DOI: 10.18129/B9.bioc.xcms  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see xcms.

LC-MS and GC-MS Data Analysis

Bioconductor version: 3.16

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 [ctb], Ralf Tautenhahn [ctb], Steffen Neumann [aut, cre] , Paul Benton [ctb], Christopher Conley [ctb], Johannes Rainer [ctb] , Michael Witting [ctb], William Kumler [ctb]

Maintainer: Steffen Neumann <sneumann at ipb-halle.de>

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


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HTML R Script Grouping FTICR-MS data with xcms
HTML R Script LC-MS feature grouping
HTML R Script LC-MS/MS data analysis with xcms
HTML R Script LCMS data preprocessing and analysis with xcms
PDF   Reference Manual
Text   NEWS


biocViews ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version 3.20.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 18 years)
License GPL (>= 2) + file LICENSE
Depends R (>= 4.0.0), BiocParallel(>= 1.8.0), MSnbase(>= 2.21.4)
Imports mzR(>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics(>= 1.25.1), lattice, RColorBrewer, plyr, RANN, MassSpecWavelet(>= 1.5.2), S4Vectors, robustbase, IRanges, SummarizedExperiment, MsCoreUtils, MsFeatures
Suggests BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata(>= 0.25.1), ncdf4, testthat, pander, magrittr, rmarkdown, multtest, MALDIquant, pheatmap, Spectra(>= 1.1.17), MsBackendMgf, progress, signal
Enhances Rgraphviz, rgl, XML
URL https://github.com/sneumann/xcms
BugReports https://github.com/sneumann/xcms/issues/new
Depends On Me CAMERA, faahKO, flagme, IPO, LOBSTAHS, Metab, metaMS, ncGTW, proFIA, PtH2O2lipids
Imports Me CAMERA, cliqueMS, cosmiq, MAIT, MobilityTransformR, Risa
Suggests Me CluMSID, msdata, msPurity, mtbls2, RforProteomics, RMassBank
Links To Me
Build Report  

Package Archives

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Source Package xcms_3.20.0.tar.gz
Windows Binary xcms_3.20.0.zip
macOS Binary (x86_64) xcms_3.20.0.tgz
macOS Binary (arm64) xcms_3.20.0.tgz
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/
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