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

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

bioconductor-recount
====================

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

   Explore and download data from the recount project

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/recount.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-recount <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-recount>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-recount/meta.yaml>`_

   Explore and download data from the recount project available at https\:\/\/jhubiostatistics.shinyapps.io\/recount\/. Using the recount package you can download RangedSummarizedExperiment objects at the gene\, exon or exon\-exon junctions level\, the raw counts\, the phenotype metadata used\, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http\:\/\/bioconductor.org\/packages\/derfinder you can perform annotation\-agnostic differential expression analyses with the data from the recount project as described at http\:\/\/www.nature.com\/nbt\/journal\/v35\/n4\/full\/nbt.3838.html.


.. conda:package:: bioconductor-recount

   |downloads_bioconductor-recount| |docker_bioconductor-recount|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.28.0-0</code>,  <code>1.26.0-0</code>,  <code>1.24.0-0</code>,  <code>1.20.0-0</code>,  <code>1.18.0-0</code>,  <code>1.16.1-0</code>,  <code>1.16.0-0</code>,  <code>1.14.0-0</code>,  <code>1.12.0-0</code>,  </span></summary>
      

      ``1.28.0-0``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.1-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.8-0``,  ``1.8.1-0``,  ``1.6.3-0``,  ``1.4.5-0``,  ``1.4.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0``
   :depends bioconductor-derfinder: ``>=1.36.0,<1.37.0``
   :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-geoquery: ``>=2.70.0,<2.71.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-downloader: 
   :depends r-rcurl: 
   :depends r-rentrez: 
   :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-recount

   and update with::

      mamba update bioconductor-recount

  To create a new environment, run::

      mamba create --name myenvname bioconductor-recount

  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-recount:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-recount";
        var versions = ["1.28.0","1.26.0","1.24.0","1.20.0","1.18.0"];
    </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/bioconductor-recount/README.html)

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