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

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

bioconductor-raresim
====================

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

   Simulation of Rare Variant Genetic Data

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/RAREsim.html
   :license: GPL-3
   :recipe: /`bioconductor-raresim <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-raresim>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-raresim/meta.yaml>`_

   Haplotype simulations of rare variant genetic data that emulates real data can be performed with RAREsim. RAREsim uses the expected number of variants in MAC bins \- either as provided by default parameters or estimated from target data \- and an abundance of rare variants as simulated HAPGEN2 to probabilistically prune variants. RAREsim produces haplotypes that emulate real sequencing data with respect to the total number of variants\, allele frequency spectrum\, haplotype structure\, and variant annotation.


.. conda:package:: bioconductor-raresim

   |downloads_bioconductor-raresim| |docker_bioconductor-raresim|

   :versions:
      
      

      ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-0``

      

   
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-nloptr: 
   :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 bioconductor-raresim

   and update with::

      mamba update bioconductor-raresim

  To create a new environment, run::

      mamba create --name myenvname bioconductor-raresim

  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-raresim:<tag>

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


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


.. raw:: html

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






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