XCMS protocols

View
description
XCMS computational protocol

XCMS specifications

Information


Unique identifier OMICS_06038
Name XCMS
Alternative names centWave, XCMS Online
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 3.2.0
Stability Stable
Requirements
methods, plyr, RColorBrewer, BiocGenerics, Biobase, testthat, S4Vectors, BiocStyle, R(>=2.14.0), lattice, multtest, caTools, magrittr, rgl, pander, faahKO, BiocParallel(>=1.8.0), MSnbase(>=2.5.10), mzR(>=2.13.1), ProtGenerics, RANN, MassSpecWavelet(>=1.5.2), knitr(>=1.1.0), msdata, ncdf4, microbenchmark
Maintained Yes

Subtool


  • Massifquant

Download


Versioning


Add your version

Information


Unique identifier OMICS_06038
Name XCMS
Alternative names centWave, XCMS Online
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • Massifquant

Publications for XCMS

XCMS IN pipelines

 (3)
2017
PMCID: 5665457
PMID: 28798136
DOI: 10.1242/dmm.030411

[…] data were converted to netcdf file format with fileconverter software available in xcalibur (thermo fisher scientific, bremen, germany). deconvolution was performed using the freely available xcms software as described previously (dunn et al., 2011b; smith et al., 2006b). data were exported from xcms as a .csv file for further data analysis. the quality of data was assessed by applying qc […]

2017
PMCID: 5665457
PMID: 28798136
DOI: 10.1242/dmm.030411

[…] fisher scientific, bremen, germany). deconvolution was performed using the freely available xcms software as described previously (dunn et al., 2011b; smith et al., 2006b). data were exported from xcms as a .csv file for further data analysis. the quality of data was assessed by applying qc data as previously described (smith et al., 2006b), with all metabolite features with an rsd >20% […]

2016
PMCID: 5126694
PMID: 27897248
DOI: 10.1038/srep37976

[…] were set to 280 °c, 280 °c, and 240 °c, respectively. the detector voltage was 0.92 kv. the ionization mode was electron impact (ei) at 70 ev., for lc-ms, peak alignment was achieved with xcms52. for ce-ms, peak deconvolution, detection and area integration were performed by using agilent masshunter qualitative and quantitative analysis software. for gc-ms, the molecular features […]

XCMS institution(s)
Leibniz Institute of Plant Biochemistry, Department of Stress and Developmental Biology, Halle, Germany

XCMS reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review XCMS