recipe bioconductor-animalcules

Interactive microbiome analysis toolkit






animalcules is an R package for utilizing up-to-date data analytics, visualization methods, and machine learning models to provide users an easy-to-use interactive microbiome analysis framework. It can be used as a standalone software package or users can explore their data with the accompanying interactive R Shiny application. Traditional microbiome analysis such as alpha/beta diversity and differential abundance analysis are enhanced, while new methods like biomarker identification are introduced by animalcules. Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights.

package bioconductor-animalcules

(downloads) docker_bioconductor-animalcules



depends bioconductor-biomformat:


depends bioconductor-deseq2:


depends bioconductor-limma:


depends bioconductor-multiassayexperiment:


depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends r-ape:

depends r-assertthat:

depends r-base:


depends r-caret:

depends r-covr:

depends r-dplyr:

depends r-dt:

depends r-forcats:

depends r-ggplot2:

depends r-glmnet:

depends r-gunifrac:

depends r-lattice:

depends r-magrittr:

depends r-matrix:

depends r-plotly:

depends r-plotroc:

depends r-rentrez:

depends r-reshape2:

depends r-scales:

depends r-shiny:

depends r-shinyjs:

depends r-tibble:

depends r-tsne:

depends r-umap:

depends r-vegan:

depends r-xml:



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-animalcules

and update with::

   mamba update bioconductor-animalcules

To create a new environment, run:

mamba create --name myenvname bioconductor-animalcules

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

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