recipe bioconductor-microbiomedatasets

Experiment Hub based microbiome datasets






microbiomeDataSets is a collection of microbiome datasets loaded from Bioconductor'S ExperimentHub infrastructure. The datasets serve as reference for workflows and vignettes published adjacent to the microbiome analysis tools on Bioconductor. Additional datasets can be added overtime and additions from authors are welcome.

package bioconductor-microbiomedatasets

(downloads) docker_bioconductor-microbiomedatasets



depends bioconductor-biocgenerics:


depends bioconductor-biostrings:


depends bioconductor-data-packages:


depends bioconductor-experimenthub:


depends bioconductor-multiassayexperiment:


depends bioconductor-summarizedexperiment:


depends bioconductor-treesummarizedexperiment:


depends curl:

depends r-ape:

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-microbiomedatasets

and update with::

   mamba update bioconductor-microbiomedatasets

To create a new environment, run:

mamba create --name myenvname bioconductor-microbiomedatasets

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

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