xcms
LC-MS and GC-MS Data Analysis
Bioconductor version: 3.23 · Package version: 4.10.1
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("xcms")Details
| Maintainer | Steffen Neumann <sneumann@ipb-halle.de> |
| Author | Colin A. Smith [aut], Ralf Tautenhahn [aut], Steffen Neumann [aut, cre] (ORCID: <https://orcid.org/0000-0002-7899-7192>), Paul Benton [aut], Christopher Conley [aut], Johannes Rainer [aut] (ORCID: <https://orcid.org/0000-0002-6977-7147>), Michael Witting [ctb], William Kumler [aut] (ORCID: <https://orcid.org/0000-0002-5022-8009>), Philippine Louail [aut] (ORCID: <https://orcid.org/0009-0007-5429-6846>), Pablo Vangeenderhuysen [ctb] (ORCID: <https://orcid.org/0000-0002-5492-6904>), Carl Brunius [ctb] (ORCID: <https://orcid.org/0000-0003-3957-870X>) |
| License | GPL (>= 2) + file LICENSE |
| URL | https://github.com/sneumann/xcms |
| Bug Reports | https://github.com/sneumann/xcms/issues/new |
| Downloads rank | 2678 |
| Source branch | RELEASE_3_23 |
| biocViews | ImmunoOncology, MassSpectrometry, Metabolomics, Software |
Documentation
- Grouping FTICR-MS data with xcms
- LC-MS data preprocessing and analysis with xcms
- Compounding (grouping) of LC-MS features
- LC-MS/MS data analysis with xcms
Download
Dependencies
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
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)
Reverse dependencies
Depends On Me (8): CAMERA, flagme, IPO, LOBSTAHS, MetaboAnnotatoR, metaMS, ncGTW, PtH2O2lipids
Imports Me (7): CAMERA, cliqueMS, cosmiq, faahKO, lcmsPlot, MAIT, squallms
Suggests Me (10): CluMSID, CorrectOverloadedPeaks, isatabr, LCMSQA, MetabolomicsBasics, msdata, msPurity, mtbls2, RforProteomics, RMassBank