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

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

bioconductor-lefser
===================

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

   R implementation of the LEfSE method for microbiome biomarker discovery

   :homepage: https://bioconductor.org/packages/3.20/bioc/html/lefser.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-lefser <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-lefser>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-lefser/meta.yaml>`_

   lefser is the R implementation of the popular microbiome biomarker discovery too\, LEfSe. It uses the Kruskal\-Wallis test\, Wilcoxon\-Rank Sum test\, and Linear Discriminant Analysis to find biomarkers from two\-level classes \(and optional sub\-classes\).


.. conda:package:: bioconductor-lefser

   |downloads_bioconductor-lefser| |docker_bioconductor-lefser|

   :versions:
      
      

      ``1.16.0-0``,  ``1.12.1-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-2``,  ``1.0.0-1``

      

   
   :depends bioconductor-ggtree: ``>=3.14.0,<3.15.0``
   :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0``
   :depends bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0``
   :depends r-base: ``>=4.4,<4.5.0a0``
   :depends r-coin: 
   :depends r-dplyr: 
   :depends r-forcats: 
   :depends r-ggplot2: 
   :depends r-mass: 
   :depends r-stringr: 
   :depends r-testthat: 
   :depends r-tibble: 
   :depends r-tidyr: 
   :requirements:

   :additional platforms:
      

   .. rubric:: Installation

  You need a conda-compatible package manager
  (currently either `micromamba <https://mamba.readthedocs.io>`_, `mamba <https://mamba.readthedocs.io>`_, or `conda <https://docs.conda.io/projects/conda>`_)
  and the Bioconda channel already activated (see :ref:`set-up-channels`).

  While any of above package managers is fine, it is currently recommended to use either
  micromamba or mamba (see `here <https://mamba.readthedocs.io>`_ 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-lefser

   and update with::

      mamba update bioconductor-lefser

  To create a new environment, run::

      mamba create --name myenvname bioconductor-lefser

  with ``myenvname`` being a reasonable name for the environment
  (see e.g. the `mamba docs <https://mamba.readthedocs.io>`_ for details and further options).

  Alternatively, use the docker container::

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

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


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


.. raw:: html

    <script>
        var package = "bioconductor-lefser";
        var versions = ["1.16.0","1.12.1","1.10.0","1.8.0","1.4.0"];
    </script>






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

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

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