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CluMSID

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

Clustering of MS2 Spectra for Metabolite Identification


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

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

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

Details

biocViews Clustering, Metabolomics, Preprocessing, Software
Version 1.19.0
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
See More
Suggests knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

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

Source Package CluMSID_1.19.0.tar.gz
Windows Binary CluMSID_1.19.0.zip
macOS Binary (x86_64) CluMSID_1.19.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/CluMSID
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CluMSID
Bioc Package Browser https://code.bioconductor.org/browse/CluMSID/
Package Short Url https://bioconductor.org/packages/CluMSID/
Package Downloads Report Download Stats