xcms
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see xcms.
LC-MS and GC-MS Data Analysis
Bioconductor version: 3.18
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 [ctb]
Maintainer: Steffen Neumann <sneumann at ipb-halle.de>
citation("xcms")
):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 prep-rocessing 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 | 4.0.2 |
In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 19 years) |
License | GPL (>= 2) + file LICENSE |
Depends | R (>= 4.0.0), BiocParallel(>= 1.8.0), MSnbase(>= 2.23.1) |
Imports | mzR(>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics(>= 1.29.1), lattice, RColorBrewer, plyr, RANN, MassSpecWavelet(>= 1.66.0), S4Vectors, robustbase, IRanges, SummarizedExperiment, MsCoreUtils(>= 1.11.5), MsFeatures, MsExperiment(>= 1.1.2), Spectra(>= 1.11.10), progress, multtest |
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, pander, rmarkdown, MALDIquant, pheatmap, MsBackendMgf, MetaboCoreUtils, signal |
Linking To | |
Enhances | Rgraphviz, rgl, XML |
Depends On Me | CAMERA, faahKO, flagme, IPO, LOBSTAHS, Metab, metaMS, ncGTW, PtH2O2lipids |
Imports Me | CAMERA, cliqueMS, cosmiq, MAIT, MobilityTransformR, Risa |
Suggests Me | CluMSID, msdata, msPurity, mtbls2, RforProteomics, RMassBank |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | xcms_4.0.2.tar.gz |
Windows Binary | xcms_4.0.2.zip (64-bit only) |
macOS Binary (x86_64) | xcms_4.0.2.tgz |
macOS Binary (arm64) | xcms_4.0.2.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 |
Old Source Packages for BioC 3.18 | Source Archive |