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

.. title:: Package Recipe 'transdecoder'
.. highlight: bash

transdecoder
============

.. conda:recipe:: transdecoder
   :replaces_section_title:
   :noindex:

   TransDecoder identifies candidate coding regions within transcript sequences\, such as those generated by de novo RNA\-Seq transcript assembly using Trinity\, or constructed based on RNA\-Seq alignments to the genome using Tophat and Cufflinks.

   :homepage: https://transdecoder.github.io/
   :developer docs: https://github.com/TransDecoder/TransDecoder
   :license: Broad Institute
   :recipe: /`transdecoder <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/transdecoder>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/transdecoder/meta.yaml>`_

   


.. conda:package:: transdecoder

   |downloads_transdecoder| |docker_transdecoder|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>5.7.1-0</code>,  <code>5.7.0-0</code>,  <code>5.5.0-5</code>,  <code>5.5.0-4</code>,  <code>5.5.0-3</code>,  <code>5.5.0-2</code>,  <code>5.5.0-1</code>,  <code>5.5.0-0</code>,  <code>5.3.0-0</code>,  </span></summary>
      

      ``5.7.1-0``,  ``5.7.0-0``,  ``5.5.0-5``,  ``5.5.0-4``,  ``5.5.0-3``,  ``5.5.0-2``,  ``5.5.0-1``,  ``5.5.0-0``,  ``5.3.0-0``,  ``5.2.0-0``,  ``5.1.0-0``,  ``5.0.2-0``,  ``3.0.1-2``,  ``3.0.1-1``,  ``3.0.1-0``,  ``2.1.0-5``,  ``2.1.0-4``,  ``2.1.0-3``,  ``2.1.0-2``,  ``2.1.0-1``,  ``2.1.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-seqlogo: 
   :depends perl: ``>=5.32.1,<6.0a0 *_perl5``
   :depends perl-db-file: 
   :depends perl-uri: 
   :depends r-ggplot2: 
   :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 transdecoder

   and update with::

      mamba update transdecoder

  To create a new environment, run::

      mamba create --name myenvname transdecoder

  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/transdecoder:<tag>

   (see `transdecoder/tags`_ for valid values for ``<tag>``)


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


.. raw:: html

    <script>
        var package = "transdecoder";
        var versions = ["5.7.1","5.7.0","5.5.0","5.5.0","5.5.0"];
    </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/transdecoder/README.html)

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