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

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

bioconductor-ensembldb
======================

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

   Utilities to create and use Ensembl\-based annotation databases

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

   The package provides functions to create and use transcript centric annotation databases\/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package\, but\, in addition to retrieve all gene\/transcript models and annotations from the database\, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally\, ensembldb provides functions to map between genomic\, transcript and protein coordinates.


.. conda:package:: bioconductor-ensembldb

   |downloads_bioconductor-ensembldb| |docker_bioconductor-ensembldb|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>2.26.0-0</code>,  <code>2.24.0-0</code>,  <code>2.22.0-0</code>,  <code>2.18.1-0</code>,  <code>2.16.0-0</code>,  <code>2.14.0-1</code>,  <code>2.14.0-0</code>,  <code>2.12.1-0</code>,  <code>2.10.0-0</code>,  </span></summary>
      

      ``2.26.0-0``,  ``2.24.0-0``,  ``2.22.0-0``,  ``2.18.1-0``,  ``2.16.0-0``,  ``2.14.0-1``,  ``2.14.0-0``,  ``2.12.1-0``,  ``2.10.0-0``,  ``2.8.0-1``,  ``2.6.3-0``,  ``2.4.1-0``,  ``2.2.2-0``,  ``2.2.0-0``,  ``2.0.4-0``,  ``1.6.2-0``,  ``1.6.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0``
   :depends bioconductor-annotationfilter: ``>=1.26.0,<1.27.0``
   :depends bioconductor-biobase: ``>=2.62.0,<2.63.0``
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0``
   :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-protgenerics: ``>=1.34.0,<1.35.0``
   :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0``
   :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-curl: 
   :depends r-dbi: 
   :depends r-rsqlite: ``>=1.1``
   :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-ensembldb

   and update with::

      mamba update bioconductor-ensembldb

  To create a new environment, run::

      mamba create --name myenvname bioconductor-ensembldb

  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-ensembldb:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-ensembldb";
        var versions = ["2.26.0","2.24.0","2.22.0","2.18.1","2.16.0"];
    </script>






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

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

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