rformassspectrometry/Spectra
Spectra Infrastructure for Mass Spectrometry Data

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Functions
616
Source code
50
Man pages
23
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rformassspectrometry/Spectra: Spectra Infrastructure for Mass Spectrometry Data
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API

API for rformassspectrometry/Spectra
Spectra Infrastructure for Mass Spectrometry Data

Global functions
$,MsBackend-method Man page
$,MsBackendCached-method Man page
$,MsBackendDataFrame-method Man page
$,MsBackendMemory-method Man page
$,Spectra-method Man page
$<-,MsBackend-method Man page
$<-,MsBackendCached-method Man page
$<-,MsBackendDataFrame-method Man page
$<-,MsBackendHdf5Peaks-method Man page
$<-,MsBackendMemory-method Man page
$<-,MsBackendMzR-method Man page
$<-,Spectra-method Man page
.adjust_dda_precursor_mz Source code
.apply_processing_queue Source code
.check_ms_level Source code
.check_peaks_data_value Source code
.chunk_factor Source code
.combine_backend_data_frame Source code
.combine_spectra Source code
.compare_spectra_chunk Source code
.compare_spectra_self Source code
.concatenate_spectra Source code
.countIdentifications Source code
.create_spectra Source code
.df_combine Source code
.df_empty_peaks_data Source code
.df_pdata_column Source code
.df_peaks_columns_data_frame Source code
.df_spectra_data Source code
.df_subset Source code
.estimate_precursor_intensity Source code
.filterSpectraHierarchy Source code
.get_column Source code
.guess_software_processing Source code
.h5_read_bare Source code
.h5_read_peaks Source code
.h5_write_peaks Source code
.has_mz Source code
.has_mz_each Source code
.hdf5_compression_level Source code
.initialize_h5peaks_file Source code
.lapply Source code
.logging Source code
.mzR_header Source code
.mzR_peaks Source code
.onLoad Source code
.parallel_processing_factor Source code
.pattern_to_cv Source code
.peaks_bin Source code
.peaks_combine Source code
.peaks_compare Source code
.peaks_deisotope Source code
.peaks_filter_intensity Source code
.peaks_filter_intensity_function Source code
.peaks_filter_mz_range Source code
.peaks_filter_mz_value Source code
.peaks_filter_precursor_keep_below Source code
.peaks_filter_precursor_ne Source code
.peaks_filter_ranges Source code
.peaks_is_centroided Source code
.peaks_pick Source code
.peaks_reduce Source code
.peaks_remove_fft_artifact Source code
.peaks_replace_intensity Source code
.peaks_scale_intensities Source code
.peaks_smooth Source code
.peaks_variables Source code
.peaksapply Source code
.plot_single_spectrum Source code
.processingQueueVariables Source code
.sel_file Source code
.spectra_data Source code
.spectra_data_mzR Source code
.subset_backend_data_frame Source code
.valid_column_datatype Source code
.valid_h5files Source code
.valid_h5peaks_file Source code
.valid_intensity_column Source code
.valid_intensity_mz_columns Source code
.valid_local_data Source code
.valid_ms_backend_data_storage Source code
.valid_ms_backend_files_exist Source code
.valid_ms_backend_files_from_file Source code
.valid_ms_backend_mod_count Source code
.valid_mz_column Source code
.valid_peaks_variable_columns Source code
.valid_processing_queue Source code
.valid_spectra_data_required_columns Source code
.values_match_mz Source code
.write_ms_data_mzR Source code
MsBackend Man page
MsBackend-class Man page
MsBackendCached Man page Source code
MsBackendCached-class Man page
MsBackendDataFrame Man page Source code
MsBackendDataFrame-class Man page
MsBackendHdf5Peaks Man page Source code
MsBackendMemory Man page Source code
MsBackendMemory-class Man page
MsBackendMzR Man page Source code
MsBackendMzR-class Man page
PrecursorMzParam Man page Source code
Spectra Man page
Spectra,ANY-method Man page
Spectra,MsBackend-method Man page
Spectra,character-method Man page
Spectra,missing-method Man page
Spectra-class Man page
[,MsBackend-method Man page
[,MsBackendCached-method Man page
[,MsBackendDataFrame-method Man page
[,MsBackendHdf5Peaks-method Man page
[,MsBackendMemory-method Man page
[,Spectra-method Man page
[[,MsBackend-method Man page
[[,Spectra-method Man page
[[<-,MsBackend-method Man page
[[<-,Spectra-method Man page
`processingChunkSize<-` Source code
acquisitionNum Man page
acquisitionNum,MsBackend-method Man page
acquisitionNum,MsBackendCached-method Man page
acquisitionNum,MsBackendDataFrame-method Man page
acquisitionNum,MsBackendMemory-method Man page
acquisitionNum,Spectra-method Man page
addProcessing Man page
addProcessing,Spectra-method Man page
applyProcessing Man page Source code
asDataFrame Man page Source code
backendBpparam Man page
backendBpparam,MsBackend-method Man page
backendBpparam,Spectra-method Man page
backendInitialize Man page
backendInitialize,MsBackend-method Man page
backendInitialize,MsBackendCached-method Man page
backendInitialize,MsBackendDataFrame-method Man page
backendInitialize,MsBackendHdf5Peaks-method Man page
backendInitialize,MsBackendMemory-method Man page
backendInitialize,MsBackendMzR-method Man page
backendMerge,MsBackend-method Man page
backendMerge,MsBackendDataFrame-method Man page
backendMerge,MsBackendHdf5Peaks-method Man page
backendMerge,MsBackendMemory-method Man page
backendMerge,list-method Man page
backendParallelFactor,MsBackend-method Man page
backendParallelFactor,MsBackendHdf5Peaks-method Man page
backendParallelFactor,MsBackendMzR-method Man page
backendRequiredSpectraVariables Man page
backendRequiredSpectraVariables,MsBackend-method Man page
backendRequiredSpectraVariables,MsBackendDataFrame-method Man page
backendRequiredSpectraVariables,MsBackendHdf5Peaks-method Man page
backendRequiredSpectraVariables,MsBackendMemory-method Man page
backendRequiredSpectraVariables,MsBackendMzR-method Man page
bin Man page
bin,Spectra-method Man page
bin,numeric-method Man page
c,Spectra-method Man page
centroided Man page
centroided,MsBackend-method Man page
centroided,MsBackendCached-method Man page
centroided,MsBackendDataFrame-method Man page
centroided,MsBackendMemory-method Man page
centroided,Spectra-method Man page
centroided<-,MsBackend-method Man page
centroided<-,MsBackendCached-method Man page
centroided<-,MsBackendDataFrame-method Man page
centroided<-,MsBackendMemory-method Man page
centroided<-,Spectra-method Man page
chunkapply Man page Source code
class:MsBackend Man page
collisionEnergy Man page
collisionEnergy,MsBackend-method Man page
collisionEnergy,MsBackendCached-method Man page
collisionEnergy,MsBackendDataFrame-method Man page
collisionEnergy,MsBackendMemory-method Man page
collisionEnergy,Spectra-method Man page
collisionEnergy<-,MsBackend-method Man page
collisionEnergy<-,MsBackendCached-method Man page
collisionEnergy<-,MsBackendDataFrame-method Man page
collisionEnergy<-,MsBackendMemory-method Man page
collisionEnergy<-,Spectra-method Man page
combinePeaks Man page
combinePeaks,Spectra-method Man page
combinePeaks,list-method Man page
combinePeaksData Man page Source code
combineSpectra Man page Source code
compareSpectra Man page
compareSpectra,Spectra,Spectra-method Man page
compareSpectra,Spectra,missing-method Man page
computeMzDeltas Man page Source code
compute_mz_deltas Source code
concatenateSpectra Man page Source code
containsMz Man page
containsMz,Spectra-method Man page
containsNeutralLoss Man page
containsNeutralLoss,Spectra-method Man page
coreSpectraVariables Man page Source code
countIdentifications Man page Source code
dataOrigin Man page
dataOrigin,MsBackend-method Man page
dataOrigin,MsBackendCached-method Man page
dataOrigin,MsBackendDataFrame-method Man page
dataOrigin,MsBackendMemory-method Man page
dataOrigin,Spectra-method Man page
dataOrigin<-,MsBackend-method Man page
dataOrigin<-,MsBackendCached-method Man page
dataOrigin<-,MsBackendDataFrame-method Man page
dataOrigin<-,MsBackendMemory-method Man page
dataOrigin<-,Spectra-method Man page
dataStorage Man page
dataStorage,MsBackend-method Man page
dataStorage,MsBackendCached-method Man page
dataStorage,MsBackendDataFrame-method Man page
dataStorage,MsBackendMemory-method Man page
dataStorage,Spectra-method Man page
dataStorage<-,MsBackend-method Man page
dataStorage<-,MsBackendDataFrame-method Man page
dataStorage<-,MsBackendMemory-method Man page
dataStorageBasePath Man page
dataStorageBasePath,MsBackend-method Man page
dataStorageBasePath,MsBackendMzR-method Man page
dataStorageBasePath,Spectra-method Man page
dataStorageBasePath<- Man page
dataStorageBasePath<-,MsBackend-method Man page
dataStorageBasePath<-,MsBackendMzR-method Man page
dataStorageBasePath<-,Spectra-method Man page
deisotopeSpectra Man page Source code
dropNaSpectraVariables Man page
dropNaSpectraVariables,MsBackend-method Man page
dropNaSpectraVariables,Spectra-method Man page
entropy Man page
entropy,ANY-method Man page
entropy,Spectra-method Man page
estimatePrecursorIntensity Man page
estimatePrecursorIntensity,Spectra-method Man page
estimatePrecursorMz Man page Source code
export Man page
export,MsBackend-method Man page
export,MsBackendMzR-method Man page
export,Spectra-method Man page
extractByIndex Man page
extractByIndex,MsBackend,ANY-method Man page
extractByIndex,MsBackend,missing-method Man page
extractByIndex,MsBackendCached,ANY-method Man page
extractByIndex,MsBackendDataFrame,ANY-method Man page
extractByIndex,MsBackendHdf5Peaks,ANY-method Man page
extractByIndex,MsBackendMemory,ANY-method Man page
fft_spectrum Man page
filterAcquisitionNum Man page
filterAcquisitionNum,MsBackend-method Man page
filterAcquisitionNum,MsBackendDataFrame-method Man page
filterAcquisitionNum,MsBackendMemory-method Man page
filterAcquisitionNum,Spectra-method Man page
filterDataOrigin Man page
filterDataOrigin,MsBackend-method Man page
filterDataOrigin,Spectra-method Man page
filterDataStorage Man page
filterDataStorage,MsBackend-method Man page
filterDataStorage,Spectra-method Man page
filterEmptySpectra Man page
filterEmptySpectra,MsBackend-method Man page
filterEmptySpectra,Spectra-method Man page
filterFourierTransformArtefacts Man page
filterFourierTransformArtefacts,Spectra-method Man page
filterIntensity Man page
filterIntensity,Spectra-method Man page
filterIsolationWindow Man page
filterIsolationWindow,MsBackend-method Man page
filterIsolationWindow,Spectra-method Man page
filterMsLevel Man page
filterMsLevel,MsBackend-method Man page
filterMsLevel,Spectra-method Man page
filterMzRange Man page
filterMzRange,Spectra-method Man page
filterMzValues Man page
filterMzValues,Spectra-method Man page
filterPeaksRanges Man page Source code
filterPolarity Man page
filterPolarity,MsBackend-method Man page
filterPolarity,Spectra-method Man page
filterPrecursorCharge Man page
filterPrecursorCharge,MsBackend-method Man page
filterPrecursorCharge,Spectra-method Man page
filterPrecursorIsotopes Man page Source code
filterPrecursorMaxIntensity Man page Source code
filterPrecursorMz,MsBackend-method Man page
filterPrecursorMz,Spectra-method Man page
filterPrecursorMzRange Man page
filterPrecursorMzRange,MsBackend-method Man page
filterPrecursorMzRange,Spectra-method Man page
filterPrecursorMzValues Man page
filterPrecursorMzValues,MsBackend-method Man page
filterPrecursorMzValues,Spectra-method Man page
filterPrecursorPeaks Man page Source code
filterPrecursorScan Man page
filterPrecursorScan,MsBackend-method Man page
filterPrecursorScan,Spectra-method Man page
filterRanges Man page
filterRanges,MsBackend-method Man page
filterRanges,Spectra-method Man page
filterRt Man page
filterRt,MsBackend-method Man page
filterRt,Spectra-method Man page
filterValues Man page
filterValues,MsBackend-method Man page
filterValues,Spectra-method Man page
hidden_aliases Man page
intensity Man page
intensity,MsBackend-method Man page
intensity,MsBackendCached-method Man page
intensity,MsBackendDataFrame-method Man page
intensity,MsBackendHdf5Peaks-method Man page
intensity,MsBackendMemory-method Man page
intensity,MsBackendMzR-method Man page
intensity,Spectra-method Man page
intensity<-,MsBackend-method Man page
intensity<-,MsBackendDataFrame-method Man page
intensity<-,MsBackendHdf5Peaks-method Man page
intensity<-,MsBackendMemory-method Man page
intensity<-,MsBackendMzR-method Man page
ionCount Man page
ionCount,MsBackend-method Man page
ionCount,MsBackendCached-method Man page
ionCount,MsBackendHdf5Peaks-method Man page
ionCount,MsBackendMemory-method Man page
ionCount,MsBackendMzR-method Man page
ionCount,Spectra-method Man page
isCentroided Man page
isCentroided,MsBackend-method Man page
isCentroided,MsBackendHdf5Peaks-method Man page
isCentroided,MsBackendMzR-method Man page
isCentroided,Spectra-method Man page
isEmpty Man page
isEmpty,MsBackend-method Man page
isEmpty,MsBackendCached-method Man page
isEmpty,MsBackendDataFrame-method Man page
isEmpty,MsBackendHdf5Peaks-method Man page
isEmpty,MsBackendMemory-method Man page
isEmpty,MsBackendMzR-method Man page
isEmpty,Spectra-method Man page
isReadOnly,MsBackend-method Man page
isolationWindowLowerMz Man page
isolationWindowLowerMz,MsBackend-method Man page
isolationWindowLowerMz,MsBackendCached-method Man page
isolationWindowLowerMz,MsBackendDataFrame-method Man page
isolationWindowLowerMz,MsBackendMemory-method Man page
isolationWindowLowerMz,Spectra-method Man page
isolationWindowLowerMz<-,MsBackend-method Man page
isolationWindowLowerMz<-,MsBackendCached-method Man page
isolationWindowLowerMz<-,MsBackendDataFrame-method Man page
isolationWindowLowerMz<-,MsBackendMemory-method Man page
isolationWindowLowerMz<-,Spectra-method Man page
isolationWindowTargetMz Man page
isolationWindowTargetMz,MsBackend-method Man page
isolationWindowTargetMz,MsBackendCached-method Man page
isolationWindowTargetMz,MsBackendDataFrame-method Man page
isolationWindowTargetMz,MsBackendMemory-method Man page
isolationWindowTargetMz,Spectra-method Man page
isolationWindowTargetMz<-,MsBackend-method Man page
isolationWindowTargetMz<-,MsBackendCached-method Man page
isolationWindowTargetMz<-,MsBackendDataFrame-method Man page
isolationWindowTargetMz<-,MsBackendMemory-method Man page
isolationWindowTargetMz<-,Spectra-method Man page
isolationWindowUpperMz Man page
isolationWindowUpperMz,MsBackend-method Man page
isolationWindowUpperMz,MsBackendCached-method Man page
isolationWindowUpperMz,MsBackendDataFrame-method Man page
isolationWindowUpperMz,MsBackendMemory-method Man page
isolationWindowUpperMz,Spectra-method Man page
isolationWindowUpperMz<-,MsBackend-method Man page
isolationWindowUpperMz<-,MsBackendCached-method Man page
isolationWindowUpperMz<-,MsBackendDataFrame-method Man page
isolationWindowUpperMz<-,MsBackendMemory-method Man page
isolationWindowUpperMz<-,Spectra-method Man page
joinPeaks Man page Source code
joinPeaksGnps Man page Source code
joinPeaksNone Man page Source code
joinSpectraData Man page Source code
length,MsBackend-method Man page
length,MsBackendCached-method Man page
length,MsBackendDataFrame-method Man page
length,MsBackendMemory-method Man page
length,Spectra-method Man page
lengths Man page
lengths,MsBackend-method Man page
lengths,MsBackendCached-method Man page
lengths,MsBackendDataFrame-method Man page
lengths,MsBackendHdf5Peaks-method Man page
lengths,MsBackendMemory-method Man page
lengths,MsBackendMzR-method Man page
lengths,Spectra-method Man page
msLeveL<-,MsBackend-method Man page
msLevel Man page
msLevel,MsBackend-method Man page
msLevel,MsBackendCached-method Man page
msLevel,MsBackendDataFrame-method Man page
msLevel,MsBackendMemory-method Man page
msLevel,Spectra-method Man page
msLevel<-,MsBackend-method Man page
msLevel<-,MsBackendDataFrame-method Man page
msLevel<-,MsBackendMemory-method Man page
mz Man page
mz,MsBackend-method Man page
mz,MsBackendCached-method Man page
mz,MsBackendDataFrame-method Man page
mz,MsBackendHdf5Peaks-method Man page
mz,MsBackendMemory-method Man page
mz,MsBackendMzR-method Man page
mz,Spectra-method Man page
mz<-,MsBackend-method Man page
mz<-,MsBackendDataFrame-method Man page
mz<-,MsBackendHdf5Peaks-method Man page
mz<-,MsBackendMemory-method Man page
mz<-,MsBackendMzR-method Man page
neutralLoss Man page
neutralLoss,Spectra,PrecursorMzParam-method Man page
peaksData Man page
peaksData,MsBackend-method Man page
peaksData,MsBackendDataFrame-method Man page
peaksData,MsBackendHdf5Peaks-method Man page
peaksData,MsBackendMemory-method Man page
peaksData,MsBackendMzR-method Man page
peaksData,Spectra-method Man page
peaksData<-,MsBackend-method Man page
peaksData<-,MsBackendDataFrame-method Man page
peaksData<-,MsBackendHdf5Peaks-method Man page
peaksData<-,MsBackendMemory-method Man page
peaksVariables Man page
peaksVariables,MsBackend-method Man page
peaksVariables,MsBackendDataFrame-method Man page
peaksVariables,MsBackendMemory-method Man page
peaksVariables,Spectra-method Man page
pickPeaks Man page
pickPeaks,Spectra-method Man page
plotMzDelta Man page Source code
plotSpectra Man page Source code
plotSpectraMirror Man page
plotSpectraMirror,Spectra-method Man page
plotSpectraOverlay Man page Source code
polarity Man page
polarity,MsBackend-method Man page
polarity,MsBackendCached-method Man page
polarity,MsBackendDataFrame-method Man page
polarity,MsBackendMemory-method Man page
polarity,Spectra-method Man page
polarity<-,MsBackend-method Man page
polarity<-,MsBackendCached-method Man page
polarity<-,MsBackendDataFrame-method Man page
polarity<-,MsBackendMemory-method Man page
polarity<-,Spectra-method Man page
ppm Man page
precScanNum,MsBackend-method Man page
precScanNum,MsBackendDataFrame-method Man page
precScanNum,MsBackendMemory-method Man page
precScanNum,Spectra-method Man page
precursorCharge Man page
precursorCharge,MsBackend-method Man page
precursorCharge,MsBackendCached-method Man page
precursorCharge,MsBackendDataFrame-method Man page
precursorCharge,MsBackendMemory-method Man page
precursorCharge,Spectra-method Man page
precursorIntensity Man page
precursorIntensity,MsBackend-method Man page
precursorIntensity,MsBackendCached-method Man page
precursorIntensity,MsBackendDataFrame-method Man page
precursorIntensity,MsBackendMemory-method Man page
precursorIntensity,Spectra-method Man page
precursorMz Man page
precursorMz,MsBackend-method Man page
precursorMz,MsBackendCached-method Man page
precursorMz,MsBackendDataFrame-method Man page
precursorMz,MsBackendMemory-method Man page
precursorMz,Spectra-method Man page
precursorMz<-,MsBackend-method Man page
precursorMz<-,Spectra-method Man page
processingChunkFactor Man page Source code
processingChunkSize Man page Source code
processingChunkSize<- Man page
processingLog Man page Source code
reduceSpectra Man page Source code
replaceIntensitiesBelow Man page
replaceIntensitiesBelow,Spectra-method Man page
reset Man page
reset,MsBackend-method Man page
reset,Spectra-method Man page
rtime Man page
rtime,MsBackend-method Man page
rtime,MsBackendCached-method Man page
rtime,MsBackendDataFrame-method Man page
rtime,MsBackendMemory-method Man page
rtime,Spectra-method Man page
rtime<-,MsBackend-method Man page
rtime<-,MsBackendCached-method Man page
rtime<-,MsBackendDataFrame-method Man page
rtime<-,MsBackendMemory-method Man page
rtime<-,Spectra-method Man page
sanitize_file_name Source code
scalePeaks Man page Source code
scanIndex Man page
scanIndex,MsBackend-method Man page
scanIndex,MsBackendCached-method Man page
scanIndex,MsBackendDataFrame-method Man page
scanIndex,MsBackendMemory-method Man page
scanIndex,Spectra-method Man page
selectSpectraVariables Man page
selectSpectraVariables,MsBackend-method Man page
selectSpectraVariables,MsBackendCached-method Man page
selectSpectraVariables,MsBackendDataFrame-method Man page
selectSpectraVariables,MsBackendMemory-method Man page
selectSpectraVariables,Spectra-method Man page
setBackend Man page
setBackend,Spectra,MsBackend-method Man page
show,MsBackendCached-method Man page
show,MsBackendDataFrame-method Man page
show,MsBackendHdf5Peaks-method Man page
show,MsBackendMemory-method Man page
show,MsBackendMzR-method Man page
show,Spectra-method Man page
smooth Man page
smooth,Spectra-method Man page
smoothed Man page
smoothed,MsBackend-method Man page
smoothed,MsBackendCached-method Man page
smoothed,MsBackendDataFrame-method Man page
smoothed,MsBackendMemory-method Man page
smoothed,Spectra-method Man page
smoothed<-,MsBackend-method Man page
smoothed<-,MsBackendCached-method Man page
smoothed<-,MsBackendDataFrame-method Man page
smoothed<-,MsBackendMemory-method Man page
smoothed<-,Spectra-method Man page
spectra-plotting Man page
spectraData Man page
spectraData,MsBackend-method Man page
spectraData,MsBackendCached-method Man page
spectraData,MsBackendDataFrame-method Man page
spectraData,MsBackendHdf5Peaks-method Man page
spectraData,MsBackendMemory-method Man page
spectraData,MsBackendMzR-method Man page
spectraData,Spectra-method Man page
spectraData<-,MsBackend-method Man page
spectraData<-,MsBackendCached-method Man page
spectraData<-,MsBackendDataFrame-method Man page
spectraData<-,MsBackendHdf5Peaks-method Man page
spectraData<-,MsBackendMemory-method Man page
spectraData<-,MsBackendMzR-method Man page
spectraData<-,Spectra-method Man page
spectraNames Man page
spectraNames,MsBackend-method Man page
spectraNames,MsBackendDataFrame-method Man page
spectraNames,MsBackendMemory-method Man page
spectraNames,MsBackendMzR-method Man page
spectraNames,Spectra-method Man page
spectraNames<-,MsBackend-method Man page
spectraNames<-,MsBackendDataFrame-method Man page
spectraNames<-,MsBackendMemory-method Man page
spectraNames<-,MsBackendMzR-method Man page
spectraNames<-,Spectra-method Man page
spectraVariableMapping Man page
spectraVariables Man page
spectraVariables,MsBackend-method Man page
spectraVariables,MsBackendCached-method Man page
spectraVariables,MsBackendDataFrame-method Man page
spectraVariables,MsBackendMemory-method Man page
spectraVariables,MsBackendMzR-method Man page
spectraVariables,Spectra-method Man page
spectrapply Man page
spectrapply,Spectra-method Man page
split Man page
split,MsBackend,ANY-method Man page
split,MsBackendDataFrame,ANY-method Man page
split,MsBackendMemory,ANY-method Man page
split,Spectra,ANY-method Man page
supportsSetBackend Man page
supportsSetBackend,MsBackend-method Man page
tic Man page
tic,MsBackend-method Man page
tic,MsBackendDataFrame-method Man page
tic,MsBackendMemory-method Man page
tic,Spectra-method Man page
uniqueMsLevels Man page
uniqueMsLevels,MsBackend-method Man page
uniqueMsLevels,Spectra-method Man page
rformassspectrometry/Spectra documentation built on Oct. 30, 2024, 5:42 a.m.

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