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

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

bioconductor-degreport
======================

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

   Report of DEG analysis

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/DEGreport.html
   :license: MIT + file LICENSE
   :recipe: /`bioconductor-degreport <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-degreport>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-degreport/meta.yaml>`_
   :links: biotools: :biotools:`degreport`, doi: :doi:`10.1038/nmeth.3252`

   Creation of a HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes\, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.


.. conda:package:: bioconductor-degreport

   |downloads_bioconductor-degreport| |docker_bioconductor-degreport|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.38.4-0</code>,  <code>1.36.0-0</code>,  <code>1.34.0-0</code>,  <code>1.30.0-0</code>,  <code>1.28.0-0</code>,  <code>1.26.0-1</code>,  <code>1.26.0-0</code>,  <code>1.24.0-0</code>,  <code>1.22.0-0</code>,  </span></summary>
      

      ``1.38.4-0``,  ``1.36.0-0``,  ``1.34.0-0``,  ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-1``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-1``,  ``1.19.1-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.8.2-1``,  ``1.8.2-0``,  ``1.7.2-1``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biobase: ``>=2.62.0,<2.63.0``
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-complexheatmap: ``>=2.18.0,<2.19.0``
   :depends bioconductor-consensusclusterplus: ``>=1.66.0,<1.67.0``
   :depends bioconductor-deseq2: ``>=1.42.0,<1.43.0``
   :depends bioconductor-edger: ``>=4.0.0,<4.1.0``
   :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-broom: 
   :depends r-circlize: 
   :depends r-cluster: 
   :depends r-cowplot: 
   :depends r-dendextend: 
   :depends r-dplyr: 
   :depends r-ggdendro: 
   :depends r-ggplot2: 
   :depends r-ggrepel: 
   :depends r-knitr: 
   :depends r-logging: 
   :depends r-magrittr: 
   :depends r-psych: 
   :depends r-rcolorbrewer: 
   :depends r-reshape: 
   :depends r-rlang: 
   :depends r-scales: 
   :depends r-stringi: 
   :depends r-stringr: 
   :depends r-tibble: 
   :depends r-tidyr: 
   :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-degreport

   and update with::

      mamba update bioconductor-degreport

  To create a new environment, run::

      mamba create --name myenvname bioconductor-degreport

  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-degreport:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-degreport";
        var versions = ["1.38.4","1.36.0","1.34.0","1.30.0","1.28.0"];
    </script>






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

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

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