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

.. title:: Package Recipe 'seacr'
.. highlight: bash

seacr
=====

.. conda:recipe:: seacr
   :replaces_section_title:
   :noindex:

   SEACR is intended to call peaks and enriched regions from sparse CUT\&RUN or chromatin profiling data in which background is dominated by \"zeroes\" \(i.e. regions with no read coverage\). It requires R \(https\:\/\/www.r\-project.org\) and Bedtools \(https\:\/\/bedtools.readthedocs.io\/en\/latest\/\) to be available in your path\, and it requires bedgraphs from paired\-end sequencing as input\, which can be generated from read pair BED files \(i.e. BED coordinates reflecting the 5\' and 3\' termini of each read pair\) using bedtools genomecov with the \"\-bg\" flag\, or alternatively from name\-sorted paired\-end BAM files as described in \"Preparing input bedgraph files\" below.

   :homepage: https://github.com/FredHutch/SEACR
   :license: https://github.com/FredHutch/SEACR/blob/master/LICENSE
   :recipe: /`seacr <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/seacr>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/seacr/meta.yaml>`_

   


.. conda:package:: seacr

   |downloads_seacr| |docker_seacr|

   :versions:
      
      

      ``1.3-2``,  ``1.3-1``,  ``1.3-0``,  ``1.1-0``

      

   
   :depends r-base: 
   :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 seacr

   and update with::

      mamba update seacr

  To create a new environment, run::

      mamba create --name myenvname seacr

  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/seacr:<tag>

   (see `seacr/tags`_ for valid values for ``<tag>``)


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


.. raw:: html

    <script>
        var package = "seacr";
        var versions = ["1.3","1.3","1.3","1.1"];
    </script>






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

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

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