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.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("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 | ||
| 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 | |
| Links To Me | |
| 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/ |
| Package Downloads Report | Download Stats |