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

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

bioconductor-wavcluster
=======================

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

   Sensitive and highly resolved identification of RNA\-protein interaction sites in PAR\-CLIP data

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/wavClusteR.html
   :license: GPL-2
   :recipe: /`bioconductor-wavcluster <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-wavcluster>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-wavcluster/meta.yaml>`_
   :links: biotools: :biotools:`wavcluster`

   The package provides an integrated pipeline for the analysis of PAR\-CLIP data. PAR\-CLIP\-induced transitions are first discriminated from sequencing errors\, SNPs and additional non\-experimental sources by a non\- parametric mixture model. The protein binding sites \(clusters\) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework. Post\-processing of the results\, data export for UCSC genome browser visualization and motif search analysis are provided. In addition\, the package allows to integrate RNA\-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. Note\: while wavClusteR was designed for PAR\-CLIP data analysis\, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions \(e.g. BisSeq\).


.. conda:package:: bioconductor-wavcluster

   |downloads_bioconductor-wavcluster| |docker_bioconductor-wavcluster|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>2.36.0-0</code>,  <code>2.34.0-0</code>,  <code>2.32.0-0</code>,  <code>2.28.0-0</code>,  <code>2.26.0-0</code>,  <code>2.24.0-1</code>,  <code>2.24.0-0</code>,  <code>2.22.0-0</code>,  <code>2.20.0-0</code>,  </span></summary>
      

      ``2.36.0-0``,  ``2.34.0-0``,  ``2.32.0-0``,  ``2.28.0-0``,  ``2.26.0-0``,  ``2.24.0-1``,  ``2.24.0-0``,  ``2.22.0-0``,  ``2.20.0-0``,  ``2.18.0-1``,  ``2.16.0-0``,  ``2.14.0-0``,  ``2.11.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0``
   :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0``
   :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-foreach: 
   :depends r-ggplot2: 
   :depends r-hmisc: 
   :depends r-mclust: 
   :depends r-seqinr: 
   :depends r-stringr: 
   :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-wavcluster

   and update with::

      mamba update bioconductor-wavcluster

  To create a new environment, run::

      mamba create --name myenvname bioconductor-wavcluster

  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-wavcluster:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-wavcluster";
        var versions = ["2.36.0","2.34.0","2.32.0","2.28.0","2.26.0"];
    </script>






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

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

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