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

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

bioconductor-hiannotator
========================

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

   Functions for annotating GRanges objects

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/hiAnnotator.html
   :license: GPL (>= 2)
   :recipe: /`bioconductor-hiannotator <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-hiannotator>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-hiannotator/meta.yaml>`_
   :links: biotools: :biotools:`hiannotator`, doi: :doi:`10.1038/nmeth.3252`

   hiAnnotator contains set of functions which allow users to annotate a GRanges object with custom set of annotations. The basic philosophy of this package is to take two GRanges objects \(query \& subject\) with common set of seqnames \(i.e. chromosomes\) and return associated annotation per seqnames and rows from the query matching seqnames and rows from the subject \(i.e. genes or cpg islands\). The package comes with three types of annotation functions which calculates if a position from query is\: within a feature\, near a feature\, or count features in defined window sizes. Moreover\, each function is equipped with parallel backend to utilize the foreach package. In addition\, the package is equipped with wrapper functions\, which finds appropriate columns needed to make a GRanges object from a common data frame.


.. conda:package:: bioconductor-hiannotator

   |downloads_bioconductor-hiannotator| |docker_bioconductor-hiannotator|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.36.0-0</code>,  <code>1.34.0-0</code>,  <code>1.32.0-0</code>,  <code>1.28.0-0</code>,  <code>1.26.0-0</code>,  <code>1.24.0-1</code>,  <code>1.24.0-0</code>,  <code>1.22.0-0</code>,  <code>1.20.0-0</code>,  </span></summary>
      

      ``1.36.0-0``,  ``1.34.0-0``,  ``1.32.0-0``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.24.0-1``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-1``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.11.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-bsgenome: ``>=1.70.0,<1.71.0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-dplyr: 
   :depends r-foreach: 
   :depends r-ggplot2: 
   :depends r-iterators: 
   :depends r-scales: 
   :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-hiannotator

   and update with::

      mamba update bioconductor-hiannotator

  To create a new environment, run::

      mamba create --name myenvname bioconductor-hiannotator

  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-hiannotator:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-hiannotator";
        var versions = ["1.36.0","1.34.0","1.32.0","1.28.0","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::

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