cliqueMS

DOI: 10.18129/B9.bioc.cliqueMS  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see cliqueMS.

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

Bioconductor version: 3.16

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.

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	MassSpectrometry, Metabolomics, Network, NetworkInference, Software
Version	1.12.2
In Bioconductor since	BioC 3.10 (R-3.6) (3.5 years)
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_1.12.2.tar.gz
Windows Binary	cliqueMS_1.12.2.zip (64-bit only)
macOS Binary (x86_64)	cliqueMS_1.12.2.tgz
macOS Binary (arm64)	cliqueMS_1.12.2.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