cliqueMS

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see cliqueMS.

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


Bioconductor version: Release (3.19)

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 praenoscere.com>

Citation (from within R, enter citation("cliqueMS")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cliqueMS")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("cliqueMS")
Annotating LC/MS data with cliqueMS HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews MassSpectrometry, Metabolomics, Network, NetworkInference, Software
Version 1.18.1
In Bioconductor since BioC 3.10 (R-3.6) (5 years)
License GPL (>= 2)
Depends R (>= 4.3.0)
Imports Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, coop, slam, matrixStats, methods
System Requirements C++11
URL http://cliquems.seeslab.net
Bug Reports https://github.com/osenan/cliqueMS/issues
See More
Suggests BiocParallel, knitr, rmarkdown, testthat, CAMERA
Linking To Rcpp, BH, RcppArmadillo
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package cliqueMS_1.18.1.tar.gz
Windows Binary (x86_64) cliqueMS_1.18.1.zip
macOS Binary (x86_64) cliqueMS_1.18.1.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/cliqueMS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cliqueMS
Package Short Url https://bioconductor.org/packages/cliqueMS/
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