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 (3.21)
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:
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")
# The following initializes usage of Bioc devel
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 |
Details
biocViews | ImmunoOncology, MassSpectrometry, Metabolomics, Software |
Version | 4.5.0 |
In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 19.5 years) |
License | GPL (>= 2) + file LICENSE |
Depends | R (>= 4.0.0), BiocParallel(>= 1.8.0) |
Imports | MSnbase(>= 2.29.3), mzR(>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics(>= 1.37.1), lattice, MassSpecWavelet(>= 1.66.0), S4Vectors, IRanges, SummarizedExperiment, MsCoreUtils(>= 1.15.5), MsFeatures, MsExperiment(>= 1.5.4), Spectra(>= 1.15.7), progress, RColorBrewer, MetaboCoreUtils(>= 1.11.2) |
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 |
Linking To | |
Enhances | Rgraphviz, rgl |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | xcms_4.5.0.tar.gz |
Windows Binary (x86_64) | |
macOS Binary (x86_64) | |
macOS Binary (arm64) | |
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 |