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

.. title:: Package Recipe 'r-dartr'
.. highlight: bash

r-dartr
=======

.. conda:recipe:: r-dartr
   :replaces_section_title:
   :noindex:

   Functions are provided that facilitate the import and analysis of SNP \(single nucleotide polymorphism\) and silicodart \(presence\/absence\) data. The main focus is on data generated by DarT \(Diversity Arrays Technology\). However\, once SNP or related fragment presence\/absence data from any source is imported into a genlight object many of the functions can be used. Functions are available for input and output of SNP and silicodart data\, for reporting on and filtering on various criteria \(e.g. CallRate\, Heterozygosity\, Reproducibility\, maximum allele frequency\). Advanced filtering is based on Linkage Disequilibrium and HWE \(Hardy\-Weinberg equilibrium\). Other functions are available for visualization after PCoA \(Principle Coordinate Analysis\)\, or to facilitate transfer of data between genlight\/genind objects and newhybrids\, related\, phylip\, structure\, faststructure packages.

   :homepage: https://CRAN.R-project.org/package=dartR
   :license: GPL3 / GPL-3.0-or-later
   :recipe: /`r-dartr <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/r-dartr>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/r-dartr/meta.yaml>`_

   


.. conda:package:: r-dartr

   |downloads_r-dartr| |docker_r-dartr|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>2.9.7-1</code>,  <code>2.9.7-0</code>,  <code>2.0.4-1</code>,  <code>2.0.4-0</code>,  <code>2.0.3-0</code>,  <code>1.9.9.1-1</code>,  <code>1.9.9.1-0</code>,  <code>1.9.6-0</code>,  <code>1.9.4-0</code>,  </span></summary>
      

      ``2.9.7-1``,  ``2.9.7-0``,  ``2.0.4-1``,  ``2.0.4-0``,  ``2.0.3-0``,  ``1.9.9.1-1``,  ``1.9.9.1-0``,  ``1.9.6-0``,  ``1.9.4-0``,  ``1.1.11-2``,  ``1.1.11-1``,  ``1.1.11-0``,  ``1.0.5-1``,  ``1.0.5-0``,  ``1.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-snprelate: 
   :depends r-adegenet: ``>=2.0.0``
   :depends r-ape: 
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-crayon: 
   :depends r-dartr.data: 
   :depends r-data.table: 
   :depends r-dplyr: 
   :depends r-fields: 
   :depends r-foreach: 
   :depends r-ggplot2: 
   :depends r-gridextra: 
   :depends r-mass: 
   :depends r-patchwork: 
   :depends r-plyr: 
   :depends r-popgenreport: 
   :depends r-raster: 
   :depends r-reshape2: 
   :depends r-shiny: 
   :depends r-sp: ``>=1.6.1``
   :depends r-stampp: 
   :depends r-stringr: 
   :depends r-tidyr: 
   :depends r-vegan: 
   :requirements:

   .. 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 r-dartr

   and update with::

      mamba update r-dartr

  To create a new environment, run::

      mamba create --name myenvname r-dartr

  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/r-dartr:<tag>

   (see `r-dartr/tags`_ for valid values for ``<tag>``)


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


.. raw:: html

    <script>
        var package = "r-dartr";
        var versions = ["2.9.7","2.9.7","2.0.4","2.0.4","2.0.3"];
    </script>






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

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