Files in Bioconductor-mirror/xcms
LC/MS and GC/MS Data Analysis

.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/AllGenerics.R R/DataClasses.R R/Deprecated.R R/MPI.R R/c.R R/cwTools.R R/databases.R R/do_adjustRtime-functions.R R/do_findChromPeaks-functions.R R/do_groupChromPeaks-functions.R R/fastMatch.R R/functions-IO.R R/functions-MsFeatureData.R R/functions-OnDiskMSnExp.R R/functions-Params.R R/functions-ProcessHistory.R R/functions-XCMSnExp.R R/functions-binning.R R/functions-normalization.R R/functions-utils.R R/functions-xcmsEIC.R R/functions-xcmsFragments.R R/functions-xcmsRaw.R R/functions-xcmsSet.R R/init.R R/matchpeaks.R R/methods-IO.R R/methods-MsFeatureData.R R/methods-OnDiskMSnExp.R R/methods-Params.R R/methods-ProcessHistory.R R/methods-XCMSnExp.R R/methods-netCdfSource.R R/methods-rampSource.R R/methods-xcmsEIC.R R/methods-xcmsFileSource.R R/methods-xcmsFragments.R R/methods-xcmsPeaks.R R/methods-xcmsRaw.R R/methods-xcmsSet.R R/models.R R/msn2xcmsRaw.R R/mzClust.R R/netCDF.R R/plotQC.R R/ramp.R R/specDist.R R/write.mzquantML.R R/writemzdata.R R/writemztab.R R/xcmsSource.R R/zzz.R
inst/CHANGELOG
inst/CITATION
inst/NEWS
inst/unitTests/Makefile
inst/unitTests/mzQuantML_1_0_0.xsd
inst/unitTests/runit.BiocParallel.R inst/unitTests/runit.Chromatogram.R inst/unitTests/runit.Param-classes.R inst/unitTests/runit.XCMSnExp.R inst/unitTests/runit.absentPresent.R inst/unitTests/runit.binning.R inst/unitTests/runit.calibrate.R inst/unitTests/runit.createProfileMatrix.R inst/unitTests/runit.diffreport.R inst/unitTests/runit.do_adjustRtime.R inst/unitTests/runit.do_findChromPeaks_MSW.R inst/unitTests/runit.do_findChromPeaks_centWave.R inst/unitTests/runit.do_findChromPeaks_centWave_isotopes.R inst/unitTests/runit.do_findChromPeaks_massifquant.R inst/unitTests/runit.do_findChromPeaks_matchedFilter.R inst/unitTests/runit.do_groupChromPeaks.R inst/unitTests/runit.fillChromPeaks.R inst/unitTests/runit.fillPeaks.R inst/unitTests/runit.findPeaksCentWave.R inst/unitTests/runit.findPeaksCentWave.fitGauss.plot.R inst/unitTests/runit.findPeaksCentWaveWithIsotopeROIs.R inst/unitTests/runit.findPeaksMassIfQuant.R inst/unitTests/runit.functions-IO.R inst/unitTests/runit.functions-XCMSnExp.R inst/unitTests/runit.functions-normalization.R inst/unitTests/runit.functions-utils.R inst/unitTests/runit.getEIC.R inst/unitTests/runit.getXcmsRaw.R inst/unitTests/runit.group.R inst/unitTests/runit.matchpeaks.R inst/unitTests/runit.msms.R inst/unitTests/runit.new_read_data.R inst/unitTests/runit.new_scanrange_subsetting.R inst/unitTests/runit.obiwarp.R inst/unitTests/runit.phenoData.R inst/unitTests/runit.processHistory.R inst/unitTests/runit.profStepPad.R inst/unitTests/runit.ramp.R inst/unitTests/runit.rawMat.R inst/unitTests/runit.sampclass.R inst/unitTests/runit.scanrage.R inst/unitTests/runit.snames.R inst/unitTests/runit.specDist.R inst/unitTests/runit.splitCombine.R inst/unitTests/runit.splitRaw.R inst/unitTests/runit.stopOnError.R inst/unitTests/runit.subset_extraction.R inst/unitTests/runit.unusedGroups.R inst/unitTests/runit.updateObject.R inst/unitTests/runit.useOriginalCode.R inst/unitTests/runit.writecdf.R inst/unitTests/runit.writemzdata.R inst/unitTests/runit.writemzquantml.R inst/unitTests/runit.xcmsRawCopy.R inst/unitTests/runit.xcmsSet.R man/AutoLockMass-methods.Rd man/GenericParam.Rd man/ProcessHistory-class.Rd man/SSgauss.Rd man/XCMSnExp-class.Rd man/XCMSnExp-filter-methods.Rd man/XCMSnExp-inherited-methods.Rd man/XCMSnExp-peak-grouping-results.Rd man/absent-methods.Rd man/adjustRtime-obiwarp.Rd man/adjustRtime-peakGroups.Rd man/adjustRtime.Rd man/binYonX.Rd man/breaks_on_binSize.Rd man/breaks_on_nBins.Rd man/c.xcmsSet.Rd man/calibrate-calibrant-mass.Rd man/calibrate.Rd man/chromatogram-method.Rd man/chromatographic-peak-detection.Rd man/colMax.Rd man/collect-methods.Rd man/descendZero.Rd man/diffreport-methods.Rd man/do_adjustRtime_peakGroups.Rd man/do_findChromPeaks_centWave.Rd man/do_findChromPeaks_centWaveWithPredIsoROIs.Rd man/do_findChromPeaks_massifquant.Rd man/do_findChromPeaks_matchedFilter.Rd man/do_findPeaks_MSW.Rd man/do_groupChromPeaks_density.Rd man/do_groupChromPeaks_nearest.Rd man/do_groupPeaks_mzClust.Rd man/doubleMatrix.Rd man/etg.Rd man/extractMsData-method.Rd man/fillChromPeaks.Rd man/fillPeaks-methods.Rd man/fillPeaks.MSW-methods.Rd man/fillPeaks.chrom-methods.Rd man/filtfft.Rd man/findChromPeaks-centWave.Rd man/findChromPeaks-centWaveWithPredIsoROIs.Rd man/findChromPeaks-massifquant.Rd man/findChromPeaks-matchedFilter.Rd man/findEqualGreater.Rd man/findMZ.Rd man/findPeaks-MSW.Rd man/findPeaks-methods.Rd man/findPeaks.MS1-methods.Rd man/findPeaks.MSW-xcmsRaw-method.Rd man/findPeaks.addPredictedIsotopeFeatures-methods.Rd man/findPeaks.centWave-methods.Rd man/findPeaks.centWaveWithPredictedIsotopeROIs-methods.Rd man/findPeaks.massifquant-methods.Rd man/findPeaks.matchedFilter-xcmsRaw-method.Rd man/findneutral.Rd man/getEIC-methods.Rd man/getPeaks-methods.Rd man/getScan-methods.Rd man/getSpec-methods.Rd man/getXcmsRaw-methods.Rd man/group-methods.Rd man/group.density.Rd man/group.mzClust.Rd man/group.nearest.Rd man/groupChromPeaks-density.Rd man/groupChromPeaks-mzClust.Rd man/groupChromPeaks-nearest.Rd man/groupChromPeaks.Rd man/groupnames-methods.Rd man/groupval-methods.Rd man/highlightChromPeaks.Rd man/image.xcmsRaw.Rd man/imputeLinInterpol.Rd man/levelplot.xcmsRaw.Rd man/loadRaw-methods.Rd man/medianFilter.Rd man/msn2xcmsRaw.Rd man/na.flatfill.Rd man/panel.cor.Rd man/peakPlots-methods.Rd man/peakTable-methods.Rd man/phenoDataFromPaths.Rd man/plot.xcmsEIC.Rd man/plotAdjustedRtime.Rd man/plotChrom-methods.Rd man/plotChromPeakDensity.Rd man/plotChromPeaks.Rd man/plotEIC-methods.Rd man/plotPeaks-methods.Rd man/plotQC.Rd man/plotRaw-methods.Rd man/plotScan-methods.Rd man/plotSpec-methods.Rd man/plotSurf-methods.Rd man/plotTIC-methods.Rd man/plotrt-methods.Rd man/profGenerate.Rd man/profMat-xcmsSet.Rd man/profMedFilt-methods.Rd man/profMethod-methods.Rd man/profRange-methods.Rd man/profStep-methods.Rd man/pval.Rd man/rawEIC-methods.Rd man/rawMat-methods.Rd man/rectUnique.Rd man/retcor-methods.Rd man/retcor.obiwarp-methods.Rd man/retcor.peakgroups-methods.Rd man/retexp.Rd man/sampnames-methods.Rd man/showError-xcmsSet-method.Rd man/specDist-methods.Rd man/specDist.cosine-methods.Rd man/specDist.meanMZmatch-methods.Rd man/specDist.peakCount-methods.Rd man/specNoise.Rd man/specPeaks.Rd man/split.xcmsRaw.Rd man/split.xcmsSet.Rd man/stitch-methods.Rd man/sub-xcmsRaw-logicalOrNumeric-missing-missing-method.Rd man/updateObject-xcmsSet-method.Rd man/useOriginalCode.Rd man/verify.mzQuantML.Rd man/write.cdf-methods.Rd man/write.mzQuantML.Rd man/write.mzdata-methods.Rd man/writeMzTab.Rd man/xcms-deprecated.Rd man/xcmsEIC-class.Rd man/xcmsFileSource-class.Rd man/xcmsFragments-class.Rd man/xcmsFragments.Rd man/xcmsPapply.Rd man/xcmsPeaks-class.Rd man/xcmsRaw-class.Rd man/xcmsRaw.Rd man/xcmsSet-class.Rd man/xcmsSet.Rd man/xcmsSource-class.Rd man/xcmsSource-methods.Rd
readme.org
src/Makevars
src/Makevars.win
src/binarySearch.h
src/binners.c
src/binners.h
src/fastMatch.c
src/massifquant/DataKeeper.cpp
src/massifquant/DataKeeper.h
src/massifquant/OpOverload.cpp
src/massifquant/OpOverload.h
src/massifquant/SegProc.cpp
src/massifquant/SegProc.h
src/massifquant/TrMgr.cpp
src/massifquant/TrMgr.h
src/massifquant/Tracker.cpp
src/massifquant/Tracker.h
src/massifquant/dpq.h
src/massifquant/nmath.h
src/massifquant/xcms_massifquant.cpp
src/mzClust_hclust.c
src/mzROI.c
src/obiwarp/lmat.h
src/obiwarp/mat.cpp
src/obiwarp/mat.h
src/obiwarp/vec.cpp
src/obiwarp/vec.h
src/obiwarp/xcms_dynprog.cpp
src/obiwarp/xcms_dynprog.h
src/obiwarp/xcms_lmat.cpp
src/util.c
src/util.h
src/xcms.c
src/xcms.h
src/xcms_obiwarp.cpp
tests/doRUnit.R
vignettes/FlowChart.graffle
vignettes/FlowChart.pdf
vignettes/benchmarking.Rmd-notrun
vignettes/biomed-central.csl
vignettes/new_functionality.Rmd
vignettes/new_functionality.org
vignettes/references.bib
vignettes/xcms-direct-injection.Rmd
vignettes/xcms.bib
vignettes/xcms.org
vignettes/xcmsMSn.Rnw
vignettes/xcmsPreprocess.Rnw-notrun
Bioconductor-mirror/xcms documentation built on Aug. 10, 2017, 11:01 a.m.