CAMERA: Collection of annotation related methods for mass spectrometry data

Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments

AuthorCarsten Kuhl, Ralf Tautenhahn, Hendrik Treutler, Steffen Neumann {ckuhl|htreutle|sneumann}@ipb-halle.de, rtautenh@scripps.edu
Date of publicationNone
MaintainerSteffen Neumann <sneumann@ipb-halle.de>
LicenseGPL (>= 2)
Version1.30.0
http://msbi.ipb-halle.de/msbi/CAMERA/

View on Bioconductor

Man pages

annotateDiffreport: Automatic deconvolution/annotation of LC/ESI-MS data

annotate-methods: Automatic deconvolution/annotation of LC/ESI-MS data

calcCaS-methods: EIC correlation grouping of LC/ESI-MS data

calcCiS-methods: Calculate peak distance matrix after EIC correlation

calcIsotopes-methods: Calculate isotope distance matrix from xsAnnotate object

calcPC.hcs-methods: Peakclustering into pseudospectra with the highly connected...

calcPC.lpc-methods: Peakclustering into pseudospectra with the...

calcPC-methods: Peakclustering into pseudospectra according to a distance...

cleanParallel: Cleans up with spawned slave processes after use

combinexsAnnos: Check CAMERA ion species annotation due to matching with...

compoundLibraries: The supported compound databases

compoundQuantiles: compoundQuantiles constructor

compoundQuantiles-class: Class compoundQuantiles encapsulates compound statistics from...

findAdducts-methods: Calculate Adducts and Annotate LC/ESI-MS Spectra

findIsotopes-methods: Deconvolute/Annotate LC/ESI-MS data

findIsotopesWithValidation-methods: Deconvolute/Annotate LC/ESI-MS data

findKendrickMasses: Find specfic mass defects using Kendrick mass scales

findNeutralLoss: Find pseudospectra that contains a specific neutral loss

findNeutralLossSpecs: Find pseudospectra that contains a specific neutral loss

getAllPeakEICs-methods: Generate EIC information from raw data

getAtomCount-compoundQuantiles-method: The number of atoms of the given element

getIsotopeCluster: Retrieve the annotatad isotopes

getIsotopeProportion-compoundQuantiles-method: The proportion of the intensities of two isotope peaks

getPeaklist-methods: Generate the annotatad peaklist

getpspectra: Retrieve a peaklist of one or more pseudospectra

groupCorr-methods: EIC correlation grouping of LC/ESI-MS data

groupDen-methods: Density-Grouping of LC/ESI-MS data

groupFWHM-methods: FWHM-Grouping of LC/ESI-MS data

massWindowSizes: The supported mass window sizes

mm14: Extract of marker mixture 14 LC/MS data

plotEIC.xsAnnotate: Plot extracted ion chromatograms from (multiple)...

plotPsSpectrum.xsAnnotate: Plot a Pseudospectrum

psDist-methods: Distance methods for xsAnnotate

pspec2metfrag: Export the putative fragments as MetFrag query files

ruleSet-class: Class 'ruleSet'

xsAnnotate: xsAnnotate constructor for an provided xcmsSet object

xsAnnotate-class: Class xsAnnotate, a class for annotated peak data

Functions

annotate Man page
annotateDiffreport Man page
annotateDiffreport,xsAnnotate-methods Man page
annotate,xcmsSet-method Man page
calcCaS Man page
calcCaS,xsAnnotate-method Man page
calcCiS Man page
calcCiS,xsAnnotate-method Man page
calcIsotopes Man page
calcIsotopes,xsAnnotate-method Man page
calcPC Man page
calcPC,calcPC-method Man page
calcPC.hcs Man page
calcPC.hcs,xsAnnotate-method Man page
calcPC.lpc Man page
calcPC.lpc,xsAnnotate-method Man page
calcPC,xsAnnotate-method Man page
class:ruleSet Man page
cleanParallel Man page
combinexsAnnos Man page
compoundLibraries Man page
compoundQuantiles Man page
compoundQuantiles-class Man page
findAdducts Man page
findAdducts,xsAnnotate-method Man page
findIsotopes Man page
findIsotopesWithValidation Man page
findIsotopesWithValidation,xsAnnotate-method Man page
findIsotopes,xsAnnotate-method Man page
findKendrickMasses Man page
findNeutralLoss Man page
findNeutralLossSpecs Man page
generateRules Man page
generateRules,ruleSet-method Man page
getAllPeakEICs Man page
getAllPeakEICs,xsAnnotate-method Man page
getAtomCount Man page
getAtomCount,compoundQuantiles-method Man page
getIsotopeCluster Man page
getIsotopeProportion Man page
getIsotopeProportion,compoundQuantiles-method Man page
getPeaklist Man page
getPeaklist,xsAnnotate-method Man page
getpspectra Man page
groupCorr Man page
groupCorr,xsAnnotate-method Man page
groupDen Man page
groupDen,xsAnnotate-method Man page
groupFWHM Man page
groupFWHM,xsAnnotate-method Man page
massWindowSizes Man page
mm14 Man page
plotEICs Man page
plotEICs.xsAnnotate Man page
plotEICs,xsAnnotate-method Man page
plotPsSpectrum Man page
plotPsSpectrum.xsAnnotate Man page
plotPsSpectrum,xsAnnotate-method Man page
psDist Man page
psDist,CAMERA-method Man page
psDist-methods Man page
pspec2metfrag Man page
pspec2metfusion Man page
readLists Man page
readLists,ruleSet-method Man page
ruleSet-class Man page
setDefaultLists Man page
setDefaultLists,ruleSet-method Man page
setDefaultParams Man page
setDefaultParams,ruleSet-method Man page
setParams Man page
setParams,ruleSet,numeric,numeric,numeric,numeric,numeric,numeri Man page
show,ruleSet-method Man page
show,xsAnnotate-method Man page
xsAnnotate Man page
xsAnnotate-class Man page

Files

CAMERA/.travis.yml
CAMERA/DESCRIPTION
CAMERA/NAMESPACE
CAMERA/R
CAMERA/R/00xsAnnotate.R CAMERA/R/compoundQuantiles.R CAMERA/R/fastMatch.R CAMERA/R/fct_findAdducts.R CAMERA/R/fct_findIsotopes.R CAMERA/R/fct_findIsotopesWithValidation.R CAMERA/R/fct_groupCorr.R CAMERA/R/init.R CAMERA/R/psDist.R CAMERA/R/pspec2metfrag.R CAMERA/R/ruleSet.R
CAMERA/R/unix
CAMERA/R/windows
CAMERA/R/xsAnnotate.R CAMERA/R/xsVisualise.R CAMERA/R/zzz.R
CAMERA/README.md
CAMERA/build
CAMERA/build/vignette.rds
CAMERA/data
CAMERA/data/mm14.rda
CAMERA/inst
CAMERA/inst/CITATION
CAMERA/inst/NEWS
CAMERA/inst/ONEWS
CAMERA/inst/doc
CAMERA/inst/doc/CAMERA.R
CAMERA/inst/doc/CAMERA.Rnw
CAMERA/inst/doc/CAMERA.pdf
CAMERA/inst/doc/IsotopeDetectionVignette.Rnw
CAMERA/inst/doc/IsotopeDetectionVignette.pdf
CAMERA/inst/doc/compoundQuantilesVignette.Rnw
CAMERA/inst/doc/compoundQuantilesVignette.pdf
CAMERA/inst/lists
CAMERA/inst/lists/ions.csv
CAMERA/inst/lists/neutraladdition.csv
CAMERA/inst/lists/neutralloss.csv
CAMERA/inst/mzdata
CAMERA/inst/mzdata/MM14.mzdata
CAMERA/inst/quantiles
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/Br_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/C_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/Cl_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/F_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/H_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/I_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/IsotopeQuantiles__iso_1.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/IsotopeQuantiles__iso_2.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/IsotopeQuantiles__iso_3.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/IsotopeQuantiles__iso_4.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/IsotopeQuantiles__iso_5.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/N_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/O_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/P_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/S_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/Si_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_10/Unknown_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/Br_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/C_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/Cl_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/F_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/H_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/I_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/IsotopeQuantiles__iso_1.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/IsotopeQuantiles__iso_2.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/IsotopeQuantiles__iso_3.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/IsotopeQuantiles__iso_4.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/IsotopeQuantiles__iso_5.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/N_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/O_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/P_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/S_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/Si_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_100/Unknown_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/Br_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/C_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/Cl_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/F_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/H_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/I_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/IsotopeQuantiles__iso_1.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/IsotopeQuantiles__iso_2.tsv
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CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/P_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/S_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/Si_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_25/Unknown_quantiles.tsv
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CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/Cl_quantiles.tsv
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CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/I_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/IsotopeQuantiles__iso_1.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/IsotopeQuantiles__iso_2.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/IsotopeQuantiles__iso_3.tsv
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CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/N_quantiles.tsv
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CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/S_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/Si_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_250/Unknown_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50
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CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/C_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/Cl_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/F_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/H_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/I_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/IsotopeQuantiles__iso_1.tsv
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CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/O_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/P_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/S_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/Si_quantiles.tsv
CAMERA/inst/quantiles/lib_LipidMaps__maxDa_500/windowSize_50/Unknown_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/Br_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/C_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/Cl_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/F_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/H_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/I_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/IsotopeQuantiles__iso_1.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/IsotopeQuantiles__iso_2.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/IsotopeQuantiles__iso_3.tsv
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CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/N_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/O_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/P_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/S_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/Si_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_10/Unknown_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_100
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CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/Cl_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/F_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/H_quantiles.tsv
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CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/IsotopeQuantiles__iso_1.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/IsotopeQuantiles__iso_2.tsv
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CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/O_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/P_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/S_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_100/Si_quantiles.tsv
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CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/C_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/Cl_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/F_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/H_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/I_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/IsotopeQuantiles__iso_1.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/IsotopeQuantiles__iso_2.tsv
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CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/N_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/O_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/P_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/S_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/Si_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_25/Unknown_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/Br_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/C_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/Cl_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/F_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/H_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/I_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/IsotopeQuantiles__iso_1.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/IsotopeQuantiles__iso_2.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/IsotopeQuantiles__iso_3.tsv
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CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/IsotopeQuantiles__iso_5.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/N_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/O_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/P_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/S_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/Si_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_250/Unknown_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_50
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/Br_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/C_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/Cl_quantiles.tsv
CAMERA/inst/quantiles/lib_chebi__maxDa_1000/windowSize_50/F_quantiles.tsv
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CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_25/H_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_25/I_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_25/IsotopeQuantiles__iso_1.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_25/IsotopeQuantiles__iso_2.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_25/IsotopeQuantiles__iso_3.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_25/IsotopeQuantiles__iso_4.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_25/IsotopeQuantiles__iso_5.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_25/N_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_25/O_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_25/P_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_25/S_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_25/Si_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_25/Unknown_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/Br_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/C_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/Cl_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/F_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/H_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/I_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/IsotopeQuantiles__iso_1.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/IsotopeQuantiles__iso_2.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/IsotopeQuantiles__iso_3.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/IsotopeQuantiles__iso_4.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/IsotopeQuantiles__iso_5.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/N_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/O_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/P_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/S_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/Si_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_250/Unknown_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/Br_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/C_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/Cl_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/F_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/H_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/I_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/IsotopeQuantiles__iso_1.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/IsotopeQuantiles__iso_2.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/IsotopeQuantiles__iso_3.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/IsotopeQuantiles__iso_4.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/IsotopeQuantiles__iso_5.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/N_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/O_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/P_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/S_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/Si_quantiles.tsv
CAMERA/inst/quantiles/lib_pubchem__maxDa_3000/windowSize_50/Unknown_quantiles.tsv
CAMERA/inst/rules
CAMERA/inst/rules/extended_adducts_neg.csv
CAMERA/inst/rules/extended_adducts_pos.csv
CAMERA/inst/rules/primary_adducts_neg.csv
CAMERA/inst/rules/primary_adducts_pos.csv
CAMERA/inst/unitTests
CAMERA/inst/unitTests/Makefile
CAMERA/inst/unitTests/test_annotateDiffreport.R
CAMERA/inst/unitTests/test_compoundQuantiles.R
CAMERA/inst/unitTests/test_findAdductsMPI.R
CAMERA/inst/unitTests/test_generateRules.R
CAMERA/inst/unitTests/test_groupCorr.R
CAMERA/inst/unitTests/test_groupFWHM.R
CAMERA/inst/unitTests/test_kendrick.R
CAMERA/inst/unitTests/test_psDist.R
CAMERA/inst/unitTests/test_pspec2metfrag.R
CAMERA/man
CAMERA/man/annotate-methods.Rd CAMERA/man/annotateDiffreport.Rd CAMERA/man/calcCaS-methods.Rd CAMERA/man/calcCiS-methods.Rd CAMERA/man/calcIsotopes-methods.Rd CAMERA/man/calcPC-methods.Rd CAMERA/man/calcPC.hcs-methods.Rd CAMERA/man/calcPC.lpc-methods.Rd CAMERA/man/cleanParallel.Rd CAMERA/man/combinexsAnnos.Rd CAMERA/man/compoundLibraries.Rd CAMERA/man/compoundQuantiles-class.Rd CAMERA/man/compoundQuantiles.Rd CAMERA/man/findAdducts-methods.Rd CAMERA/man/findIsotopes-methods.Rd CAMERA/man/findIsotopesWithValidation-methods.Rd CAMERA/man/findKendrickMasses.Rd CAMERA/man/findNeutralLoss.Rd CAMERA/man/findNeutralLossSpecs.Rd CAMERA/man/getAllPeakEICs-methods.Rd CAMERA/man/getAtomCount-compoundQuantiles-method.Rd CAMERA/man/getIsotopeCluster.Rd CAMERA/man/getIsotopeProportion-compoundQuantiles-method.Rd CAMERA/man/getPeaklist-methods.Rd CAMERA/man/getpspectra.Rd CAMERA/man/groupCorr-methods.Rd CAMERA/man/groupDen-methods.Rd CAMERA/man/groupFWHM-methods.Rd CAMERA/man/massWindowSizes.Rd CAMERA/man/mm14.Rd CAMERA/man/plotEIC.xsAnnotate.Rd CAMERA/man/plotPsSpectrum.xsAnnotate.Rd CAMERA/man/psDist-methods.Rd CAMERA/man/pspec2metfrag.Rd CAMERA/man/ruleSet-class.Rd CAMERA/man/xsAnnotate-class.Rd CAMERA/man/xsAnnotate.Rd
CAMERA/src
CAMERA/src/fastMatch.c
CAMERA/tests
CAMERA/tests/runTests.R
CAMERA/vignettes
CAMERA/vignettes/CAMERA.Rnw
CAMERA/vignettes/IsotopeDetectionVignette.Rnw
CAMERA/vignettes/compoundQuantilesVignette.Rnw

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