xcms

DOI: 10.18129/B9.bioc.xcms  

LC-MS and GC-MS Data Analysis

Bioconductor version: Release (3.17)

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 [ctb], Ralf Tautenhahn [ctb], Steffen Neumann [aut, cre] , Paul Benton [ctb], Christopher Conley [ctb], Johannes Rainer [ctb] , Michael Witting [ctb], William Kumler [ctb]

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

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")

 

HTML	R Script	Grouping FTICR-MS data with xcms
HTML	R Script	LC-MS feature grouping
HTML	R Script	LC-MS/MS data analysis with xcms
HTML	R Script	LCMS data preprocessing and analysis with xcms
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version	3.22.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 18.5 years)
License	GPL (>= 2) + file LICENSE
Depends	R (>= 4.0.0), BiocParallel(>= 1.8.0), MSnbase(>= 2.21.4)
Imports	mzR(>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics(>= 1.25.1), lattice, RColorBrewer, plyr, RANN, MassSpecWavelet(>= 1.61.3), S4Vectors, robustbase, IRanges, SummarizedExperiment, MsCoreUtils(>= 1.11.3), MsFeatures, multtest
LinkingTo
Suggests	BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata(>= 0.25.1), ncdf4, testthat, pander, magrittr, rmarkdown, MALDIquant, pheatmap, Spectra(>= 1.1.17), MsBackendMgf, progress, signal
SystemRequirements
Enhances	Rgraphviz, rgl, XML
URL	https://github.com/sneumann/xcms
BugReports	https://github.com/sneumann/xcms/issues/new
Depends On Me	CAMERA, faahKO, flagme, IPO, LOBSTAHS, Metab, metaMS, ncGTW, proFIA, PtH2O2lipids
Imports Me	CAMERA, cliqueMS, cosmiq, MAIT, MobilityTransformR, Risa
Suggests Me	CluMSID, msdata, msPurity, mtbls2, RforProteomics, RMassBank
Links To Me
Build Report

Package Archives

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

Source Package	xcms_3.22.0.tar.gz
Windows Binary	xcms_3.22.0.zip
macOS Binary (x86_64)	xcms_3.22.0.tgz
macOS Binary (arm64)	xcms_3.22.0.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 3.17	Source Archive