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

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

bioconductor-sarks
==================

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

   Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi\-motif domains

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/sarks.html
   :license: BSD_3_clause + file LICENSE
   :recipe: /`bioconductor-sarks <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-sarks>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-sarks/meta.yaml>`_

   Suffix Array Kernel Smoothing \(see https\:\/\/academic.oup.com\/bioinformatics\/article\-abstract\/35\/20\/3944\/5418797\)\, or SArKS\, identifies sequence motifs whose presence correlates with numeric scores \(such as differential expression statistics\) assigned to the sequences \(such as gene promoters\). SArKS smooths over sequence similarity\, quantified by location within a suffix array based on the full set of input sequences. A second round of smoothing over spatial proximity within sequences reveals multi\-motif domains. Discovered motifs can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing.


.. conda:package:: bioconductor-sarks

   |downloads_bioconductor-sarks| |docker_bioconductor-sarks|

   :versions:
      
      

      ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-1``,  ``1.2.0-0``

      

   
   :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends openjdk: 
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-binom: 
   :depends r-cluster: 
   :depends r-rjava: 
   :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-sarks

   and update with::

      mamba update bioconductor-sarks

  To create a new environment, run::

      mamba create --name myenvname bioconductor-sarks

  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-sarks:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-sarks";
        var versions = ["1.14.0","1.12.0","1.10.0","1.6.0","1.4.0"];
    </script>






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-----------------

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

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