Files in Cardinal

A mass spectrometry imaging toolbox for statistical analysis

README.md R/process-normalize.R R/selectROI.R R/process2-peakAlign.R R/methods-ResultSet.R R/image2-ImagingResult.R R/image2-AnnotatedImage.R R/plot2-AnnotatedImagingExperiment.R R/facet-raster.R R/stats-spatialShrunkenCentroids.R R/image2-formula.R R/tools2-slice.R R/fastmap.R R/plot2-AnnotatedImage.R R/methods-IAnnotatedDataFrame.R R/process-reduceBaseline.R R/stats2-spatialDGMM.R R/methods2-PositionDataFrame.R R/tools2-subset.R R/apply-pixelApply.R R/image3d.R R/methods-MIAPE-Imaging.R R/methods2-MassDataFrame.R R/generateSpectrum.R R/methods2-MSContinuousImagingSpectraList.R R/process2-mzBin.R R/logger.R R/process2-reduceBaseline.R R/parseFormula2.R R/apply-crossValidate.R R/stats2-spatialKMeans.R R/process2-process.R R/readAnalyze.R R/plot-SImageSet.R R/tools2-colocalized.R R/image2-PositionDataFrame.R R/facet-count.R R/stats-spatialFastmap.R R/AllGenerics.R R/plot2-ImagingResult.R R/dplyr-mutate.R R/tools-topFeatures.R R/methods2-ImagingExperiment.R R/plot2-DataFrame.R R/methods2-ImagingResult.R R/methods2-AnnotatedImage.R R/facet-plot.R R/utils.R R/plot-MSImageSet.R R/methods-SImageData.R R/stats-PLS.R R/plot2-utils.R R/dplyr-group_by.R R/stats2-PCA.R R/readImzML.R R/process2-peakPick.R R/tools2-topFeatures.R R/readMSIData.R R/process-peakFilter.R R/methods-iSet.R R/dplyr-summarize.R R/process-peakPick.R R/image-MSImageSet.R R/mz.R R/plot2-MSImagingExperiment.R R/methods-SImageSet.R R/generateImage.R R/plot2-SparseImagingExperiment.R R/image2-SparseImagingExperiment.R R/methods-MSImageProcess.R R/nipals.R R/methods2-AnnotatedImageList.R R/colors.R R/apply-spatialApply.R R/dplyr-slice.R R/apply-featureApply.R R/methods2-MSContinuousImagingExperiment.R R/process-batchProcess.R R/methods-ImageData.R R/process2-peakBin.R R/writeAnalyze.R R/options.R R/DataClasses2.R R/DIP.R R/stats2-meansTest.R R/process-standardizeRuns.R R/stats2-PLS.R R/methods2-ImageList.R R/process2-mzAlign.R R/tools2-summary.R R/stats2-segmentationTest.R R/zzz.R R/spatial.R R/methods2-SparseImagingExperiment.R R/methods2-SummaryDataFrame.R R/process2-smoothSignal.R R/image-SImageSet.R R/plot-ResultSet.R R/methods2-MSImagingInfo.R R/stats2-spatialShrunkenCentroids.R R/tools2-aggregate.R R/dplyr-filter.R R/methods-Hashmat.R R/process-smoothSignal.R R/parseFormula.R R/dplyr-arrange.R R/process2-mzFilter.R R/utils2.R R/stats-spatialKMeans.R R/tools-summary.R R/facet-image.R R/methods2-MSProcessedImagingSpectraList.R R/writeImzML.R R/methods2-MSImagingExperiment.R R/methods-MSImageData.R R/methods2-ImageArrayList.R R/tools-coregister.R R/methods2-XDataFrame.R R/image2-MSImagingExperiment.R R/methods-MSImageSet.R R/dplyr-select.R R/process-peakAlign.R R/simulateSpectrum.R R/facet-boxplot.R R/plot2-ImagingSummary.R R/stats-PCA.R R/DataClasses.R R/methods2-AnnotatedImagingExperiment.R R/process2-normalize.R R/image2-ImagingSummary.R R/stats2-spatialFastmap.R R/process-reduceDimension.R R/simulateImage.R R/writeMSIData.R R/image2-AnnotatedImagingExperiment.R R/image-ResultSet.R R/methods2-MSProcessedImagingExperiment.R vignettes/rcc-mz810.pdf vignettes/Cardinal-2-stats.Rmd vignettes/pig206-mz256.pdf vignettes/rcc-sscg.pdf vignettes/Cardinal-2-guide.Rmd vignettes/pig206-sscg.pdf man/crossValidate-methods.Rd man/peakAlign-methods.Rd man/mzAlign-methods.Rd man/ImageList-class.Rd man/deprecated.Rd man/spatialKMeans-methods.Rd man/simulateSpectrum.Rd man/subset-methods.Rd man/colocalized-methods.Rd man/Cardinal-package.Rd man/ImagingResult-class.Rd man/normalize-methods.Rd man/pixelApply-methods.Rd man/internal.Rd man/colors-functions.Rd man/ImagingExperiment-class.Rd man/defunct.Rd man/readMSIData.Rd man/MSImagingExperiment-class.Rd man/reexports.Rd man/peakBin-methods.Rd man/topFeatures-methods.Rd man/findNeighbors-methods.Rd man/spatialShrunkenCentroids-methods.Rd man/PLS-methods.Rd man/mzFilter-methods.Rd man/legacy.Rd man/mz-methods.Rd man/PositionDataFrame-class.Rd man/selectROI-methods.Rd man/aggregate-methods.Rd man/MSContinuousImagingExperiment-class.Rd man/spatialFastmap-methods.Rd man/PCA-methods.Rd man/XDataFrame-class.Rd man/MSProcessedImagingExperiment-class.Rd man/spatialDGMM-methods.Rd man/MSImagingInfo-class.Rd man/meansTest-methods.Rd man/slice-methods.Rd man/peakPick-methods.Rd man/mzBin-methods.Rd man/reduceBaseline-methods.Rd man/SparseImagingExperiment-class.Rd man/writeMSIData.Rd man/plot-methods.Rd man/MassDataFrame-class.Rd man/smoothSignal-methods.Rd man/AnnotatedImagingExperiment-class.Rd man/process-methods.Rd man/image-methods.Rd man/AnnotatedImage-class.Rd tests/testthat.R tests/testthat/test-apply.R tests/testthat/test-io.R tests/testthat/test-AnnotatedImageList.R tests/testthat/test-ImageList.R tests/testthat/test-PositionDataFrame.R tests/testthat/test-ImageArrayList.R tests/testthat/test-AnnotatedImagingExperiment.R tests/testthat/test-stats.R tests/testthat/test-ImagingExperiment.R tests/testthat/test-MassDataFrame.R tests/testthat/test-SparseImagingExperiment.R tests/testthat/test-processing.R tests/testthat/test-MSImagingExperiment.R tests/testthat/test-manip.R tests/testthat/test-XDataFrame.R inst/doc/Cardinal-2-stats.Rmd inst/doc/Cardinal-2-guide.Rmd inst/doc/Cardinal-2-guide.R inst/doc/Cardinal-2-stats.R