CluMSID
This is the released version of CluMSID; for the devel version, see CluMSID.
Clustering of MS2 Spectra for Metabolite Identification
Bioconductor version: Release (3.23)
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("CluMSID")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.28.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 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_1.28.0.tar.gz |
| Windows Binary (x86_64) | CluMSID_1.28.0.zip |
| macOS Binary (big-sur-x86_64) | CluMSID_1.28.0.tgz |
| macOS Binary (sonoma-arm64) | CluMSID_1.28.0.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 |