To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("xcms")

In most cases, you don't need to download the package archive at all.

xcms

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see xcms.

LC/MS and GC/MS Data Analysis

Bioconductor version: 3.4

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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("xcms")

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("xcms")
PDF R Script Grouping FTICR-MS data with xcms
PDF Installation Instructions for xcms
PDF R Script LC/MS Preprocessing and Analysis with xcms
PDF R Script Processing Tandem-MS and MS$^n$ data with xcms
PDF Reference Manual
Text NEWS
Text LICENSE

Details

biocViews MassSpectrometry, Metabolomics, Software
Version 1.50.1
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 12 years)
License GPL (>= 2) + file LICENSE
Depends R (>= 2.14.0), methods, mzR(>= 1.1.6), BiocGenerics, ProtGenerics, Biobase
Imports lattice, RColorBrewer, plyr, RANN, multtest, MassSpecWavelet(>= 1.5.2), BiocParallel, S4Vectors
LinkingTo
Suggests BiocStyle, knitr (>= 1.1.0), faahKO, msdata, ncdf4, rgl, RUnit
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 MassSpecWavelet, msdata, msPurity, mtbls2, RforProteomics, RMassBank, ropls
Build Report

Package Archives

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

Package Source xcms_1.50.1.tar.gz
Windows Binary xcms_1.50.1.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) xcms_1.50.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/xcms/tree/release-3.4
Package Short Url http://bioconductor.org/packages/xcms/
Package Downloads Report Download Stats

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