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 (2.14)

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 <hpaul.benton08 at imperial.ac.uk>, 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 1.40.0
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, metaMS
Imports Me CAMERA, Risa
Suggests Me MassSpecWavelet, msdata, RforProteomics, RMassBank

Package Archives

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

Package Source xcms_1.40.0.tar.gz
Windows Binary xcms_1.40.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) xcms_1.40.0.tgz
Mac OS X 10.9 (Mavericks) xcms_1.40.0.tgz
Browse/checkout source (username/password: readonly)
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