recipe bioconductor-microbiomebenchmarkdata

Datasets for benchmarking in microbiome research






The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available.

package bioconductor-microbiomebenchmarkdata

(downloads) docker_bioconductor-microbiomebenchmarkdata



depends bioconductor-biocfilecache:


depends bioconductor-data-packages:


depends bioconductor-s4vectors:


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-microbiomebenchmarkdata

and update with::

   mamba update bioconductor-microbiomebenchmarkdata

To create a new environment, run:

mamba create --name myenvname bioconductor-microbiomebenchmarkdata

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

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