recipe bioconductor-eudysbiome

Cartesian plot and contingency test on 16S Microbial data







biotools: eudysbiome, doi: 10.1186/s12918-016-0344-6

eudysbiome a package that permits to annotate the differential genera as harmful/harmless based on their ability to contribute to host diseases (as indicated in literature) or unknown based on their ambiguous genus classification. Further, the package statistically measures the eubiotic (harmless genera increase or harmful genera decrease) or dysbiotic(harmless genera decrease or harmful genera increase) impact of a given treatment or environmental change on the (gut-intestinal, GI) microbiome in comparison to the microbiome of the reference condition.

package bioconductor-eudysbiome

(downloads) docker_bioconductor-eudysbiome



depends bioconductor-biostrings:


depends bioconductor-rsamtools:


depends r-base:


depends r-plyr:

depends r-r.utils:



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-eudysbiome

and update with::

   mamba update bioconductor-eudysbiome

To create a new environment, run:

mamba create --name myenvname bioconductor-eudysbiome

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

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