Files in sgibb/MALDIquant

Quantitative Analysis of Mass Spectrometry Data

.Rbuildignore

.editorconfig

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.github/workflows/codemeta-github-actions.yml

.github/workflows/test-coverage.yaml

.github/workflows/update-citation-cff.yaml

.gitignore

.lintr

CITATION.cff

DESCRIPTION

NAMESPACE

NEWS

R/AllClasses.R R/AllGenerics.R R/Deprecated.R R/alignSpectra-functions.R R/approxfun-methods.R R/as-methods.R R/as.list-functions.R R/as.matrix-functions.R R/as.matrix-methods.R R/averageMassSpectra-functions.R R/binPeaks-functions.R R/calculateLabelPositions-functions.R R/calibrateIntensity-functions.R R/calibrateIntensity-methods.R R/colMedians-functions.R R/constructor-functions.R R/coordinates-methods.R R/deprecated-functions.R R/detectPeaks-methods.R R/determineWarpingFunctions-functions.R R/doByLabels-functions.R R/estimateBaseline-functions.R R/estimateBaseline-methods.R R/estimateNoise-functions.R R/estimateNoise-methods.R R/filterPeaks-functions.R R/findEmptyMassObjects-functions.R R/findLocalMaxima-methods.R R/grouper-functions.R R/intensity-methods.R R/intensityMatrix-functions.R R/irregular-functions.R R/isEmpty-methods.R R/isFunctionList-functions.R R/isMassObject-functions.R R/isMassObjectList-functions.R R/isRegular-methods.R R/isValidHalfWindowSize-functions.R R/labelPeaks-methods.R R/lapply-functions.R R/length-methods.R R/lines-methods.R R/localMaxima-functions.R R/mapply-functions.R R/mass-methods.R R/match.closest-functions.R R/memoryUsage-functions.R R/merge-functions.R R/metaData-methods.R R/monoisotopic-functions.R R/monoisotopicPeaks-methods.R R/morphologicalFilter-functions.R R/msiSlices-functions.R R/mz-methods.R R/onAttach.R R/plot-methods.R R/plotMsiSlice-functions.R R/plotMsiSlice-methods.R R/points-methods.R R/range-functions.R R/referencePeaks-functions.R R/removeBaseline-methods.R R/removeEmptyMassObjects-functions.R R/reorder-functions.R R/replaceNegativeIntensityValues-functions.R R/show-functions.R R/show-methods.R R/smoothIntensity-methods.R R/smoothingFilters-functions.R R/snr-methods.R R/subset-methods.R R/totalIonCurrent-methods.R R/transformIntensity-methods.R R/trim-methods.R R/unlist-functions.R R/valid-methods.R R/warp-functions.R R/warpingFunction-functions.R README.md

codemeta.json

data/fiedler2009subset.RData

demo/00Index

demo/MALDIquant.R demo/baseline.R demo/peaks.R demo/warping.R demo/workflow.R

inst/CITATION

man/AbstractMassObject-class.Rd man/MALDIquant-defunct.Rd man/MALDIquant-deprecated.Rd man/MALDIquant-package.Rd man/MALDIquant-parallel.Rd man/MassPeaks-class.Rd man/MassSpectrum-class.Rd man/alignSpectra-functions.Rd man/averageMassSpectra-functions.Rd man/binPeaks-functions.Rd man/calibrateIntensity-methods.Rd man/createMassPeaks-functions.Rd man/createMassSpectrum-functions.Rd man/detectPeaks-methods.Rd man/determineWarpingFunctions-functions.Rd man/estimateBaseline-methods.Rd man/estimateNoise-methods.Rd man/fiedler2009subset.Rd man/filterPeaks-functions.Rd man/findEmptyMassObjects-functions.Rd man/intensityMatrix-functions.Rd man/isMassObject-functions.Rd man/isMassObjectList-functions.Rd man/labelPeaks-methods.Rd man/match.closest.Rd man/mergeMassPeaks-functions.Rd man/monoisotopicPeaks-methods.Rd man/msiSlices-functions.Rd man/plot-methods.Rd man/plotMsiSlice-methods.Rd man/referencePeaks-functions.Rd man/removeBaseline-methods.Rd man/smoothIntensity-methods.Rd man/transformIntensity-methods.Rd man/trim-methods.Rd man/warp-functions.Rd

src/MALDIquant.h

src/colMedians.c

src/init.c

src/localMaxima.c

src/lowerConvexHull.c

src/morphologicalFilters.c

src/snip.c

tests/testthat.R tests/testthat/test_alignSpectra-functions.R tests/testthat/test_approxfun-methods.R tests/testthat/test_as-methods.R tests/testthat/test_as.list-functions.R tests/testthat/test_as.matrix-functions.R tests/testthat/test_as.matrix-methods.R tests/testthat/test_averageMassSpectra-functions.R tests/testthat/test_binPeaks-functions.R tests/testthat/test_calculateLabelPositions-functions.R tests/testthat/test_calibrateIntensity-methods.R tests/testthat/test_colMedians-functions.R tests/testthat/test_constructor-functions.R tests/testthat/test_coordinates-methods.R tests/testthat/test_deprecated-functions.R tests/testthat/test_detectPeaks-methods.R tests/testthat/test_determineWarpingFunctions-functions.R tests/testthat/test_doByLabel-functions.R tests/testthat/test_estimateBaseline-methods.R tests/testthat/test_estimateNoise-methods.R tests/testthat/test_filterPeaks-functions.R tests/testthat/test_findEmptyMassObjects-functions.R tests/testthat/test_findLocalMaximaLogical-methods.R tests/testthat/test_grouper-functions.R tests/testthat/test_intensity-methods.R tests/testthat/test_intensityMatrix-functions.R tests/testthat/test_irregular-functions.R tests/testthat/test_isEmpty-methods.R tests/testthat/test_isMassObject-functions.R tests/testthat/test_isMassObjectList-functions.R tests/testthat/test_isRegular-methods.R tests/testthat/test_labelPeaks-methods.R tests/testthat/test_length-methods.R tests/testthat/test_localMaxima-functions.R tests/testthat/test_mapply-functions.R tests/testthat/test_mass-methods.R tests/testthat/test_match.closest-functions.R tests/testthat/test_merge-functions.R tests/testthat/test_metaData-methods.R tests/testthat/test_monoisotopic-functions.R tests/testthat/test_monoisotopicPeaks-methods.R tests/testthat/test_morphologicalFilter-functions.R tests/testthat/test_msiSlices-functions.R tests/testthat/test_mz-methods.R tests/testthat/test_plotMsiSlice-functions.R tests/testthat/test_plotMsiSlice-methods.R tests/testthat/test_range-functions.R tests/testthat/test_referencePeaks-functions.R tests/testthat/test_removeBaseline-methods.R tests/testthat/test_removeEmptyMassObjects-functions.R tests/testthat/test_reorder.R tests/testthat/test_replaceNegativeIntensityValues.R tests/testthat/test_show-methods.R tests/testthat/test_smoothIntensity-methods.R tests/testthat/test_smoothingFilters-functions.R tests/testthat/test_snr-methods.R tests/testthat/test_subset-methods.R tests/testthat/test_totalIonCurrent-methods.R tests/testthat/test_transformIntensity-methods.R tests/testthat/test_trim-methods.R tests/testthat/test_unlist-functions.R tests/testthat/test_valid-functions.R tests/testthat/test_warp-functions.R tests/testthat/test_warpingFunctions-functions.R

vignettes/MALDIquant-intro.Rnw

vignettes/bibliography.bib

sgibb/MALDIquant documentation built on Jan. 26, 2024, 10:04 a.m.