CluMSID

DOI: 10.18129/B9.bioc.CluMSID    

This is the development version of CluMSID; to use it, please install the devel version of Bioconductor.

Clustering of MS2 Spectra for Metabolite Identification

Bioconductor version: Development (3.10)

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>

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

Installation

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

if (!requireNamespace("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")

 

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 1.1.0
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_1.1.0.tar.gz
Windows Binary CluMSID_1.1.0.zip
Mac OS X 10.11 (El Capitan) CluMSID_1.1.0.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

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