recipe bioconductor-ahpubmeddbs

SQLites, tibbles, and data.tables for AnnotationHub






Supplies AnnotationHub with some preprocessed sqlite, tibble, and data.table datasets of PubMed. All the datasets are generated by our Snakemake workflow [pubmed-workflow]( For the details, see the of pubmed-workflow.

package bioconductor-ahpubmeddbs

(downloads) docker_bioconductor-ahpubmeddbs



depends bioconductor-annotationhub:


depends bioconductor-data-packages:


depends curl:

depends r-base:




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-ahpubmeddbs

and update with::

   mamba update bioconductor-ahpubmeddbs

To create a new environment, run:

mamba create --name myenvname bioconductor-ahpubmeddbs

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

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