xcms

DOI: 10.18129/B9.bioc.xcms    

LC-MS and GC-MS Data Analysis

Bioconductor version: Release (3.13)

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>

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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/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 3.14.1
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 16 years)
License GPL (>= 2) + file LICENSE
Depends R (>= 4.0.0), BiocParallel(>= 1.8.0), MSnbase(>= 2.17.7)
Imports mzR(>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics(>= 1.23.7), lattice, RColorBrewer, plyr, RANN, MassSpecWavelet(>= 1.5.2), S4Vectors, robustbase, IRanges, SummarizedExperiment, MsCoreUtils
LinkingTo
Suggests BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata(>= 0.25.1), ncdf4, testthat, pander, magrittr, rmarkdown, multtest, MALDIquant, pheatmap, Spectra(>= 1.1.17), MsBackendMgf
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, Risa
Suggests Me CluMSID, MassSpecWavelet, 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_3.14.1.tar.gz
Windows Binary xcms_3.14.1.zip
macOS 10.13 (High Sierra) xcms_3.14.1.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 3.13 Source Archive

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