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
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LC/MS and GC/MS Data Analysis
Bioconductor version: Release (3.5)
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")
| R Script | Grouping FTICR-MS data with xcms | |
| Installation Instructions for xcms | ||
| R Script | LC/MS Preprocessing and Analysis with xcms | |
| R Script | Processing Tandem-MS and MS$^n$ data with xcms | |
| HTML | R Script | New and modified functionality in xcms |
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | MassSpectrometry, Metabolomics, Software |
| Version | 1.52.0 |
| 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(>= 2.1.10) |
| 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 |
| 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, RforProteomics, RMassBank, ropls |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | xcms_1.52.0.tar.gz |
| Windows Binary | xcms_1.52.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | xcms_1.52.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/xcms |
| Package Short Url | http://bioconductor.org/packages/xcms/ |
| Package Downloads Report | Download Stats |
Documentation »
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