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

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

bioconductor-oder
=================

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

   Optimising the Definition of Expressed Regions

   :homepage: https://bioconductor.org/packages/3.17/bioc/html/ODER.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-oder <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-oder>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-oder/meta.yaml>`_

   The aim of ODER is to identify previously unannotated expressed regions \(ERs\) using RNA\-sequencing data. For this purpose\, ODER defines and optimises the definition of ERs\, then connected these ERs to genes using junction data. In this way\, ODER improves gene annotation. Gene annotation is a staple input of many bioinformatic pipelines and a more complete gene annotation can enable more accurate interpretation of disease associated variants.


.. conda:package:: bioconductor-oder

   |downloads_bioconductor-oder| |docker_bioconductor-oder|

   :versions:
      
      

      ``1.6.0-0``,  ``1.4.0-0``,  ``1.0.0-0``

      

   
   :depends bioconductor-biocfilecache: ``>=2.8.0,<2.9.0``
   :depends bioconductor-biocgenerics: ``>=0.46.0,<0.47.0``
   :depends bioconductor-dasper: ``>=1.9.0,<1.10.0``
   :depends bioconductor-derfinder: ``>=1.34.0,<1.35.0``
   :depends bioconductor-genomeinfodb: ``>=1.36.0,<1.37.0``
   :depends bioconductor-genomicranges: ``>=1.52.0,<1.53.0``
   :depends bioconductor-iranges: ``>=2.34.0,<2.35.0``
   :depends bioconductor-megadepth: ``>=1.10.0,<1.11.0``
   :depends bioconductor-rtracklayer: ``>=1.60.0,<1.61.0``
   :depends bioconductor-s4vectors: ``>=0.38.0,<0.39.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-data.table: 
   :depends r-dplyr: 
   :depends r-ggplot2: 
   :depends r-ggpubr: 
   :depends r-ggrepel: 
   :depends r-magrittr: 
   :depends r-plyr: 
   :depends r-purrr: 
   :depends r-stringr: 
   :depends r-tibble: 
   :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-oder

   and update with::

      mamba update bioconductor-oder

  To create a new environment, run::

      mamba create --name myenvname bioconductor-oder

  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-oder:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-oder";
        var versions = ["1.6.0","1.4.0","1.0.0"];
    </script>






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

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

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