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] 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 (from within R, enter citation("xcms")):

Installation

To install this package, start R (version "4.6") 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version	4.11.0
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

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
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
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (big-sur-arm64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/xcms
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/xcms
Package Short Url	https://bioconductor.org/packages/xcms/
Package Downloads Report	Download Stats