Package: cliqueMS 1.21.0

Oriol Senan Campos

cliqueMS: Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data

Annotates data from liquid chromatography coupled to mass spectrometry (LC/MS) metabolomics experiments. Based on a network algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O. Yanes, R.Guimerà and M. Sales-Pardo, Bioinformatics, 35(20), 2019), 'CliqueMS' builds a weighted similarity network where nodes are features and edges are weighted according to the similarity of this features. Then it searches for the most plausible division of the similarity network into cliques (fully connected components). Finally it annotates metabolites within each clique, obtaining for each annotated metabolite the neutral mass and their features, corresponding to isotopes, ionization adducts and fragmentation adducts of that metabolite.

Authors:Oriol Senan Campos [aut, cre], Antoni Aguilar-Mogas [aut], Jordi Capellades [aut], Miriam Navarro [aut], Oscar Yanes [aut], Roger Guimera [aut], Marta Sales-Pardo [aut]

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NEWS

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

Peer review:

Bug tracker:https://github.com/osenan/cliquems/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:cliqueMS-1.21.0(bioc 3.21)cliqueMS-1.20.0(bioc 3.20)

metabolomicsmassspectrometrynetworknetworkinferencecpp

6.91 score 12 stars 25 scripts 194 downloads 3 mentions 20 exports 140 dependencies

Last updated 2 months agofrom:6b0f4ec681. Checks:OK: 1 NOTE: 4 WARNING: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 21 2024
R-4.5-win-x86_64NOTENov 21 2024
R-4.5-linux-x86_64NOTEDec 21 2024
R-4.4-win-x86_64NOTENov 21 2024
R-4.4-mac-x86_64WARNINGDec 21 2024
R-4.4-mac-aarch64WARNINGDec 21 2024
R-4.3-win-x86_64NOTENov 21 2024
R-4.3-mac-x86_64WARNINGDec 21 2024
R-4.3-mac-aarch64WARNINGDec 21 2024

Exports:computeCliquescreateanCliquecreateNetworkgetAnnotationgetCliquesgetIsolistanCliquegetIsotopesgetlistofCliquesgetlistofCliques<-getNetanCliquegetNetanClique<-getPeaklistanCliquegetPeaklistanClique<-hasAnnotationhasAnnotation<-hasCliqueshasCliques<-hasIsotopeshasIsotopes<-show

Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbslibcachemcliclueclustercodetoolscolorspacecoopcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmgcvmimeMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmeopensslpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchpurrrQFeaturesR6rappdirsRColorBrewerRcppRcppArmadilloreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorssassscalesslamsnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitevsnwithrxcmsxfunXMLXVectoryamlzlibbioc

Annotating LC/MS data with cliqueMS

Rendered fromannotate_features.Rmdusingknitr::rmarkdownon Dec 21 2024.

Last update: 2024-08-03
Started: 2018-03-22

Readme and manuals

Help Manual

Help pageTopics
'anClique' class constructoranClique
'anClique' S4 class for annotating isotopes and adductsanClique-class getIsolistanClique getIsolistanClique,anClique-method getIsolistanClique<- getIsolistanClique<-,anClique-method getlistofCliques getlistofCliques,anClique-method getlistofCliques<- getlistofCliques<-,anClique-method getNetanClique getNetanClique,anClique-method getNetanClique<- getNetanClique<-,anClique-method getPeaklistanClique getPeaklistanClique,anClique-method getPeaklistanClique<- getPeaklistanClique<-,anClique-method hasAnnotation hasAnnotation,anClique-method hasAnnotation<- hasAnnotation<-,anClique-method hasCliques hasCliques,anClique-method hasCliques<- hasCliques<-,anClique-method hasIsotopes hasIsotopes,anClique-method hasIsotopes<- hasIsotopes<-,anClique-method show,anClique-method
'cliqueMS' annotates isotopes and adducts in m/z datacliqueMS-package cliqueMS
Computes clique groups from a similarity networkcomputeCliques
'createanClique' generic function to create an object of class 'anClique'.createanClique createanClique,XCMSnExp-method createanClique,xcmsSet-method
Generic function to create a similarity network from processed m/z datacreateNetwork createNetwork,XCMSnExp-method createNetwork,xcmsSet-method
Example m/z processed dataex.cliqueGroups
Annotate adducts and fragmentsgetAnnotation
Compute clique groups from processed m/z datagetCliques
Annotate isotopesgetIsotopes
Default list of negative charged adductsnegative.adinfo
Default list of positive charged adductspositive.adinfo