To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("xcms")

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

xcms

LC/MS and GC/MS Data Analysis

Bioconductor version: Release (3.0)

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>

Maintainer: Ralf Tautenhahn <rtautenh at gmail.com>

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

Installation

To install this package, start R and enter:

source("http://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 R Script 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 1.42.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier
License GPL (>= 2) + file LICENSE
Depends R (>= 2.14.0), methods, mzR(>= 1.1.6), BiocGenerics, Biobase
Imports
Suggests faahKO, msdata, ncdf, multtest, rgl, MassSpecWavelet(>= 1.5.2), RANN, RUnit
System Requirements
URL http://metlin.scripps.edu/download/ and https://github.com/sneumann/xcms
Depends On Me CAMERA, faahKO, flagme, Metab, metaMS
Imports Me CAMERA, cosmiq, MAIT, Risa
Suggests Me MassSpecWavelet, msdata, RforProteomics, RMassBank

Package Archives

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

Package Source xcms_1.42.0.tar.gz
Windows Binary xcms_1.42.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) xcms_1.42.0.tgz
Mac OS X 10.9 (Mavericks) xcms_1.42.0.tgz
Browse/checkout source (username/password: readonly)
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