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>
citation("CluMSID")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, Metabolomics, Preprocessing, Software |
| Version | 1.0.0 |
| 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 | |
| Links To Me | |
| Build Report | 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 [email protected]:packages/CluMSID |
| Bioc Package Browser | https://code.bioconductor.org/browse/CluMSID/ |
| Package Short Url | https://bioconductor.org/packages/CluMSID/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |