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 (3.24)
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]
, Paul Benton [aut], Christopher Conley [aut], Johannes Rainer [aut]
, Michael Witting [ctb], William Kumler [aut]
, Philippine Louail [aut]
, Pablo Vangeenderhuysen [ctb]
, Carl Brunius [ctb]
Maintainer: Steffen Neumann <sneumann at ipb-halle.de>
citation("xcms")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("xcms")
For older versions of R, please refer to the appropriate Bioconductor 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 | 4.11.1 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | GPL (>= 2) + file LICENSE |
| 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(>= 1.21.5), 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, ncdf4, testthat (>= 3.1.9), pander, rmarkdown, MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal, mgcv, rhdf5, MsDataHub(>= 1.11.2) |
| Linking To | |
| Enhances | Rgraphviz, rgl |
| Depends On Me | CAMERA, flagme, IPO, LOBSTAHS, MetaboAnnotatoR, metaMS, ncGTW, PtH2O2lipids |
| Imports Me | CAMERA, cliqueMS, cosmiq, lcmsPlot, squallms, faahKO |
| Suggests Me | CluMSID, msPurity, RMassBank, msdata, mtbls2, RforProteomics, CorrectOverloadedPeaks, isatabr, LCMSQA, MetabolomicsBasics, specmine |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | xcms_4.11.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | xcms_4.11.1.tgz |
| macOS Binary (sonoma-arm64) | xcms_4.11.1.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 |