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

.. title:: Package Recipe 'paralyzer'
.. highlight: bash

paralyzer
=========

.. conda:recipe:: paralyzer
   :replaces_section_title:
   :noindex:

   We developed the PARalyzer algorithm to generate a high resolution map of interaction sites between RNA\-binding proteins and their targets. The algorithm utilizes the deep sequencing reads generated by PAR\-CLIP \(Photoactivatable\-Ribonucleoside\-Enhanced Crosslinking and Immunoprecipitation\) protocol.The use of photoactivatable nucleotides in the PAR\-CLIP protocol results in more efficient crosslinking between the RNA\-binding protein and its target relative to other CLIP methods\; in addition a nucleotide substitution occurs at the site of crosslinking\, providing for single\-nucleotide resolution binding information. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein\-RNA interaction sites.

   :homepage: https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/
   :license: PARalyzer is provided for academic use only, if you wish to use it in another setting please contact Uwe Ohler.
   :recipe: /`paralyzer <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/paralyzer>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/paralyzer/meta.yaml>`_
   :links: biotools: :biotools:`paralyzer`

   


.. conda:package:: paralyzer

   |downloads_paralyzer| |docker_paralyzer|

   :versions:
      
      

      ``1.5-3``,  ``1.5-2``,  ``1.5-1``,  ``1.5-0``

      

   
   :depends openjdk: 
   :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 paralyzer

   and update with::

      mamba update paralyzer

  To create a new environment, run::

      mamba create --name myenvname paralyzer

  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/paralyzer:<tag>

   (see `paralyzer/tags`_ for valid values for ``<tag>``)


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


.. raw:: html

    <script>
        var package = "paralyzer";
        var versions = ["1.5","1.5","1.5","1.5"];
    </script>






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

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

Link to this page
-----------------

Render an |install-with-bioconda| badge with the following MarkDown::

   [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/paralyzer/README.html)

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