:orphan:  .. only available via index, not via toctree

.. title:: Package Recipe 'bioconductor-animalcules'
.. highlight: bash

bioconductor-animalcules
========================

.. conda:recipe:: bioconductor-animalcules
   :replaces_section_title:
   :noindex:

   Interactive microbiome analysis toolkit

   :homepage: https://bioconductor.org/packages/3.14/bioc/html/animalcules.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-animalcules <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-animalcules>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-animalcules/meta.yaml>`_

   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.


.. conda:package:: bioconductor-animalcules

   |downloads_bioconductor-animalcules| |docker_bioconductor-animalcules|

   :versions:
      
      

      ``1.10.0-0``,  ``1.6.0-1``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.6-0``

      

   
   :depends bioconductor-biomformat: ``>=1.22.0,<1.23.0``
   :depends bioconductor-deseq2: ``>=1.34.0,<1.35.0``
   :depends bioconductor-limma: ``>=3.50.0,<3.51.0``
   :depends bioconductor-multiassayexperiment: ``>=1.20.0,<1.21.0``
   :depends bioconductor-s4vectors: ``>=0.32.0,<0.33.0``
   :depends bioconductor-summarizedexperiment: ``>=1.24.0,<1.25.0``
   :depends r-ape: 
   :depends r-assertthat: 
   :depends r-base: ``>=4.1,<4.2.0a0``
   :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: 
   :requirements:

   .. rubric:: Installation

   With an activated Bioconda channel (see :ref:`set-up-channels`), install with::

      conda install bioconductor-animalcules

   and update with::

      conda update bioconductor-animalcules

   or use the docker container::

      docker pull quay.io/biocontainers/bioconductor-animalcules:<tag>

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


.. |downloads_bioconductor-animalcules| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-animalcules.svg?style=flat
   :target: https://anaconda.org/bioconda/bioconductor-animalcules
   :alt:   (downloads)
.. |docker_bioconductor-animalcules| image:: https://quay.io/repository/biocontainers/bioconductor-animalcules/status
   :target: https://quay.io/repository/biocontainers/bioconductor-animalcules
.. _`bioconductor-animalcules/tags`: https://quay.io/repository/biocontainers/bioconductor-animalcules?tab=tags


.. raw:: html

    <script>
        var package = "bioconductor-animalcules";
        var versions = ["1.10.0","1.6.0","1.6.0","1.4.0","1.2.0"];
    </script>






Download stats
-----------------

.. raw:: html
    :file: ../../templates/package_dashboard.html

Link to this page
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Render an |install-with-bioconda| badge with the following MarkDown::

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.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/bioconductor-animalcules/README.html