Package: cliqueMS
Type: Package
Title: Annotation of Isotopes, Adducts and Fragmentation Adducts for
        in-Source LC/MS Metabolomics Data
Version: 1.24.0
Date: 2024-25-04
Authors@R: c(
	   person("Oriol", "Senan Campos", email = "oriol.senan@praenoscere.com", role = c("aut","cre")),
	   person("Antoni", "Aguilar-Mogas", role = "aut"),
	   person("Jordi", "Capellades", role = "aut"),
	   person("Miriam", "Navarro", role = "aut"),
	   person("Oscar", "Yanes", role = "aut"),
	   person("Roger", "Guimera", role = "aut"),
	   person("Marta", "Sales-Pardo", role = "aut")
	   )
Description: 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.
License: GPL (>= 2)
Depends: R (>= 4.3.0)
Imports: Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, coop,
        slam, matrixStats, methods
LinkingTo: Rcpp, BH, RcppArmadillo
URL: http://cliquems.seeslab.net
BugReports: https://github.com/osenan/cliqueMS/issues
biocViews: Metabolomics, MassSpectrometry, Network, NetworkInference
SystemRequirements: C++11
Encoding: UTF-8
RoxygenNote: 7.3.2
Collate: 'allGenerics.R' 'allClasses.R' 'buildNetwork.R' 'cliqueMS.R'
        'ex.cliqueGroups.R' 'findAnnotation.R' 'findCliques.R'
        'findIsotopes.R' 'negative.adinfo.R' 'positive.adinfo.R'
        'RcppExports.R'
Suggests: BiocParallel, knitr, rmarkdown, testthat, CAMERA
VignetteBuilder: knitr
Config/pak/sysreqs: libglpk-dev make libicu-dev libxml2-dev
        libnetcdf-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:31:29 UTC
RemoteUrl: https://github.com/bioc/cliqueMS
RemoteRef: RELEASE_3_22
RemoteSha: ce55a9e16b759585e9596904f88185e309405a90
NeedsCompilation: yes
Packaged: 2025-11-11 13:41:29 UTC; root
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@praenoscere.com>
Built: R 4.5.2; x86_64-w64-mingw32; 2025-11-11 13:49:57 UTC; windows
Archs: x64
