Package: cliqueMS 1.19.3
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:
cliqueMS_1.19.3.tar.gz
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cliqueMS_1.19.3.tgz(r-4.4-x86_64)cliqueMS_1.19.3.tgz(r-4.4-arm64)cliqueMS_1.19.3.tgz(r-4.3-x86_64)cliqueMS_1.19.3.tgz(r-4.3-arm64)
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cliqueMS_1.19.3.tgz(r-4.4-emscripten)cliqueMS_1.19.3.tgz(r-4.3-emscripten)
cliqueMS.pdf |cliqueMS.html✨
cliqueMS/json (API)
NEWS
| # Install 'cliqueMS' in R: |
| install.packages('cliqueMS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/osenan/cliquems/issues
- ex.cliqueGroups - Example m/z processed data
- negative.adinfo - Default list of negative charged adducts
- positive.adinfo - Default list of positive charged adducts
On BioConductor:cliqueMS-1.19.2(bioc 3.20)cliqueMS-1.18.1(bioc 3.19)
metabolomicsmassspectrometrynetworknetworkinference
Last updated 3 days agofrom:cea456a921. Checks:OK: 1 NOTE: 4 WARNING: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 20 2024 |
| R-4.5-win-x86_64 | NOTE | Oct 20 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 20 2024 |
| R-4.4-win-x86_64 | NOTE | Oct 20 2024 |
| R-4.4-mac-x86_64 | WARNING | Oct 20 2024 |
| R-4.4-mac-aarch64 | WARNING | Oct 20 2024 |
| R-4.3-win-x86_64 | NOTE | Oct 20 2024 |
| R-4.3-mac-x86_64 | WARNING | Oct 20 2024 |
| R-4.3-mac-aarch64 | WARNING | Oct 20 2024 |
Exports:computeCliquescreateanCliquecreateNetworkgetAnnotationgetCliquesgetIsolistanCliquegetIsotopesgetlistofCliquesgetlistofCliques<-getNetanCliquegetNetanClique<-getPeaklistanCliquegetPeaklistanClique<-hasAnnotationhasAnnotation<-hasCliqueshasCliques<-hasIsotopeshasIsotopes<-show
Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbslibcachemcliclueclustercodetoolscolorspacecoopcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmgcvmimeMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmeopensslpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchpurrrQFeaturesR6rappdirsRColorBrewerRcppRcppArmadilloreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorssassscalesslamsnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitevsnwithrxcmsxfunXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 'anClique' class constructor | anClique |
| 'anClique' S4 class for annotating isotopes and adducts | anClique-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 data | cliqueMS-package cliqueMS |
| Computes clique groups from a similarity network | computeCliques |
| '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 data | createNetwork createNetwork,XCMSnExp-method createNetwork,xcmsSet-method |
| Example m/z processed data | ex.cliqueGroups |
| Annotate adducts and fragments | getAnnotation |
| Compute clique groups from processed m/z data | getCliques |
| Annotate isotopes | getIsotopes |
| Default list of negative charged adducts | negative.adinfo |
| Default list of positive charged adducts | positive.adinfo |
