sneumann/RMassBank
Workflow to process tandem MS files and build MassBank records

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Functions
329
Source code
37
Man pages
92
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sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records
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API

API for sneumann/RMassBank
Workflow to process tandem MS files and build MassBank records

Global functions
.annotateFormulaToEnviPatTable Source code
.buildRecord.RmbSpectraSet Man page Source code
.buildRecord.RmbSpectrum2 Source code
.checkMbSettings Source code
.cleanElnoise.df Source code
.fillSlots Source code
.fillback Source code
.findMatchingPeaks Source code
.findPattern Source code
.findProgress.v1 Source code
.locb Source code
.locf Source code
.msmsWorkspace Man page
.normalize.int Source code
.onLoad Source code
.parseTitleString Man page Source code
.peakReasoner Source code
.propertySet Source code
.pubChemOnline Source code
.selfDefinedAccessionBuilder Source code
.setData.main Source code
.setData.properties Source code
.simpleAccessionBuilder Source code
.standardAccessionBuilder Source code
.translateLevel Source code
.unitTestRMB2 Source code
.unitTestmzR Source code
.updateObject.RmbSpectraSet.updatePolarity Source code
.updateObject.RmbSpectrum2.formulaSource Man page Source code
.updateObject.RmbWorkspace.1to2 Source code
.updateObject.RmbWorkspace.RmbSpectraSet Source code
.updateObject.aggregated Source code
.updateObject.refiltered Source code
.updateObject.spectra Source code
CTS.externalIdSubset Man page Source code
CTS.externalIdTypes Man page Source code
RmbDefaultSettings Man page Source code
RmbSettings Man page
RmbSettingsTemplate Man page Source code
add.formula Man page Source code
addMB Man page Source code
addPeaks Man page Source code
addPeaksManually Man page Source code
addProperty Man page
addProperty,RmbSpectrum2,character,character-method Man page
addProperty,data.frame,character,character-method Man page
aggregateSpectra Man page Source code
analyzeMsMs Man page Source code
analyzeMsMs.formula Man page Source code
analyzeMsMs.formula.optimized Source code
analyzeMsMs.intensity Man page Source code
analyzeMsMs.optimized Source code
annotator.default Man page Source code
archiveResults Man page Source code
checkIsotopes Man page Source code
checkSpectra Man page
checkSpectra,RmbSpectraSet,character-method Man page
cleanElnoise Man page
cleanElnoise,RmbSpectrum2List,numeric,numeric-method Man page
combineMultiplicities Man page Source code
createMolfile Man page Source code
createSpecsFromPeaklists Source code
dbe Man page Source code
decimalavoidance Source code
deprofile Man page Source code
deprofile.fwhm Man page Source code
deprofile.localMax Man page Source code
deprofile.scan Man page Source code
deprofile.spline Man page Source code
exportMassbank Man page Source code
exportMassbank_moldata Source code
exportMassbank_recdata Source code
fillback Man page
filterLowaccResults Man page Source code
filterMultiplicity Man page Source code
filterPeakSatellites Man page Source code
filterPeaksMultiplicity Man page Source code
filter_spectrum Source code
findCAS Man page Source code
findEIC Man page Source code
findFormula Man page Source code
findLevel Man page Source code
findMass Man page Source code
findMsMsHR Man page Source code
findMsMsHR.direct Man page Source code
findMsMsHR.mass Man page Source code
findMsMsHR.ticMS2 Man page
findMsMsHR.ticms2 Man page Source code
findMsMsHR.ticms2.d Source code
findMsMsHR.ticms2.file Source code
findMsMsHRperMsp Source code
findMsMsHRperMsp.direct Source code
findMsMsHRperxcms Man page Source code
findMsMsHRperxcms.direct Man page Source code
findMz Man page Source code
findMz.formula Man page Source code
findName Man page Source code
findPeaksInFracData Source code
findProgress Man page Source code
findRt Man page Source code
findSmiles Man page Source code
flatten Man page Source code
formulastring.to.list Man page Source code
fragDataIndexing Source code
gatherCompound Man page
gatherData Man page Source code
gatherDataBabel Man page Source code
gatherDataMinimal.cpd Source code
gatherDataMinimal.spectrum Source code
gatherDataUnknown Man page Source code
gatherPubChem Man page Source code
gatherSpectrum Man page
getAdductInformation Source code
getAdductProperties Source code
getAnalyticalInfo Man page Source code
getBlockHash Source code
getBlockHist Source code
getCSID Man page Source code
getCactus Man page Source code
getCompTox Man page Source code
getCtsKey Man page Source code
getCtsRecord Man page Source code
getData Man page
getData,RmbSpectrum2-method Man page
getMolecule Man page Source code
getMonoisotopicMass Source code
getPcCHEBI Source code
getPcId Man page Source code
getPcInchiKey Source code
getPcSDF Source code
getSplash Source code
integer2base36 Source code
is.sub.formula Source code
is.valid.formula Man page Source code
knownAdducts Source code
list.to.formula Man page Source code
loadInfolist Man page Source code
loadInfolists Man page Source code
loadList Man page Source code
loadMsmsWorkspace Man page Source code
loadRmbSettings Man page Source code
loadRmbSettingsFromEnv Man page Source code
makeMollist Man page Source code
makePeaksCache Man page Source code
makeRecalibration Man page Source code
mbWorkflow Man page Source code
mbWorkspace-class Man page
mergePeaks.df Man page Source code
mergeSpectra.RmbSpectrum2List Source code
msmsRead Man page Source code
msmsRead.RAW Man page Source code
msmsRead.ticms2 Source code
msmsWorkflow Man page Source code
msmsWorkspace-class Man page
multiply.formula Man page Source code
newMbWorkspace Man page Source code
newMsmsWorkspace Man page Source code
newStep2WorkFlow Source code
nist2matrix Source code
order.formula Man page Source code
parseMassBank Man page Man page Source code
parseMbRecord Man page Source code
parseMbRecords Source code
peaksMatched Man page
peaksMatched,data.frame-method Man page
peaksMatched,msmsWorkspace-method Man page
peaksUnmatched Man page
peaksUnmatched,data.frame-method Man page
peaksUnmatched,msmsWorkspace-method Man page
plotMbWorkspaces Man page Source code
plotRecalibration Man page Source code
plotRecalibration.direct Man page Source code
ppm Man page Source code
problematicPeaks Man page Source code
processProblematicPeaks Man page Source code
progressBarHook Man page Source code
read.msp Source code
readMbdata Man page Source code
reanalyzeFailpeak Man page Source code
reanalyzeFailpeaks Man page Source code
recalibrate Man page Source code
recalibrate.addMS1data Man page Source code
recalibrate.identity Man page Source code
recalibrate.linear Man page Source code
recalibrate.loess Man page Source code
recalibrate.mean Man page Source code
recalibrateSingleSpec Man page Source code
recalibrateSpectra Man page Source code
renderPeaks Source code
resetInfolists Man page Source code
resetList Man page Source code
retrieveDataWithRetry Source code
selectPeaks Man page
selectPeaks,RmbSpectraSetList-method Man page
selectPeaks,RmbSpectrum2-method Man page
selectPeaks,RmbSpectrum2List-method Man page
selectPeaks,data.frame-method Man page
selectPeaks,msmsWorkspace-method Man page
selectSpectra Man page
selectSpectra,RmbSpectraSetList,character-method Man page
selectSpectra,msmsWorkspace,character-method Man page
setData Man page
setData,RmbSpectrum2,data.frame-method Man page
show,mbWorkspace-method Man page
show,msmsWorkspace-method Man page
smiles2mass Man page Source code
spectraCount Man page
spectraCount,RmbSpectraSet-method Man page
spectraCount,RmbSpectraSetList-method Man page
spectraCount,msmsWorkspace-method Man page
split.formula.posneg Source code
to.limits.rcdk Man page Source code
toMassbank Man page
toRMB Man page Source code
translate_base Source code
updateSettings Man page Source code
validate Man page Source code
writeMgfRmbSpectrum2List Source code
writeMgfSpectraSet Source code
sneumann/RMassBank documentation built on Oct. 20, 2020, 3:19 p.m.

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