recipe bioconductor-compounddb

Creating and Using (Chemical) Compound Annotation Databases






CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor's Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.

package bioconductor-compounddb

(downloads) docker_bioconductor-compounddb



depends bioconductor-annotationfilter:


depends bioconductor-biobase:


depends bioconductor-biocgenerics:


depends bioconductor-biocparallel:


depends bioconductor-chemminer:


depends bioconductor-iranges:


depends bioconductor-metabocoreutils:


depends bioconductor-mscoreutils:


depends bioconductor-protgenerics:


depends bioconductor-s4vectors:


depends bioconductor-spectra:


depends r-base:


depends r-dbi:

depends r-dbplyr:

depends r-dplyr:

depends r-jsonlite:

depends r-rsqlite:

depends r-tibble:

depends r-xml2:



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-compounddb

and update with::

   mamba update bioconductor-compounddb

To create a new environment, run:

mamba create --name myenvname bioconductor-compounddb

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-compounddb/tags`_ for valid values for ``<tag>``)

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