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 3.2 of Bioconductor; for the stable, up-to-date release version, see xcms.
LC/MS and GC/MS Data Analysis
Bioconductor version: 3.2
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")
| Grouping FTICR-MS data with xcms | ||
| Installation Instructions for xcms | ||
| LC/MS Preprocessing and Analysis with xcms | ||
| Processing Tandem-MS and MS$^n$ data with xcms | ||
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | MassSpectrometry, Metabolomics, Software |
| Version | 1.46.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 11 years) |
| License | GPL (>= 2) + file LICENSE |
| Depends | R (>= 2.14.0), methods, mzR(>= 1.1.6), BiocGenerics, ProtGenerics, Biobase |
| Imports | lattice, RColorBrewer |
| LinkingTo | |
| Suggests | faahKO, msdata, ncdf, multtest, rgl, MassSpecWavelet(>= 1.5.2), RANN, RUnit, parallel |
| 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, Metab, metaMS |
| Imports Me | CAMERA, cosmiq, MAIT, metaX, Risa |
| Suggests Me | MassSpecWavelet, msdata, mtbls2, RforProteomics, RMassBank |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | xcms_1.46.0.tar.gz |
| Windows Binary | xcms_1.46.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | xcms_1.46.0.tgz |
| Mac OS X 10.9 (Mavericks) | xcms_1.46.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/xcms/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/xcms/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
