Package: cliqueMS 1.14.1

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]

cliqueMS_1.14.1.tar.gz
cliqueMS_1.14.1.zip(r-4.7)cliqueMS_1.14.1.zip(r-4.6)cliqueMS_1.7.1.zip(r-4.5)
cliqueMS_1.14.1.tgz(r-4.6-x86_64)cliqueMS_1.14.1.tgz(r-4.6-arm64)cliqueMS_1.7.1.tgz(r-4.5-x86_64)cliqueMS_1.7.1.tgz(r-4.5-arm64)
cliqueMS_1.14.1.tar.gz(r-4.7-arm64)cliqueMS_1.14.1.tar.gz(r-4.7-x86_64)cliqueMS_1.14.1.tar.gz(r-4.6-arm64)cliqueMS_1.14.1.tar.gz(r-4.6-x86_64)
cliqueMS_1.14.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
cliqueMS/json (API)
NEWS

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

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

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

On BioConductor:cliqueMS-1.27.0(bioc 3.24)cliqueMS-1.26.0(bioc 3.23)

metabolomicsmassspectrometrynetworknetworkinferencecpp

3.81 score 32 scripts 11 downloads 20 exports 140 dependencies

Last updated from:b06c0fd579. Checks:9 ERROR, 3 FAIL, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR379
linux-devel-x86_64ERROR374
source / vignettesERROR375
linux-release-arm64ERROR360
linux-release-x86_64ERROR427
macos-release-arm64ERROR374
macos-release-x86_64ERROR468
macos-oldrel-arm64FAIL124
macos-oldrel-x86_64FAIL198
windows-develERROR682
windows-releaseERROR460
windows-oldrelFAIL427
wasm-releaseOK206

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

Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocManagerBiocParallelbslibcachemcliclueclustercodetoolscpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdir.expirydocoptdoParalleldplyrevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmzIDmzRncdf4opensslotelpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchPTModspurrrQFeaturesqlcMatrixR6rappdirsRColorBrewerRcppRcppArmadilloreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfoslamsnowSparseArraysparsesvdSpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitevsnwithrxcmsxfunXMLXVectoryaml

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