Package: CluMSID 1.23.0

Tobias Depke

CluMSID: Clustering of MS2 Spectra for Metabolite Identification

CluMSID is a tool that aids the identification of features in untargeted LC-MS/MS analysis by the use of MS2 spectra similarity and unsupervised statistical methods. It offers functions for a complete and customisable workflow from raw data to visualisations and is interfaceable with the xmcs family of preprocessing packages.

Authors:Tobias Depke [aut, cre], Raimo Franke [ctb], Mark Broenstrup [ths]

CluMSID_1.23.0.tar.gz
CluMSID_1.23.0.zip(r-4.5)CluMSID_1.23.0.zip(r-4.4)CluMSID_1.23.0.zip(r-4.3)
CluMSID_1.23.0.tgz(r-4.4-any)CluMSID_1.23.0.tgz(r-4.3-any)
CluMSID_1.23.0.tar.gz(r-4.5-noble)CluMSID_1.23.0.tar.gz(r-4.4-noble)
CluMSID_1.23.0.tgz(r-4.4-emscripten)CluMSID_1.23.0.tgz(r-4.3-emscripten)
CluMSID.pdf |CluMSID.html✨
CluMSID/json (API)
NEWS

# Install 'CluMSID' in R:
install.packages('CluMSID', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/tdepke/clumsid/issues

On BioConductor:CluMSID-1.23.0(bioc 3.21)CluMSID-1.22.0(bioc 3.20)

metabolomicspreprocessingclustering

6.04 score 10 stars 22 scripts 176 downloads 1 mentions 34 exports 145 dependencies

Last updated 2 months agofrom:e5261c43cd. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-winWARNINGNov 30 2024
R-4.5-linuxWARNINGNov 30 2024
R-4.4-winWARNINGNov 30 2024
R-4.4-macWARNINGNov 30 2024
R-4.3-winWARNINGNov 30 2024
R-4.3-macWARNINGNov 30 2024

Exports:accessAnnotationaccessIDaccessNeutralLossesaccessPolarityaccessPrecursoraccessRTaccessSpectrumaddAnnotationsas.MS2spectrumcossimdistanceMatrixextractMS2spectraextractPseudospectrafeatureListfindFragmentfindNLgetSimilaritiesgetSpectrumHCplotHCtblintensityMDSplotmergeMS2spectramznetworkplotOPTICSplotOPTICStblpeaksCountprecursorMzrtimeshowspecplotsplitPolaritieswriteFeaturelist

Dependencies:abindaffyaffyioAnnotationFilterapeaskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbitopsbslibcachemcaToolscliclueclustercodacodetoolscolorspacecpp11crayoncrosstalkcurldata.tabledbscanDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforcatsforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGGallyggplot2ggstatsgluegplotsgtablegtoolshighrhmshtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMsCoreUtilsMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4networknlmeopensslpatchworkpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchpurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorssassscalessnasnowSparseArraystatmodstatnet.commonstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitevsnwithrxfunXMLXVectoryamlzlibbioc

Clustering Spectra from High Resolution DI-MS/MS Data Using CluMSID

Tobias Depke

Rendered fromCluMSID_DI-MSMS.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2018-12-15
Started: 2018-11-12

Clustering Mass Spectra from Low Resolution GC-EI-MS Data Using CluMSID

Tobias Depke

Rendered fromCluMSID_GC-EI-MS.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2018-12-15
Started: 2018-11-11

Clustering Mass Spectra from Low Resolution LC-MS/MS Data Using CluMSID

Tobias Depke

Rendered fromCluMSID_lowres-LC-MSMS.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2018-12-15
Started: 2018-11-12

Using CluMSID with a Publicly Available MetaboLights Data Set

Tobias Depke

Rendered fromCluMSID_MTBLS.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2018-12-15
Started: 2018-11-12

CluMSID --- Clustering of MS^2^ Spectra for Metabolite Identification

Tobias Depke

Rendered fromCluMSID_tutorial.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2019-01-02
Started: 2018-04-19

Readme and manuals

Help Manual

Help pageTopics
Accessor functions for individual slots of 'MS2spectrum' and 'pseudospectrum' objectsaccessAnnotation accessID accessNeutralLosses accessors accessPolarity accessPrecursor accessRT accessSpectrum
Adding external annotations to list of 'MS2spectrum' objectsaddAnnotations
Convert spectra from 'MSnbase' classesas.MS2spectrum
Calculate cosine similarity between two spectracossim cossim,MS2spectrum,MS2spectrum-method cossim,pseudospectrum,pseudospectrum-method
Create distance matrix from list of spectradistanceMatrix
Extract MS2 spectra from raw data filesextractMS2spectra
Extract pseudospectraextractPseudospectra
Generate a 'data.frame' with feature information from list of 'MS2spectrum' objectsfeatureList
Find spectra that contain a specific fragmentfindFragment
Find spectra that contain a specific neutral lossfindNL
Match one spectrum against a set of spectragetSimilarities
Access individual spectra from a list of spectra by various slot entriesgetSpectrum
Generate cluster dendrogram or heatmap from spectral similarity dataHCplot
Hierarchical clustering of spectral similarity dataHCtbl
Multidimensional scaling of spectral similarity dataMDSplot
Merge MS2 spectra with or without external peak tablemergeMS2spectra
A custom S4 class for MS2 spectra, neutral loss patterns and respective metainformationintensity,MS2spectrum-method MS2spectrum-class mz,MS2spectrum-method peaksCount,MS2spectrum,ANY-method precursorMz,MS2spectrum-method rtime,MS2spectrum-method show,MS2spectrum-method
Correlation network from spectral similarity datanetworkplot
Visualisation of density-based clustering of spectral similarity dataOPTICSplot
Density-based clustering of spectral similarity dataOPTICStbl
A custom S4 class for MS1 pseudospectra and respective metainformationpseudospectrum-class
Create a basic plot of MS2 spectraspecplot
Separate spectra with different polarities from the same runsplitPolarities
Write feature information from list of 'MS2spectrum' objectswriteFeaturelist