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

DOI: 10.18129/B9.bioc.xcms    

This is the development version of xcms; for the stable release version, see xcms.

LC/MS and GC/MS Data Analysis

Bioconductor version: Development (3.7)

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

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 MassSpectrometry, Metabolomics, Software
Version 3.1.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 12.5 years)
License GPL (>= 2) + file LICENSE
Depends R (>= 2.14.0), methods, Biobase, BiocParallel(>= 1.8.0), MSnbase(>= 2.3.11)
Imports mzR(>= 1.1.6), BiocGenerics, ProtGenerics, lattice, RColorBrewer, plyr, RANN, multtest, MassSpecWavelet(>= 1.5.2), S4Vectors
LinkingTo
Suggests BiocStyle, knitr (>= 1.1.0), faahKO, msdata, ncdf4, rgl, microbenchmark, RUnit, pander
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, RMassBank, ropls
Build Report  

Package Archives

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

Source Package xcms_3.1.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) xcms_3.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/xcms
Package Short Url http://bioconductor.org/packages/xcms/
Package Downloads Report Download Stats

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