cliqueMS
This is the released version of cliqueMS; for the devel version, see cliqueMS.
All Bioconductor versions of cliqueMS
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
Bioconductor version: 3.23 · Package version: 1.26.0
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>
Citation
From within R, enter citation("cliqueMS"):
Oriol Senan Campos, Antoni Aguilar-Mogas, Jordi Capellades, Miriam Navarro, Oscar Yanes, Roger Guimera, Marta Sales-Pardo. cliqueMS: Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data. doi:10.18129/B9.bioc.cliqueMS, R package version 1.26.0, https://bioconductor.org/packages/cliqueMS.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 1.26.0 |
| License | GPL (>= 2) |
| URL | http://cliquems.seeslab.net |
| Bug Reports | https://github.com/osenan/cliqueMS/issues |
| System Requirements | C++11 |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.10 (R-3.6) (6 years) |
| Downloads rank | 1545 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | MassSpectrometry, Metabolomics, Network, NetworkInference, Software |
| Package Short Url | https://bioconductor.org/packages/cliqueMS/ |
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 | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | cliqueMS_1.26.0.tar.gz |
| Windows binary (x86_64) | cliqueMS_1.26.0.zip |
| macOS binary (arm64) | cliqueMS_1.26.0.tgz |
| macOS binary (x86_64) | cliqueMS_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cliqueMS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cliqueMS |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.3.0)
Imports: Rcpp (>= 0.12.15), xcms (>= 3.0.0), MSnbase, igraph, coop, slam, matrixStats, methods
LinkingTo: Rcpp, BH, RcppArmadillo
Suggests: BiocParallel, knitr, rmarkdown, testthat, CAMERA