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 2.12 of Bioconductor; for the stable, up-to-date release version, see xcms.

LC/MS and GC/MS Data Analysis

Bioconductor version: 2.12

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 scripps.edu>, Steffen Neumann <sneumann at ipb-halle.de>, Paul Benton <hpaul.benton08 at imperial.ac.uk>

Maintainer: Ralf Tautenhahn <rtautenh at scripps.edu>

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		FlowChart.pdf
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	1.36.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 11 years)
License	GPL (>= 2)
Depends	R (>= 2.14.0), methods, mzR(>= 1.1.6), BiocGenerics, Biobase
Imports
LinkingTo
Suggests	faahKO, msdata, ncdf, multtest, rgl, MassSpecWavelet(>= 1.5.2), RANN, RUnit
SystemRequirements
Enhances	Rgraphviz, KEGGSOAP, Rmpi
URL	http://metlin.scripps.edu/download/
Depends On Me	CAMERA, faahKO, flagme
Imports Me	CAMERA, Risa
Suggests Me	MassSpecWavelet, msdata, RforProteomics, RMassBank
Build Report

Package Archives

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

Package Source	xcms_1.36.0.tar.gz
Windows Binary	xcms_1.36.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	xcms_1.36.0.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/xcms/tree/release-2.12
Package Short Url	http://bioconductor.org/packages/xcms/
Package Downloads Report	Download Stats