This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

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 (3.18)

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 "4.3") 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 1.17.0
In Bioconductor since BioC 3.9 (R-3.6) (4.5 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
Linking To
Suggests knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms
System Requirements
Enhances
URL https://github.com/tdepke/CluMSID
Bug Reports https://github.com/tdepke/CluMSID/issues
See More
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_1.17.0.tar.gz
Windows Binary CluMSID_1.17.0.zip
macOS Binary (x86_64) CluMSID_1.17.0.tgz
macOS Binary (arm64) CluMSID_1.17.0.tgz
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