method Man page
prochistory,MSImageProcess-method Man page
protocolData<-,iSet-method Man page
protocolData,iSet-method Man page
pubMedIds<-,MIAPE-Imaging-method Man page
pubMedIds,MIAPE-Imaging-method Man page
rbind,Binmat-method Man page
rbind,Hashmat-method Man page
readAnalyze Man page
readImzML Man page
readMSIData Man page
reduceBaseline Man page
reduceBaseline.median Man page
reduceBaseline-methods Man page
reduceBaseline,MSImageSet-method Man page
reduceDimension Man page
reduceDimension.bin Man page
reduceDimension-methods Man page
reduceDimension,MSImageSet,missing-method Man page
reduceDimension,MSImageSet,MSImageSet-method Man page
reduceDimension,MSImageSet,numeric-method Man page
reduceDimension.peaks Man page
reduceDimension.resample Man page
regeneratePositions Man page
regeneratePositions,SImageData-method Man page
regeneratePositions,SImageSet-method Man page
resultData Man page
resultData<- Man page
resultData<-,ResultSet-method Man page
resultData,ResultSet-method Man page
ResultSet Man page
[,ResultSet,ANY,ANY,ANY-method Man page
[[,ResultSet,ANY,ANY-method Man page
ResultSet-class Man page
[,ResultSet-method Man page
[[,ResultSet-method Man page
$,ResultSet-method Man page
risk.colors Man page
rownames<-,Binmat-method Man page
rownames,Binmat-method Man page
rownames<-,Hashmat-method Man page
rownames,Hashmat-method Man page
sampleNames<-,IAnnotatedDataFrame,ANY-method Man page
sampleNames<-,IAnnotatedDataFrame-method Man page
sampleNames,IAnnotatedDataFrame-method Man page
sampleNames<-,iSet,ANY-method Man page
sampleNames<-,iSet-method Man page
sampleNames,iSet-method Man page
samples,MIAPE-Imaging-method Man page
scanDirection Man page
scanDirection<- Man page
scanDirection<-,MIAPE-Imaging-method Man page
scanDirection,MIAPE-Imaging-method Man page
scanPattern Man page
scanPattern<- Man page
scanPattern<-,MIAPE-Imaging-method Man page
scanPattern,MIAPE-Imaging-method Man page
scanPolarity Man page
scanPolarity<- Man page
scanPolarity<-,MIAPE-Imaging-method Man page
scanPolarity,MIAPE-Imaging-method Man page
scanType Man page
scanType<- Man page
scanType<-,MIAPE-Imaging-method Man page
scanType,MIAPE-Imaging-method Man page
select Man page
select-methods Man page
select,SImageSet-method Man page
show,Binmat-method Man page
show,Hashmat-method Man page
show,ImageData-method Man page
show,MIAPE-Imaging-method Man page
show,MSImageProcess-method Man page
show,ResultSet-method Man page
SImageData Man page
[,SImageData,ANY,ANY,ANY-method Man page
SImageData-class Man page
[,SImageData-method Man page
SImageSet Man page
[,SImageSet,ANY,ANY,ANY-method Man page
SImageSet-class Man page
[,SImageSet-method Man page
smoothing Man page
smoothing<- Man page
smoothing<-,MSImageProcess-method Man page
smoothing,MSImageProcess-method Man page
softwareName Man page
softwareName<- Man page
softwareName<-,MIAPE-Imaging-method Man page
softwareName,MIAPE-Imaging-method Man page
softwareVersion Man page
softwareVersion<- Man page
softwareVersion<-,MIAPE-Imaging-method Man page
softwareVersion,MIAPE-Imaging-method Man page
spatialKMeans Man page
SpatialKMeans-class Man page
spatialKMeans-methods Man page
spatialKMeans,SImageSet-method Man page
spatialShrunkenCentroids Man page
SpatialShrunkenCentroids-class Man page
spatialShrunkenCentroids-methods Man page
spatialShrunkenCentroids,SImageSet,character-method Man page
spatialShrunkenCentroids,SImageSet,factor-method Man page
spatialShrunkenCentroids,SImageSet,missing-method Man page
specimenOrigin Man page
specimenOrigin<- Man page
specimenOrigin<-,MIAPE-Imaging-method Man page
specimenOrigin,MIAPE-Imaging-method Man page
specimenType Man page
specimenType<- Man page
specimenType<-,MIAPE-Imaging-method Man page
specimenType,MIAPE-Imaging-method Man page
spectra Man page
spectra<- Man page
spectra-methods Man page
spectra<-,MSImageSet-method Man page
spectra,MSImageSet-method Man page
spectrumRepresentation Man page
spectrumRepresentation<- Man page
spectrumRepresentation<-,MSImageProcess-method Man page
spectrumRepresentation,MSImageProcess-method Man page
stainingMethod Man page
stainingMethod<- Man page
stainingMethod<-,MIAPE-Imaging-method Man page
stainingMethod,MIAPE-Imaging-method Man page
standardizeSamples Man page
standardizeSamples-methods Man page
standardizeSamples,MSImageSet-method Man page
standardizeSamples.sum Man page
storageMode<-,ImageData,character-method Man page
storageMode,ImageData-method Man page
storageMode<-,iSet,ANY-method Man page
storageMode<-,iSet,character-method Man page
storageMode,iSet-method Man page
summary,CrossValidated-method Man page
summary,iSet-method Man page
summary,OPLS-method Man page
summary,PCA-method Man page
summary,PLS-method Man page
summary,SpatialKMeans-method Man page
summary,SpatialShrunkenCentroids-method Man page
tissueThickness Man page
tissueThickness<- Man page
tissueThickness<-,MIAPE-Imaging-method Man page
tissueThickness,MIAPE-Imaging-method Man page
tissueWash Man page
tissueWash<- Man page
tissueWash<-,MIAPE-Imaging-method Man page
tissueWash,MIAPE-Imaging-method Man page
topLabels Man page
topLabels,CrossValidated-method Man page
topLabels-methods Man page
topLabels,OPLS-method Man page
topLabels,PCA-method Man page
topLabels,PLS-method Man page
topLabels,ResultSet-method Man page
topLabels,SpatialKMeans-method Man page
topLabels,SpatialShrunkenCentroids-method Man page
varLabels<-,iSet-method Man page
varLabels,iSet-method Man page
varMetadata<-,iSet,ANY-method Man page
varMetadata<-,iSet-method Man page
varMetadata,iSet-method Man page

Files

Cardinal/DESCRIPTION
Cardinal/NAMESPACE
Cardinal/NEWS
Cardinal/R
Cardinal/R/AllGenerics.R Cardinal/R/DataClasses.R Cardinal/R/analysis-OPLS.R Cardinal/R/analysis-PCA.R Cardinal/R/analysis-PLS.R Cardinal/R/analysis-spatialKMeans.R Cardinal/R/analysis-spatialShrunkenCentroids.R Cardinal/R/colors.R Cardinal/R/combine.R Cardinal/R/contrast.R Cardinal/R/coregister.R Cardinal/R/fastmap.R Cardinal/R/format.R Cardinal/R/generateImage.R Cardinal/R/generateSpectrum.R Cardinal/R/image3d.R Cardinal/R/interpolate.R Cardinal/R/log.R Cardinal/R/math.R Cardinal/R/methods-Binmat.R Cardinal/R/methods-Hashmat.R Cardinal/R/methods-IAnnotatedDataFrame.R Cardinal/R/methods-ImageData.R Cardinal/R/methods-MIAPE-Imaging.R Cardinal/R/methods-MSImageData.R Cardinal/R/methods-MSImageProcess.R Cardinal/R/methods-MSImageSet.R Cardinal/R/methods-ResultSet.R Cardinal/R/methods-SImageData.R Cardinal/R/methods-SImageSet.R Cardinal/R/methods-iSet.R Cardinal/R/nipals.R Cardinal/R/normalize.R Cardinal/R/plotting-MSImageSet.R Cardinal/R/plotting-ResultSet.R Cardinal/R/plotting-SImageSet.R Cardinal/R/processing-batchProcess.R Cardinal/R/processing-normalize.R Cardinal/R/processing-peakAlign.R Cardinal/R/processing-peakFilter.R Cardinal/R/processing-peakPick.R Cardinal/R/processing-reduceBaseline.R Cardinal/R/processing-reduceDimension.R Cardinal/R/processing-smoothSignal.R Cardinal/R/processing-standardizeSamples.R Cardinal/R/readAnalyze.R Cardinal/R/readImzML.R Cardinal/R/readMSIData.R Cardinal/R/smooth.R Cardinal/R/spatial.R Cardinal/R/summary.R Cardinal/R/topLabels.R Cardinal/R/utils.R Cardinal/R/zzz.R
Cardinal/README.md
Cardinal/TODO
Cardinal/build
Cardinal/build/vignette.rds
Cardinal/inst
Cardinal/inst/CITATION
Cardinal/inst/doc
Cardinal/inst/doc/Cardinal-development.R
Cardinal/inst/doc/Cardinal-development.Rnw
Cardinal/inst/doc/Cardinal-development.pdf
Cardinal/inst/doc/Cardinal-walkthrough.R
Cardinal/inst/doc/Cardinal-walkthrough.Rnw
Cardinal/inst/doc/Cardinal-walkthrough.pdf
Cardinal/inst/tests
Cardinal/man
Cardinal/man/Binmat-class.Rd Cardinal/man/Cardinal-package.Rd Cardinal/man/Hashmat-class.Rd Cardinal/man/IAnnotatedDataFrame-class.Rd Cardinal/man/ImageData-class.Rd Cardinal/man/MIAPE-Imaging-class.Rd Cardinal/man/MSImageData-class.Rd Cardinal/man/MSImageProcess-class.Rd Cardinal/man/MSImageSet-class.Rd Cardinal/man/OPLS-methods.Rd Cardinal/man/PCA-methods.Rd Cardinal/man/PLS-methods.Rd Cardinal/man/ResultSet-class.Rd Cardinal/man/SImageData-class.Rd Cardinal/man/SImageSet-class.Rd Cardinal/man/batchProcess-methods.Rd Cardinal/man/colors-functions.Rd Cardinal/man/coord-methods.Rd Cardinal/man/coregister-methods.Rd Cardinal/man/cvApply-methods.Rd Cardinal/man/generateImage.Rd Cardinal/man/generateSpectrum.Rd Cardinal/man/iSet-class.Rd Cardinal/man/image-methods.Rd Cardinal/man/imageData-methods.Rd Cardinal/man/mz-methods.Rd Cardinal/man/normalize-methods.Rd Cardinal/man/peakAlign-methods.Rd Cardinal/man/peakFilter-methods.Rd Cardinal/man/peakPick-methods.Rd Cardinal/man/pixelApply-methods.Rd Cardinal/man/pixelData-methods.Rd Cardinal/man/pixelNames-methods.Rd Cardinal/man/pixels-methods.Rd Cardinal/man/plot-methods.Rd Cardinal/man/processingData-methods.Rd Cardinal/man/readMSIData.Rd Cardinal/man/reduceBaseline-methods.Rd Cardinal/man/reduceDimension-methods.Rd Cardinal/man/select-methods.Rd
Cardinal/man/smoothSignal-methods.R.rd
Cardinal/man/spatialKMeans-methods.Rd Cardinal/man/spatialShrunkenCentroids-methods.Rd Cardinal/man/standardizeSamples-methods.Rd Cardinal/man/topLabels-methods.Rd
Cardinal/src
Cardinal/src/OBO-IMS.h
Cardinal/src/OBO-MS.h
Cardinal/src/OBO-UO.h
Cardinal/src/dynamicAlign.c
Cardinal/src/fastmap.c
Cardinal/src/fastmap.h
Cardinal/src/localMaxima.c
Cardinal/src/pugiconfig.h
Cardinal/src/pugixml.cpp
Cardinal/src/pugixml.h
Cardinal/src/readAnalyze.cpp
Cardinal/src/readImzML.cpp
Cardinal/src/smooth.c
Cardinal/src/spatial.c
Cardinal/src/utils.cpp
Cardinal/src/utils.h
Cardinal/tests
Cardinal/tests/testthat
Cardinal/tests/testthat.R
Cardinal/tests/testthat/test-Hashmat.R
Cardinal/tests/testthat/test-IAnnotatedDataFrame.R
Cardinal/tests/testthat/test-ImageData.R
Cardinal/tests/testthat/test-MIAPE-Imaging.R
Cardinal/tests/testthat/test-MSImageData.R
Cardinal/tests/testthat/test-MSImageProcess.R
Cardinal/tests/testthat/test-MSImageSet.R
Cardinal/tests/testthat/test-OPLS.R
Cardinal/tests/testthat/test-PCA.R
Cardinal/tests/testthat/test-PLS.R
Cardinal/tests/testthat/test-SImageData.R
Cardinal/tests/testthat/test-SImageSet.R
Cardinal/tests/testthat/test-fastmap.R
Cardinal/tests/testthat/test-generatePositionArray.R
Cardinal/tests/testthat/test-iSet.R
Cardinal/tests/testthat/test-nipals.R
Cardinal/tests/testthat/test-processing.R
Cardinal/tests/testthat/test-spatialKMeans.R
Cardinal/tests/testthat/test-spatialShrunkenCentroids.R
Cardinal/vignettes
Cardinal/vignettes/Cardinal-development.Rnw
Cardinal/vignettes/Cardinal-walkthrough.Rnw
Cardinal/vignettes/Cardinal.bib
Cardinal/vignettes/pig206-mz256.pdf
Cardinal/vignettes/pig206-optical.png
Cardinal/vignettes/pig206-sscg.pdf
Cardinal/vignettes/preprocessingRoughDraft.pdf
Cardinal/vignettes/rcc-MH0204_33.png
Cardinal/vignettes/rcc-mz810.pdf
Cardinal/vignettes/rcc-sscg.pdf

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