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

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

bioconductor-chippeakanno
=========================

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

   Batch annotation of the peaks identified from either ChIP\-seq\, ChIP\-chip experiments or any experiments resulted in large number of chromosome ranges

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/ChIPpeakAnno.html
   :license: GPL (>= 2)
   :recipe: /`bioconductor-chippeakanno <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-chippeakanno>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-chippeakanno/meta.yaml>`_
   :links: biotools: :biotools:`chippeakanno`

   The package includes functions to retrieve the sequences around the peak\, obtain enriched Gene Ontology \(GO\) terms\, find the nearest gene\, exon\, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5\, new functions have been added for finding the peaks with bi\-directional promoters with summary statistics \(peaksNearBDP\)\, for summarizing the occurrence of motifs in peaks \(summarizePatternInPeaks\) and for adding other IDs to annotated peaks or enrichedGO \(addGeneIDs\). This package leverages the biomaRt\, IRanges\, Biostrings\, BSgenome\, GO.db\, multtest and stat packages.


.. conda:package:: bioconductor-chippeakanno

   |downloads_bioconductor-chippeakanno| |docker_bioconductor-chippeakanno|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>3.36.0-0</code>,  <code>3.34.1-0</code>,  <code>3.32.0-0</code>,  <code>3.28.0-0</code>,  <code>3.26.0-0</code>,  <code>3.24.1-0</code>,  <code>3.24.0-0</code>,  <code>3.22.0-0</code>,  <code>3.20.0-0</code>,  </span></summary>
      

      ``3.36.0-0``,  ``3.34.1-0``,  ``3.32.0-0``,  ``3.28.0-0``,  ``3.26.0-0``,  ``3.24.1-0``,  ``3.24.0-0``,  ``3.22.0-0``,  ``3.20.0-0``,  ``3.18.2-0``,  ``3.16.0-0``,  ``3.14.2-0``,  ``3.12.0-0``,  ``3.10.2-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0``
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-biomart: ``>=2.58.0,<2.59.0``
   :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0``
   :depends bioconductor-ensembldb: ``>=2.26.0,<2.27.0``
   :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicalignments: ``>=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-graph: ``>=1.80.0,<1.81.0``
   :depends bioconductor-interactionset: ``>=1.30.0,<1.31.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-keggrest: ``>=1.42.0,<1.43.0``
   :depends bioconductor-multtest: ``>=2.58.0,<2.59.0``
   :depends bioconductor-rbgl: ``>=1.78.0,<1.79.0``
   :depends bioconductor-regioner: ``>=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 bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-dbi: 
   :depends r-dplyr: 
   :depends r-ggplot2: 
   :depends r-matrixstats: 
   :depends r-venndiagram: 
   :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-chippeakanno

   and update with::

      mamba update bioconductor-chippeakanno

  To create a new environment, run::

      mamba create --name myenvname bioconductor-chippeakanno

  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-chippeakanno:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-chippeakanno";
        var versions = ["3.36.0","3.34.1","3.32.0","3.28.0","3.26.0"];
    </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-chippeakanno/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-chippeakanno/README.html