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

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

bioconductor-chipseeker
=======================

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

   ChIPseeker for ChIP peak Annotation\, Comparison\, and Visualization

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

   This package implements functions to retrieve the nearest genes around the peak\, annotate genomic region of the peak\, statstical methods for estimate the significance of overlap among ChIP peak data sets\, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment\, average profile and heatmap of peaks binding to TSS regions\, genomic annotation\, distance to TSS\, and overlap of peaks or genes.


.. conda:package:: bioconductor-chipseeker

   |downloads_bioconductor-chipseeker| |docker_bioconductor-chipseeker|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.38.0-0</code>,  <code>1.36.0-0</code>,  <code>1.34.0-0</code>,  <code>1.32.0-0</code>,  <code>1.30.0-0</code>,  <code>1.28.3-1</code>,  <code>1.28.3-0</code>,  <code>1.26.2-0</code>,  <code>1.26.0-0</code>,  </span></summary>
      

      ``1.38.0-0``,  ``1.36.0-0``,  ``1.34.0-0``,  ``1.32.0-0``,  ``1.30.0-0``,  ``1.28.3-1``,  ``1.28.3-0``,  ``1.26.2-0``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-1``,  ``1.18.0-0``,  ``1.16.1-0``,  ``1.14.2-0``,  ``1.14.0-0``,  ``1.12.1-0``,  ``1.10.0-0``,  ``1.6.6-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0``
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-enrichplot: ``>=1.22.0,<1.23.0``
   :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-rtracklayer: ``>=1.62.0,<1.63.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene: ``>=3.2.0,<3.3.0``
   :depends r-aplot: 
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-boot: 
   :depends r-dplyr: 
   :depends r-ggplot2: 
   :depends r-gplots: 
   :depends r-gtools: 
   :depends r-magrittr: 
   :depends r-plotrix: 
   :depends r-tibble: 
   :depends r-yulab.utils: 
   :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-chipseeker

   and update with::

      mamba update bioconductor-chipseeker

  To create a new environment, run::

      mamba create --name myenvname bioconductor-chipseeker

  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-chipseeker:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-chipseeker";
        var versions = ["1.38.0","1.36.0","1.34.0","1.32.0","1.30.0"];
    </script>






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

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

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