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cliqueMS

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


Bioconductor version: Release (3.18)

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 "4.3") 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 1.16.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL (>= 2)
Depends R (>= 3.6.0)
Imports Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, qlcMatrix, matrixStats, methods
System Requirements C++11
URL http://cliquems.seeslab.net
Bug Reports https://github.com/osenan/cliqueMS/issues
See More
Suggests knitr, rmarkdown, testthat, CAMERA
Linking To Rcpp, BH, RcppArmadillo
Enhances
Depends On Me
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Package Archives

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

Source Package cliqueMS_1.16.0.tar.gz
Windows Binary cliqueMS_1.16.0.zip
macOS Binary (x86_64) cliqueMS_1.16.0.tgz
macOS Binary (arm64) cliqueMS_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cliqueMS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cliqueMS
Bioc Package Browser https://code.bioconductor.org/browse/cliqueMS/
Package Short Url https://bioconductor.org/packages/cliqueMS/
Package Downloads Report Download Stats