MetaboCoreUtils
This is the released version of MetaboCoreUtils; for the devel version, see MetaboCoreUtils.
Core Utils for Metabolomics Data
Bioconductor version: Release (3.23)
MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound mass-to-charge ratios and masses or functions to work with chemical formulas. The package provides also a set of adduct definitions and information on some commercially available internal standard mixes commonly used in MS experiments.
Author: Johannes Rainer [aut, cre]
, Michael Witting [aut]
, Andrea Vicini [aut], Liesa Salzer [ctb]
, Sebastian Gibb [aut]
, Michael Stravs [ctb]
, Roger Gine [aut]
, William Kumler [aut]
, Philippine Louail [aut]
, Gabriele Tomè [aut] (ORCID:
, 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("MetaboCoreUtils")):
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")
BiocManager::install("MetaboCoreUtils")
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("MetaboCoreUtils")| Core Utils for Metabolomics Data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, MassSpectrometry, Metabolomics, Software |
| Version | 1.20.1 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0) |
| Imports | utils, MsCoreUtils, BiocParallel, methods, stats |
| System Requirements | |
| URL | https://github.com/RforMassSpectrometry/MetaboCoreUtils |
| Bug Reports | https://github.com/RforMassSpectrometry/MetaboCoreUtils/issues |
See More
| Suggests | BiocStyle, testthat, knitr, rmarkdown, robustbase |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | CompoundDb, MetaboAnnotation, MsQuality, Spectra, xcms, pubchem.bio |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MetaboCoreUtils_1.20.1.tar.gz |
| Windows Binary (x86_64) | MetaboCoreUtils_1.20.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | MetaboCoreUtils_1.20.1.tgz |
| macOS Binary (sonoma-arm64) | MetaboCoreUtils_1.20.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MetaboCoreUtils |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MetaboCoreUtils |
| Bioc Package Browser | https://code.bioconductor.org/browse/MetaboCoreUtils/ |
| Package Short Url | https://bioconductor.org/packages/MetaboCoreUtils/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |