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Bioconductor - xcms

xcms

This is the released version of xcms; for the devel version, see xcms.

LC-MS and GC-MS Data Analysis

Bioconductor version: Release (3.21)

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] ORCID: 0000-0002-7899-7192 , Paul Benton [aut], Christopher Conley [aut], Johannes Rainer [aut] ORCID: 0000-0002-6977-7147 , Michael Witting [ctb], William Kumler [aut] ORCID: 0000-0002-5022-8009 , Philippine Louail [aut] ORCID: 0009-0007-5429-6846 , Pablo Vangeenderhuysen [ctb] ORCID: 0000-0002-5492-6904 , Carl Brunius [ctb] ORCID: 0000-0003-3957-870X

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

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

To install this package, start R (version "4.5") 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")

Details biocViews ImmunoOncology, MassSpectrometry, Metabolomics, Software Version 4.6.3 In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 20 years) License GPL (>= 2) + file LICENSE Depends R (>= 4.1.0), BiocParallel(>= 1.8.0) Imports MSnbase(>= 2.33.3), mzR(>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics(>= 1.37.1), lattice, MassSpecWavelet(>= 1.66.0), S4Vectors, IRanges, SummarizedExperiment, MsCoreUtils(>= 1.15.5), MsFeatures, MsExperiment(>= 1.10.1), Spectra(>= 1.15.7), progress, 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, flagme, IPO, LOBSTAHS, metaMS, ncGTW, PtH2O2lipids Imports Me CAMERA, cliqueMS, cosmiq, squallms, faahKO Suggests Me CluMSID, msPurity, RMassBank, msdata, mtbls2, RforProteomics, CorrectOverloadedPeaks, isatabr, LCMSQA, MetabolomicsBasics Links To Me Build Report Build Report Package Archives

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

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