CluMSID

DOI: 10.18129/B9.bioc.CluMSID    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CluMSID.

Clustering of MS2 Spectra for Metabolite Identification

Bioconductor version: 3.9

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 <tobias.depke at helmholtz-hzi.de>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML	R Script	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
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, Metabolomics, Preprocessing, Software
Version	1.0.0
In Bioconductor since	BioC 3.9 (R-3.6) (< 6 months)
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
LinkingTo
Suggests	knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms
SystemRequirements
Enhances
URL	https://github.com/tdepke/CluMSID
BugReports	https://github.com/tdepke/CluMSID/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	CluMSID_1.0.0.tar.gz
Windows Binary	CluMSID_1.0.0.zip
Mac OS X 10.11 (El Capitan)	CluMSID_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CluMSID
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CluMSID
Package Short Url	https://bioconductor.org/packages/CluMSID/
Package Downloads Report	Download Stats