DOI: 10.18129/B9.bioc.xcms    

LC/MS and GC/MS Data Analysis

Bioconductor version: Release (3.6)

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 and enter:

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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 MassSpectrometry, Metabolomics, Software
Version 3.0.2
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 13 years)
License GPL (>= 2) + file LICENSE
Depends R (>= 2.14.0), methods, Biobase, BiocParallel(>= 1.8.0), MSnbase(>= 2.3.11)
Imports mzR(>= 1.1.6), BiocGenerics, ProtGenerics, lattice, RColorBrewer, plyr, RANN, multtest, MassSpecWavelet(>= 1.5.2), S4Vectors
Suggests BiocStyle, knitr (>= 1.1.0), faahKO, msdata, ncdf4, rgl, microbenchmark, RUnit, pander
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, ropls
Build Report  

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Source Package xcms_3.0.2.tar.gz
Windows Binary xcms_3.0.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) xcms_3.0.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/xcms
Package Short Url http://bioconductor.org/packages/xcms/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.6 Source Archive

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