Cardinal: A mass spectrometry imaging toolbox for statistical analysis

Share:

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

Author
Kylie A. Bemis <k.bemis@northeastern.edu>
Date of publication
None
Maintainer
Kylie A. Bemis <k.bemis@northeastern.edu>
License
Artistic-2.0
Version
1.6.0
URLs

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

Files in this package

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