DOI: 10.18129/B9.bioc.xcms    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see xcms.

LC/MS and GC/MS Data Analysis

Bioconductor version: 3.8

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 <csmith at scripps.edu>, Ralf Tautenhahn <rtautenh at gmail.com>, Steffen Neumann <sneumann at ipb-halle.de>, Paul Benton <hpbenton at scripps.edu>, Christopher Conley <cjconley at ucdavis.edu>, Johannes Rainer <Johannes.Rainer at eurac.edu>

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

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


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Grouping FTICR-MS data with xcms
HTML R Script LCMS data preprocessing and analysis with xcms
HTML R Script New and modified functionality in xcms
HTML R Script Processing Tandem-MS and MSn data with xcms
PDF   Reference Manual
Text   NEWS


biocViews ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version 3.4.4
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 14 years)
License GPL (>= 2) + file LICENSE
Depends R (>= 2.14.0), methods, Biobase, BiocParallel(>= 1.8.0), MSnbase(>= 2.7.8)
Imports mzR(>= 2.13.1), BiocGenerics, ProtGenerics, lattice, RColorBrewer, plyr, RANN, multtest, MassSpecWavelet(>= 1.5.2), S4Vectors, robustbase
Suggests BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata, ncdf4, rgl, microbenchmark, testthat, pander, magrittr, MALDIquant
Enhances Rgraphviz, Rmpi, XML
URL http://metlin.scripps.edu/download/ and https://github.com/sneumann/xcms
BugReports https://github.com/sneumann/xcms/issues/new
Depends On Me CAMERA, faahKO, flagme, IPO, LOBSTAHS, Metab, metaMS, proFIA, PtH2O2lipids
Imports Me CAMERA, cosmiq, MAIT, Risa
Suggests Me MassSpecWavelet, msdata, msPurity, mtbls2, RforProteomics, RMassBank
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package xcms_3.4.4.tar.gz
Windows Binary xcms_3.4.4.zip
Mac OS X 10.11 (El Capitan) xcms_3.4.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/xcms
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/xcms
Package Short Url http://bioconductor.org/packages/xcms/
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