recipe bioconductor-microbiomedasim

Microbiome Differential Abundance Simulation






A toolkit for simulating differential microbiome data designed for longitudinal analyses. Several functional forms may be specified for the mean trend. Observations are drawn from a multivariate normal model. The objective of this package is to be able to simulate data in order to accurately compare different longitudinal methods for differential abundance.

package bioconductor-microbiomedasim

(downloads) docker_bioconductor-microbiomedasim



depends bioconductor-biobase:


depends bioconductor-metagenomeseq:


depends bioconductor-phyloseq:


depends r-base:


depends r-ggplot2:

depends r-mass:

depends r-matrix:

depends r-mvtnorm:

depends r-pbapply:

depends r-tmvtnorm:



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-microbiomedasim

and update with::

   mamba update bioconductor-microbiomedasim

To create a new environment, run:

mamba create --name myenvname bioconductor-microbiomedasim

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

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