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

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

bioconductor-recoup
===================

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

   An R package for the creation of complex genomic profile plots

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/recoup.html
   :license: GPL (>= 3)
   :recipe: /`bioconductor-recoup <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-recoup>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-recoup/meta.yaml>`_
   :links: biotools: :biotools:`recoup`, doi: :doi:`10.1038/nmeth.3252`

   recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently\, recoup supports genomic profile plots for reads derived from ChIP\-Seq and RNA\-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.


.. conda:package:: bioconductor-recoup

   |downloads_bioconductor-recoup| |docker_bioconductor-recoup|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.30.0-0</code>,  <code>1.28.0-0</code>,  <code>1.26.0-0</code>,  <code>1.22.0-0</code>,  <code>1.20.0-0</code>,  <code>1.18.0-1</code>,  <code>1.18.0-0</code>,  <code>1.16.0-0</code>,  <code>1.14.0-0</code>,  </span></summary>
      

      ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-1``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-biomart: ``>=2.58.0,<2.59.0``
   :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0``
   :depends bioconductor-complexheatmap: ``>=2.18.0,<2.19.0``
   :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0``
   :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-circlize: 
   :depends r-ggplot2: 
   :depends r-httr: 
   :depends r-rsqlite: 
   :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-recoup

   and update with::

      mamba update bioconductor-recoup

  To create a new environment, run::

      mamba create --name myenvname bioconductor-recoup

  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-recoup:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-recoup";
        var versions = ["1.30.0","1.28.0","1.26.0","1.22.0","1.20.0"];
    </script>






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

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

Link to this page
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