recipe bioconductor-biodb

biodb, a library and a development framework for connecting to chemical and biological databases






The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, …), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.

package bioconductor-biodb

(downloads) docker_bioconductor-biodb



depends bioconductor-biocfilecache:


depends bioconductor-biocfilecache:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends r-base:


depends r-chk:

depends r-git2r:

depends r-jsonlite:

depends r-lgr:

depends r-lifecycle:

depends r-openssl:

depends r-plyr:

depends r-progress:

depends r-r6:

depends r-rappdirs:

depends r-rcpp:

depends r-rcurl:

depends r-rsqlite:

depends r-stringr:

depends r-testthat:

depends r-withr:

depends r-xml:

depends r-yaml:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-biodb

and update with::

   mamba update bioconductor-biodb

To create a new environment, run:

mamba create --name myenvname bioconductor-biodb

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-biodb/tags`_ for valid values for ``<tag>``)

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