Package: cliqueMS
Type: Package
Title: Annotation of Isotopes, Adducts and Fragmentation Adducts for
        in-Source LC/MS Metabolomics Data
Version: 1.22.0
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
git_url: https://git.bioconductor.org/packages/cliqueMS
git_branch: RELEASE_3_21
git_last_commit: c7c2873
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: yes
Packaged: 2025-04-15 23:45:39 UTC; biocbuild
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 4.5.0; x86_64-w64-mingw32; 2025-04-16 14:08:26 UTC; windows
Archs: x64
