├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE.txt ├── NAMESPACE ├── R ├── AverageSpectrum.R ├── DataImportAndProcessWizard.R ├── DetectPeaks.R ├── ExportROISummary.R ├── LoadStorePeakMat.R ├── Process.R ├── RcppExports.R ├── ReferenceSpectrum.R ├── Smoothing.R ├── adductAnnotation.R ├── annotation.R ├── api.R ├── fileBrowseWidget.R ├── ggplot_additional_graphics.R ├── isotopeAnnotation.R ├── mass_calibration.R ├── peakList2imzML.R ├── plotPeakMatrix.R ├── rmsicdataio.R └── zzz.R ├── README.md ├── man ├── ArrangeMultipleImg2Plot.Rd ├── AverageSpectrum_rMSIproc.Rd ├── CPeakList2PeakMatrix.Rd ├── CalibrateImage.Rd ├── CalibrationWindow.Rd ├── DeisotopingOutputFormat.Rd ├── DetectPeaks.Rd ├── DetectPeaks_C.Rd ├── ExportROIAverages.Rd ├── ExportROIAveragesMultiple.Rd ├── ExportROIPeaks.Rd ├── FormatPeakMatrix.Rd ├── InternalReferenceSpectrum.Rd ├── InternalReferenceSpectrumMultipleDatasets.Rd ├── LoadPeakMatrix.Rd ├── LoadPeakMatrixC.Rd ├── MergePeakMatrices.Rd ├── MergeTwoMassAxis.Rd ├── MergerMSIDataSets.Rd ├── NoiseEstimationFFTCosWin.Rd ├── NoiseEstimationFFTCosWinMat.Rd ├── NoiseEstimationFFTExpWin.Rd ├── NoiseEstimationFFTExpWinMat.Rd ├── PeakList2PeakMatrix.Rd ├── ProcessImage.Rd ├── ProcessWizard.Rd ├── SaveProcessingParams.Rd ├── Smoothing.Rd ├── Smoothing_SavitzkyGolay.Rd ├── StorePeakMatrix.Rd ├── StorePeakMatrixC.Rd ├── TestAreaWindow.Rd ├── TestHanningWindow.Rd ├── TestPeakInterpolation_C.Rd ├── adductAnnotation.Rd ├── buildImgIdVectorFromPeakMatrix.Rd ├── calMzAxis.Rd ├── chemFormula2Expression.Rd ├── export_imzMLpeakList.Rd ├── getImgIdsFromPeakMatrixRows.Rd ├── getPeakMatrixRowsFromImgIds.Rd ├── getrMSIdataInfo.Rd ├── getrMSIdataInfoMultipleDataSets.Rd ├── hello.Rd ├── import_imzMLpeakList.Rd ├── isotopeAnnotation.Rd ├── loadDataCube.Rd ├── plot.rMSIprocPeakMatrix.Rd ├── plotClusterImage.Rd ├── plotClusterImageG.Rd ├── plotMassDriftComparedG.Rd ├── plotMassDriftG.Rd ├── plotMassDriftImageComparedG.Rd ├── plotMassDriftImageG.Rd ├── plotPeakImage.Rd ├── plotPeakImageG.Rd ├── plotValuesImage.Rd ├── plotValuesImageG.Rd ├── print.rMSIprocPeakMatrix.Rd ├── printrMSIdataInfo.Rd ├── rMSIannotation.Rd ├── rMSIproc.Rd ├── rcpp_hello.Rd ├── sub-.rMSIprocPeakMatrix.Rd ├── summary.rMSIprocPeakMatrix.Rd └── theme_black.Rd ├── rMSIproc.Rproj ├── rMSIproc_0.3.pdf ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp ├── adductannotation.cpp ├── adductannotation.h ├── fftw3_win │ ├── fftw3.f │ ├── fftw3.f03 │ ├── fftw3.h │ ├── fftw3l.f03 │ ├── fftw3q.f03 │ ├── lib32 │ │ └── libfftw3-3.dll │ └── lib64 │ │ └── libfftw3-3.dll ├── install.libs.R ├── isotopeannotation.cpp ├── isotopeannotation.h ├── labelfreealign.cpp ├── labelfreealign.h ├── mergeTwoMassAxes.cpp ├── mtaverage.cpp ├── mtaverage.h ├── mtbitdepthreduction.cpp ├── mtbitdepthreduction.h ├── mtlabelfreealign.cpp ├── mtlabelfreealign.h ├── mtpeakpicking.cpp ├── mtpeakpicking.h ├── mtreplacezeropeaks.cpp ├── mtreplacezeropeaks.h ├── mtsmoothing.cpp ├── mtsmoothing.h ├── 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