recipe bioconductor-microstasis

Microbiota STability ASsessment via Iterative cluStering






The toolkit 'µSTASIS', or microSTASIS, has been developed for the stability analysis of microbiota in a temporal framework by leveraging on iterative clustering. Concretely, the core function uses Hartigan-Wong k-means algorithm as many times as possible for stressing out paired samples from the same individuals to test if they remain together for multiple numbers of clusters over a whole data set of individuals. Moreover, the package includes multiple functions to subset samples from paired times, validate the results or visualize the output.

package bioconductor-microstasis

(downloads) docker_bioconductor-microstasis



depends bioconductor-biocparallel:


depends bioconductor-treesummarizedexperiment:


depends r-base:


depends r-ggplot2:

depends r-ggside:

depends r-rlang:

depends r-stringr:



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-microstasis

and update with::

   mamba update bioconductor-microstasis

To create a new environment, run:

mamba create --name myenvname bioconductor-microstasis

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

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