CluMSID

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see CluMSID.

Clustering of MS2 Spectra for Metabolite Identification

Bioconductor version: 3.15

CluMSID is a tool that aids the identification of features in untargeted LC-MS/MS analysis by the use of MS2 spectra similarity and unsupervised statistical methods. It offers functions for a complete and customisable workflow from raw data to visualisations and is interfaceable with the xmcs family of preprocessing packages.

Author: Tobias Depke [aut, cre], Raimo Franke [ctb], Mark Broenstrup [ths]

Maintainer: Tobias Depke <depke at mailbox.org>

Citation (from within R, enter citation("CluMSID")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("CluMSID")

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("CluMSID")

CluMSID DI-MS/MS Tutorial HTML R Script

CluMSID GC-EI-MS Tutorial HTML R Script

CluMSID LowRes Tutorial HTML R Script

CluMSID MTBLS Tutorial HTML R Script

CluMSID Tutorial HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, Metabolomics, Preprocessing, Software

Version 1.12.0

In Bioconductor since BioC 3.9 (R-3.6) (5 years)

License MIT + file LICENSE

Depends R (>= 3.6)

Imports mzR, S4Vectors, dbscan, RColorBrewer, ape, network, GGally, ggplot2, plotly, methods, utils, stats, sna, grDevices, graphics, Biobase, gplots, MSnbase

System Requirements

URL https://github.com/tdepke/CluMSID

Bug Reports https://github.com/tdepke/CluMSID/issues

Suggests knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms

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