MsBackendMetabolomicsWorkbench
This is the development version of MsBackendMetabolomicsWorkbench; to use it, please install the devel version of Bioconductor.
Retrieve Mass Spectrometry Data from Metabolomics Workbench
Bioconductor version: Development (3.24)
Metabolomics Workbench is one of the main public repositories for storage of metabolomics experiments. The MsBackendMetabolomicsWorkbench package provides functionality to retrieve and represent mass spectrometry (MS) data from Metabolomics Workbench. 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 MsBackendMetabolomicsWorkbench package.
Author: Gabriele Tomè [aut, cre] (ORCID:
, fnd: MetaRbolomics4Galaxy project (CUP: D53C25001030003) co-funded by the Autonomous Province of Bolzano under the Joint Projects South Tyrol–Germany 2025 program.), Philippine Louail [aut]
, Johannes Rainer [aut]
Maintainer: Gabriele Tomè <gabriele.tome at eurac.edu>
citation("MsBackendMetabolomicsWorkbench")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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("MsBackendMetabolomicsWorkbench")
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("MsBackendMetabolomicsWorkbench")| Retrieve and Use Mass Spectrometry Data from Metabolomics Workbench | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL-3 |
| Depends | R (>= 4.2.0), Spectra(>= 1.15.12) |
| Imports | rvest, httr2, curl, ProtGenerics, BiocFileCache, S4Vectors, methods, MsCoreUtils(>= 1.23.9), jsonlite, plyr, tidyr, archive |
| System Requirements | |
| URL | https://github.com/RforMassSpectrometry/MsBackendMetabolomicsWorkbench |
| Bug Reports | https://github.com/RforMassSpectrometry/MsBackendMetabolomicsWorkbench/issues |
See More
| Suggests | testthat, rmarkdown, mzR, knitr, BiocStyle |
| Linking To | |
| Enhances | |
| 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 | MsBackendMetabolomicsWorkbench_0.99.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | MsBackendMetabolomicsWorkbench_0.99.1.tgz |
| macOS Binary (sonoma-arm64) | MsBackendMetabolomicsWorkbench_0.99.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MsBackendMetabolomicsWorkbench |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MsBackendMetabolomicsWorkbench |
| Bioc Package Browser | https://code.bioconductor.org/browse/MsBackendMetabolomicsWorkbench/ |
| Package Short Url | https://bioconductor.org/packages/MsBackendMetabolomicsWorkbench/ |
| Package Downloads Report | Download Stats |