cliqueMS

DOI: 10.18129/B9.bioc.cliqueMS    

This is the development version of cliqueMS; for the stable release version, see cliqueMS.

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

Bioconductor version: Development (3.11)

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 "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

HTML R Script Annotating LC/MS data with cliqueMS
PDF   Reference Manual
Text   NEWS

Details

biocViews MassSpectrometry, Metabolomics, Network, NetworkInference, Software
Version 1.1.1
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
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
Enhances
URL http://cliquems.seeslab.net
BugReports https://github.com/osenan/cliqueMS/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package cliqueMS_1.1.1.tar.gz
Windows Binary cliqueMS_1.1.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) cliqueMS_1.1.1.tgz
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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