recipe bioconductor-microbiomeexplorer

Microbiome Exploration App






The MicrobiomeExplorer R package is designed to facilitate the analysis and visualization of marker-gene survey feature data. It allows a user to perform and visualize typical microbiome analytical workflows either through the command line or an interactive Shiny application included with the package. In addition to applying common analytical workflows the application enables automated analysis report generation.

package bioconductor-microbiomeexplorer

(downloads) docker_bioconductor-microbiomeexplorer



depends bioconductor-biobase:


depends bioconductor-biomformat:


depends bioconductor-deseq2:


depends bioconductor-limma:


depends bioconductor-metagenomeseq:


depends r-base:


depends r-broom:

depends r-car:

depends r-dplyr:

depends r-dt:


depends r-forcats:

depends r-heatmaply:

depends r-knitr:

depends r-lubridate:

depends r-magrittr:

depends r-matrixstats:

depends r-plotly:


depends r-purrr:

depends r-rcolorbrewer:

depends r-readr:

depends r-reshape2:

depends r-rlang:

depends r-rmarkdown:


depends r-shiny:

depends r-shinycssloaders:

depends r-shinydashboard:

depends r-shinyjs:


depends r-shinywidgets:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

depends r-vegan:



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-microbiomeexplorer

and update with::

   mamba update bioconductor-microbiomeexplorer

To create a new environment, run:

mamba create --name myenvname bioconductor-microbiomeexplorer

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

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