xcms
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see xcms.
LC-MS and GC-MS Data Analysis
Bioconductor version: 3.19
Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.
Author: Colin A. Smith [aut], Ralf Tautenhahn [aut], Steffen Neumann [aut, cre] 
, Paul Benton [aut], Christopher Conley [aut], Johannes Rainer [aut] , Michael Witting [ctb], William Kumler [aut] , Philippine Louail [aut] , Pablo Vangeenderhuysen [ctb] , Carl Brunius [ctb]
Maintainer: Steffen Neumann <sneumann at ipb-halle.de>
citation("xcms")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("xcms")
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("xcms")| Grouping FTICR-MS data with xcms | HTML | R Script |
| LC-MS data preprocessing and analysis with xcms | HTML | R Script |
| LC-MS feature grouping | HTML | R Script |
| LC-MS/MS data analysis with xcms | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Metabolomics, Software |
| Version | 4.2.3 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 19.5 years) |
| License | GPL (>= 2) + file LICENSE |
| Depends | R (>= 4.0.0), BiocParallel(>= 1.8.0) |
| Imports | MSnbase(>= 2.29.3), mzR(>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics(>= 1.35.4), lattice, MassSpecWavelet(>= 1.66.0), S4Vectors, IRanges, SummarizedExperiment, MsCoreUtils(>= 1.15.5), MsFeatures, MsExperiment(>= 1.5.4), Spectra(>= 1.13.7), progress, jsonlite, RColorBrewer, MetaboCoreUtils(>= 1.11.2) |
| System Requirements | |
| URL | https://github.com/sneumann/xcms |
| Bug Reports | https://github.com/sneumann/xcms/issues/new |
See More
| Suggests | BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata(>= 0.25.1), ncdf4, testthat (>= 3.1.9), pander, rmarkdown, MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal, mgcv |
| Linking To | |
| Enhances | Rgraphviz, rgl |
| Depends On Me | CAMERA, IPO, LOBSTAHS, flagme, metaMS, ncGTW, faahKO, PtH2O2lipids |
| Imports Me | CAMERA, cliqueMS, cosmiq |
| Suggests Me | CluMSID, RMassBank, msPurity, msdata, mtbls2, RforProteomics, CorrectOverloadedPeaks, enviGCMS, isatabr, LCMSQA, MetabolomicsBasics, RAMClustR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | xcms_4.2.3.tar.gz |
| Windows Binary (x86_64) | xcms_4.2.3.zip (64-bit only) |
| macOS Binary (x86_64) | xcms_4.2.1.tgz |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/xcms |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/xcms |
| Bioc Package Browser | https://code.bioconductor.org/browse/xcms/ |
| Package Short Url | https://bioconductor.org/packages/xcms/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |