MsBackendMetaboLights

Retrieve Mass Spectrometry Data from MetaboLights


Bioconductor version: Release (3.20)

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] , Philippine Louail [aut]

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

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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

Details

biocViews DataImport, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 1.0.0
In Bioconductor since BioC 3.20 (R-4.4) (< 6 months)
License Artistic-2.0
Depends R (>= 4.2.0), Spectra(>= 1.15.12)
Imports curl, ProtGenerics, BiocFileCache, S4Vectors, methods
System Requirements
URL https://github.com/RforMassSpectrometry/MsBackendMetaboLights
Bug Reports https://github.com/RforMassSpectrometry/MsBackendMetaboLights/issues
See More
Suggests testthat, rmarkdown, mzR, knitr, BiocStyle
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Package Archives

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

Source Package MsBackendMetaboLights_1.0.0.tar.gz
Windows Binary (x86_64) MsBackendMetaboLights_1.0.0.zip
macOS Binary (x86_64) MsBackendMetaboLights_1.0.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/MsBackendMetaboLights
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MsBackendMetaboLights
Bioc Package Browser https://code.bioconductor.org/browse/MsBackendMetaboLights/
Package Short Url https://bioconductor.org/packages/MsBackendMetaboLights/
Package Downloads Report Download Stats