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

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

bioconductor-fishpond
=====================

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

   Fishpond\: downstream methods and tools for expression data

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

   Fishpond contains methods for differential transcript and gene expression analysis of RNA\-seq data using inferential replicates for uncertainty of abundance quantification\, as generated by Gibbs sampling or bootstrap sampling. Also the package contains a number of utilities for working with Salmon and Alevin quantification files.


.. conda:package:: bioconductor-fishpond

   |downloads_bioconductor-fishpond| |docker_bioconductor-fishpond|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>2.8.0-0</code>,  <code>2.6.2-0</code>,  <code>2.4.0-0</code>,  <code>2.0.1-1</code>,  <code>2.0.1-0</code>,  <code>2.0.0-0</code>,  <code>1.8.0-0</code>,  <code>1.6.0-1</code>,  <code>1.6.0-0</code>,  </span></summary>
      

      ``2.8.0-0``,  ``2.6.2-0``,  ``2.4.0-0``,  ``2.0.1-1``,  ``2.0.1-0``,  ``2.0.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-qvalue: ``>=2.34.0,<2.35.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends r-abind: 
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-gtools: 
   :depends r-jsonlite: 
   :depends r-matrix: 
   :depends r-matrixstats: 
   :depends r-svmisc: 
   :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-fishpond

   and update with::

      mamba update bioconductor-fishpond

  To create a new environment, run::

      mamba create --name myenvname bioconductor-fishpond

  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-fishpond:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-fishpond";
        var versions = ["2.8.0","2.6.2","2.4.0","2.0.1","2.0.1"];
    </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-fishpond/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-fishpond/README.html