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

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

bioconductor-genomation
=======================

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

   Summary\, annotation and visualization of genomic data

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/genomation.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-genomation <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-genomation>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-genomation/meta.yaml>`_
   :links: biotools: :biotools:`genomation`

   A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre\-defined functional regions\, such as promoters\, exons\, introns\, etc. The genomic intervals represent regions with a defined chromosome position\, which may be associated with a score\, such as aligned reads from HT\-seq experiments\, TF binding sites\, methylation scores\, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition\, It can use BAM or BigWig files as input.


.. conda:package:: bioconductor-genomation

   |downloads_bioconductor-genomation| |docker_bioconductor-genomation|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.34.0-0</code>,  <code>1.32.0-0</code>,  <code>1.30.0-1</code>,  <code>1.30.0-0</code>,  <code>1.26.0-2</code>,  <code>1.26.0-1</code>,  <code>1.26.0-0</code>,  <code>1.24.0-0</code>,  <code>1.22.0-1</code>,  </span></summary>
      

      ``1.34.0-0``,  ``1.32.0-0``,  ``1.30.0-1``,  ``1.30.0-0``,  ``1.26.0-2``,  ``1.26.0-1``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-1``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-1``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.6.0-0``,  ``1.4.2-0``,  ``1.2.2-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0``
   :depends bioconductor-biostrings: ``>=2.70.1,<2.71.0a0``
   :depends bioconductor-bsgenome: ``>=1.70.0,<1.71.0``
   :depends bioconductor-bsgenome: ``>=1.70.1,<1.71.0a0``
   :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomeinfodb: ``>=1.38.1,<1.39.0a0``
   :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0a0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-genomicranges: ``>=1.54.1,<1.55.0a0``
   :depends bioconductor-impute: ``>=1.76.0,<1.77.0``
   :depends bioconductor-impute: ``>=1.76.0,<1.77.0a0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0``
   :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0``
   :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0a0``
   :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0``
   :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0a0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-s4vectors: ``>=0.40.2,<0.41.0a0``
   :depends bioconductor-seqpattern: ``>=1.34.0,<1.35.0``
   :depends bioconductor-seqpattern: ``>=1.34.0,<1.35.0a0``
   :depends libblas: ``>=3.9.0,<4.0a0``
   :depends libgcc-ng: ``>=12``
   :depends liblapack: ``>=3.9.0,<4.0a0``
   :depends libstdcxx-ng: ``>=12``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-data.table: 
   :depends r-ggplot2: 
   :depends r-gridbase: 
   :depends r-matrixstats: 
   :depends r-plotrix: 
   :depends r-plyr: 
   :depends r-rcpp: ``>=0.12.14``
   :depends r-readr: 
   :depends r-reshape2: 
   :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-genomation

   and update with::

      mamba update bioconductor-genomation

  To create a new environment, run::

      mamba create --name myenvname bioconductor-genomation

  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-genomation:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-genomation";
        var versions = ["1.34.0","1.32.0","1.30.0","1.30.0","1.26.0"];
    </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/bioconductor-genomation/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-genomation/README.html