xcms

DOI: 10.18129/B9.bioc.xcms    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see xcms.

LC/MS and GC/MS Data Analysis

Bioconductor version: 3.9

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>

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

Installation

To install this package, start R (version "3.6") 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	LCMS data preprocessing and analysis with xcms
HTML	R Script	New and modified functionality in xcms
HTML	R Script	Processing Tandem-MS and MSn data with xcms
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version	3.6.2
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 14.5 years)
License	GPL (>= 2) + file LICENSE
Depends	R (>= 2.14.0), methods, Biobase, BiocParallel(>= 1.8.0), MSnbase(>= 2.9.3)
Imports	mzR(>= 2.13.3), BiocGenerics, ProtGenerics, lattice, RColorBrewer, plyr, RANN, multtest, MassSpecWavelet(>= 1.5.2), S4Vectors, robustbase
LinkingTo
Suggests	BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata, ncdf4, rgl, microbenchmark, testthat, pander, magrittr, MALDIquant, pheatmap
SystemRequirements
Enhances	Rgraphviz, Rmpi, XML
URL	http://metlin.scripps.edu/download/ and https://github.com/sneumann/xcms
BugReports	https://github.com/sneumann/xcms/issues/new
Depends On Me	CAMERA, faahKO, flagme, IPO, LOBSTAHS, Metab, metaMS, proFIA, PtH2O2lipids
Imports Me	CAMERA, 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_3.6.2.tar.gz
Windows Binary	xcms_3.6.2.zip
Mac OS X 10.11 (El Capitan)	xcms_3.6.2.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