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

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

bioconductor-sseq
=================

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

   Shrinkage estimation of dispersion in Negative Binomial models for RNA\-seq experiments with small sample size

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/sSeq.html
   :license: GPL (>= 3)
   :recipe: /`bioconductor-sseq <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-sseq>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-sseq/meta.yaml>`_
   :links: biotools: :biotools:`sseq`, doi: :doi:`10.1093/bioinformatics/btt143`

   The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA\-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial \(NB\) distribution using a shrinkage approach for dispersion estimation. The method of moment \(MM\) estimates for dispersion are shrunk towards an estimated target\, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per\-gene probability under the NB model is calculated\, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.


.. conda:package:: bioconductor-sseq

   |downloads_bioconductor-sseq| |docker_bioconductor-sseq|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.40.0-0</code>,  <code>1.38.0-0</code>,  <code>1.36.0-0</code>,  <code>1.32.0-0</code>,  <code>1.30.0-0</code>,  <code>1.28.0-1</code>,  <code>1.28.0-0</code>,  <code>1.26.0-0</code>,  <code>1.24.0-0</code>,  </span></summary>
      

      ``1.40.0-0``,  ``1.38.0-0``,  ``1.36.0-0``,  ``1.32.0-0``,  ``1.30.0-0``,  ``1.28.0-1``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-1``,  ``1.22.0-0``,  ``1.20.1-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-catools: 
   :depends r-rcolorbrewer: 
   :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-sseq

   and update with::

      mamba update bioconductor-sseq

  To create a new environment, run::

      mamba create --name myenvname bioconductor-sseq

  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-sseq:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-sseq";
        var versions = ["1.40.0","1.38.0","1.36.0","1.32.0","1.30.0"];
    </script>






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

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

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