DOI: 10.18129/B9.bioc.cliqueMS  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see cliqueMS.

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

Bioconductor version: 3.16

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.GuimerĂ  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.

Author: 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]

Maintainer: Oriol Senan Campos <oriol.senan at>

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biocViews MassSpectrometry, Metabolomics, Network, NetworkInference, Software
Version 1.12.2
In Bioconductor since BioC 3.10 (R-3.6) (3.5 years)
License GPL (>= 2)
Depends R (>= 3.6.0)
Imports Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, qlcMatrix, matrixStats, methods
LinkingTo Rcpp, BH, RcppArmadillo
Suggests knitr, rmarkdown, testthat, CAMERA
SystemRequirements C++11
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