recipe bioconductor-miasim

Microbiome Data Simulation



Artistic-2.0 | file LICENSE



Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.

package bioconductor-miasim

(downloads) docker_bioconductor-miasim



depends bioconductor-matrixgenerics:


depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends bioconductor-treesummarizedexperiment:


depends r-base:


depends r-desolve:

depends r-powerlaw:



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-miasim

and update with::

   mamba update bioconductor-miasim

To create a new environment, run:

mamba create --name myenvname bioconductor-miasim

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

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