DOI: 10.18129/B9.bioc.biodbHmdb  

biodbHmdb, a library for connecting to the HMDB Database

Bioconductor version: Release (3.17)

The biodbHmdb library is an extension of the biodb framework package that provides access to the HMDB Metabolites database. It allows to download the whole HMDB Metabolites database locally, access entries and search for entries by name or description. A future version of this package will also include a search by mass and mass spectra annotation.

Author: Pierrick Roger [aut, cre]

Maintainer: Pierrick Roger <pierrick.roger at>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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HTML R Script Introduction to the biodbHmdb package.
PDF   Reference Manual
Text   NEWS


biocViews DataImport, Infrastructure, Software
Version 1.6.1
In Bioconductor since BioC 3.14 (R-4.1) (2 years)
License AGPL-3
Depends R (>= 4.1)
Imports R6, biodb(>= 1.3.2), Rcpp, zip
LinkingTo Rcpp, testthat
Suggests BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, lgr
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package biodbHmdb_1.6.1.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) biodbHmdb_1.6.1.tgz
macOS Binary (arm64) biodbHmdb_1.6.1.tgz
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