xcms

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see xcms.

LC-MS and GC-MS Data Analysis

Bioconductor version: 3.10

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 <csmith at scripps.edu>, Ralf Tautenhahn <rtautenh at gmail.com>, Steffen Neumann <sneumann at ipb-halle.de>, Paul Benton <hpbenton at scripps.edu>, Christopher Conley <cjconley at ucdavis.edu>, Johannes Rainer <Johannes.Rainer at eurac.edu>, Michael Witting <michael.witting at helmholtz-muenchen.de>

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

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

Installation

To install this package, start R (version "3.6") 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/MS data analysis with xcms HTML R Script

LCMS data preprocessing and analysis with xcms HTML R Script

New and modified functionality in 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 3.8.2

In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)

License GPL (>= 2) + file LICENSE

Depends R (>= 2.14.0), methods, Biobase, BiocParallel(>= 1.8.0), MSnbase(>= 2.9.3)

Imports mzR(>= 2.19.5), BiocGenerics, ProtGenerics(>= 1.17.2), lattice, RColorBrewer, plyr, RANN, multtest, MassSpecWavelet(>= 1.5.2), S4Vectors, robustbase, IRanges

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, msdata(>= 0.25.1), ncdf4, rgl, microbenchmark, testthat, pander, magrittr, MALDIquant, pheatmap

Linking To

Enhances Rgraphviz, Rmpi, XML

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

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