MsBackendMetaboLights

This is the development version of MsBackendMetaboLights; for the stable release version, see MsBackendMetaboLights.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20

Retrieve Mass Spectrometry Data from MetaboLights

Bioconductor version: Development (3.24)

MetaboLights is one of the main public repositories for storage of metabolomics experiments, which includes analysis results as well as raw data. The MsBackendMetaboLights package provides functionality to retrieve and represent mass spectrometry (MS) data from MetaboLights. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMetaboLights package.

Author: Johannes Rainer [aut, cre] ORCID: 0000-0002-6977-7147 , Philippine Louail [aut] ORCID: 0009-0007-5429-6846 , Gabriele Tomè [aut] (ORCID: ORCID: 0000-0002-3976-6068 , fnd: MetaRbolomics4Galaxy project (CUP: D53C25001030003) co-funded by the Autonomous Province of Bolzano under the Joint Projects South Tyrol–Germany 2025 program.)

Maintainer: Johannes Rainer <Johannes.Rainer at eurac.edu>

Citation (from within R, enter citation("MsBackendMetaboLights")):

Johannes Rainer, Philippine Louail, Gabriele Tomè. MsBackendMetaboLights: Retrieve Mass Spectrometry Data from MetaboLights. doi:10.18129/B9.bioc.MsBackendMetaboLights, R package version 1.7.7, https://bioconductor.org/packages/MsBackendMetaboLights.

Generated from the package metadata; it may differ from the package's own citation.

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("MsBackendMetaboLights")

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("MsBackendMetaboLights")

Retrieve and Use Mass Spectrometry Data from MetaboLights	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version	1.7.7
In Bioconductor since	BioC 3.20 (R-4.4) (2 years)
License	Artistic-2.0
Depends	R (>= 4.2.0), Spectra (>= 1.15.12)
Imports	curl, ProtGenerics, BiocFileCache, S4Vectors, methods, progress, utils, MsCoreUtils (>= 1.23.8)
System Requirements
URL	https://github.com/RforMassSpectrometry/MsBackendMetaboLights
Bug Reports	https://github.com/RforMassSpectrometry/MsBackendMetaboLights/issues

Suggests	testthat, rmarkdown, mzR, knitr, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	Chromatograms, RmzTabM
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MsBackendMetaboLights_1.7.7.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	MsBackendMetaboLights_1.7.7.tgz
macOS Binary (sonoma-arm64)	MsBackendMetaboLights_1.7.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MsBackendMetaboLights
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MsBackendMetaboLights
Package Short Url	https://bioconductor.org/packages/MsBackendMetaboLights/
Package Downloads Report	Download Stats