xcms
This is thereleased version of xcms; for the devel version, seexcms.
LC-MS and GC-MS Data Analysis
Bioconductor version: Release (3.22)
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 [aut], Ralf Tautenhahn [aut], Steffen Neumann [aut, cre]
ORCID: 0000-0002-7899-7192, Paul Benton [aut], Christopher Conley [aut], Johannes Rainer [aut] ORCID: 0000-0002-6977-7147, Michael Witting [ctb], William Kumler [aut] ORCID: 0000-0002-5022-8009, Philippine Louail [aut] ORCID: 0009-0007-5429-6846, Pablo Vangeenderhuysen [ctb] ORCID: 0000-0002-5492-6904, Carl Brunius [ctb] ORCID: 0000-0003-3957-870X
Maintainer: Steffen Neumann <sneumann at ipb-halle.de>
citation("xcms")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("xcms")For older versions of R, please refer to the appropriateBioconductor release.
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 | HTML | R Script |
| LC-MS data preprocessing and analysis with xcms | HTML | R Script |
| LC-MS feature grouping | HTML | R Script |
| LC-MS/MS data analysis with xcms | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ImmunoOncology,MassSpectrometry,Metabolomics,Software |
| Version | 4.8.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 20.5 years) |
| License | GPL (>= 2) + fileLICENSE |
| Depends | R (>= 4.1.0),BiocParallel(>= 1.8.0) |
| Imports | MSnbase(>= 2.33.3),mzR(>= 2.25.3), methods,Biobase,BiocGenerics,ProtGenerics(>= 1.37.1),lattice,MassSpecWavelet(>= 1.66.0),S4Vectors,IRanges,SummarizedExperiment,MsCoreUtils(>= 1.19.2),MsFeatures,MsExperiment(>= 1.5.4),Spectra(>= 1.16.1),progress,RColorBrewer,MetaboCoreUtils(>= 1.11.2),data.table |
| System Requirements | |
| URL | https://github.com/sneumann/xcms |
| Bug Reports | https://github.com/sneumann/xcms/issues/new |
See More
| Suggests | BiocStyle,caTools,knitr (>= 1.1.0),faahKO,msdata(>= 0.25.1),ncdf4,testthat (>= 3.1.9),pander,rmarkdown,MALDIquant,pheatmap,RANN,multtest,MsBackendMgf,signal,mgcv,rhdf5 |
| Linking To | |
| Enhances | Rgraphviz,rgl |
| Depends On Me | CAMERA,flagme,IPO,LOBSTAHS,metaMS,ncGTW,PtH2O2lipids |
| Imports Me | CAMERA,cliqueMS,cosmiq,squallms,faahKO |
| Suggests Me | CluMSID,msPurity,RMassBank,msdata,mtbls2,RforProteomics,CorrectOverloadedPeaks,isatabr,LCMSQA,MetabolomicsBasics |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | xcms_4.8.0.tar.gz |
| Windows Binary (x86_64) | xcms_4.8.0.zip |
| macOS Binary (x86_64) | xcms_4.8.0.tgz |
| macOS Binary (arm64) | xcms_4.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/xcms |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/xcms |
| Bioc Package Browser | https://code.bioconductor.org/browse/xcms/ |
| Package Short Url | https://bioconductor.org/packages/xcms/ |
| Package Downloads Report | Download Stats |