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biodbHmdb, a library for connecting to the HMDB Database

Bioconductor version: Release (3.19)

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 "4.4") and enter:

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


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


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews DataImport, Infrastructure, Software
Version 1.10.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License AGPL-3
Depends R (>= 4.1)
Imports R6, biodb(>= 1.3.2), Rcpp, zip
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Suggests BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, lgr
Linking To Rcpp, testthat
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Package Archives

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

Source Package biodbHmdb_1.10.0.tar.gz
Windows Binary
macOS Binary (x86_64) biodbHmdb_1.10.0.tgz
macOS Binary (arm64) biodbHmdb_1.10.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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