xcms

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

LC-MS and GC-MS Data Analysis

Bioconductor version: Release (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: 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")):

Colin A. Smith, Ralf Tautenhahn, Steffen Neumann, Paul Benton, Christopher Conley, Johannes Rainer, William Kumler, Philippine Louail. xcms: LC-MS and GC-MS Data Analysis. doi:10.18129/B9.bioc.xcms, R package version 4.10.1, https://bioconductor.org/packages/xcms.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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 preprocessing and analysis with xcms	HTML	R Script
Compounding (grouping) of LC-MS features	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	4.10.1
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 21.5 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 (>= 1.21.5), 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

Suggests	BiocStyle, caTools, knitr (>= 1.1.0), faahKO, ncdf4, testthat (>= 3.1.9), pander, rmarkdown, MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal, mgcv, rhdf5, MsDataHub (>= 1.11.2)
Linking To
Enhances	Rgraphviz, rgl
Depends On Me	CAMERA, flagme, IPO, LOBSTAHS, MetaboAnnotatoR, metaMS, ncGTW, PtH2O2lipids
Imports Me	CAMERA, cliqueMS, cosmiq, faahKO, lcmsPlot, MAIT, squallms
Suggests Me	CluMSID, CorrectOverloadedPeaks, isatabr, LCMSQA, MetabolomicsBasics, msdata, msPurity, mtbls2, RforProteomics, RMassBank, specmine
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	xcms_4.10.1.tar.gz
Windows Binary (x86_64)	xcms_4.10.1.zip
macOS Binary (big-sur-x86_64)	xcms_4.10.1.tgz
macOS Binary (sonoma-arm64)	xcms_4.10.1.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	https://bioconductor.org/packages/xcms/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive