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xcms (development version)

xcms

This is the development version of xcms; for the stable release version, see xcms.

LC-MS and GC-MS Data Analysis

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DOI: 10.18129/B9.bioc.xcms

Bioconductor version: Development (3.23)

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 iD ORCID: 0000-0002-7899-7192 , Paul Benton [aut], Christopher Conley [aut], Johannes Rainer [aut] ORCID iD ORCID: 0000-0002-6977-7147 , Michael Witting [ctb], William Kumler [aut] ORCID iD ORCID: 0000-0002-5022-8009 , Philippine Louail [aut] ORCID iD ORCID: 0009-0007-5429-6846 , Pablo Vangeenderhuysen [ctb] ORCID iD ORCID: 0000-0002-5492-6904 , Carl Brunius [ctb] ORCID iD 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 "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 preprocessing 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ImmunoOncology, MassSpectrometry, Metabolomics, Software

Version 4.9.0

In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 20.5 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(>= 1.19.2), MsFeatures, MsExperiment(>= 1.5.4), Spectra(>= 1.16.1), progress, RColorBrewer, MetaboCoreUtils(>= 1.11.2), data.table

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, rhdf5

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.

Source Package xcms_4.9.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

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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