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xcms

LC-MS and GC-MS Data Analysis


Bioconductor version: Release (3.18)

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 [ctb]

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

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

Installation

To install this package, start R (version "4.3") 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 prep-rocessing 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 PDF
NEWS Text
LICENSE Text

Details

biocViews ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version 4.0.2
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License GPL (>= 2) + file LICENSE
Depends R (>= 4.0.0), BiocParallel(>= 1.8.0), MSnbase(>= 2.23.1)
Imports mzR(>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics(>= 1.29.1), lattice, RColorBrewer, plyr, RANN, MassSpecWavelet(>= 1.66.0), S4Vectors, robustbase, IRanges, SummarizedExperiment, MsCoreUtils(>= 1.11.5), MsFeatures, MsExperiment(>= 1.1.2), Spectra(>= 1.11.10), progress, multtest
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, pander, rmarkdown, MALDIquant, pheatmap, MsBackendMgf, MetaboCoreUtils, signal
Linking To
Enhances Rgraphviz, rgl, XML
Depends On Me CAMERA, faahKO, flagme, IPO, LOBSTAHS, Metab, metaMS, ncGTW, PtH2O2lipids
Imports Me CAMERA, cliqueMS, cosmiq, MAIT, MobilityTransformR, Risa
Suggests Me CluMSID, msdata, msPurity, mtbls2, RforProteomics, RMassBank
Links To Me
Build Report Build Report

Package Archives

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

Source Package xcms_4.0.2.tar.gz
Windows Binary xcms_4.0.2.zip
macOS Binary (x86_64) xcms_4.0.2.tgz
macOS Binary (arm64) xcms_4.0.2.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive