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

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

bioconductor-synapsis
=====================

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

   An R package to automate the analysis of double\-strand break repair during meiosis

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

   Synapsis is a Bioconductor software package for automated \(unbiased and reproducible\) analysis of meiotic immunofluorescence datasets. The primary functions of the software can i\) identify cells in meiotic prophase that are labelled by a synaptonemal complex axis or central element protein\, ii\) isolate individual synaptonemal complexes and measure their physical length\, iii\) quantify foci and co\-localise them with synaptonemal complexes\, iv\) measure interference between synaptonemal complex\-associated foci. The software has applications that extend to multiple species and to the analysis of other proteins that label meiotic prophase chromosomes. The software converts meiotic immunofluorescence images into R data frames that are compatible with machine learning methods. Given a set of microscopy images of meiotic spread slides\, synapsis crops images around individual single cells\, counts colocalising foci on strands on a per cell basis\, and measures the distance between foci on any given strand.


.. conda:package:: bioconductor-synapsis

   |downloads_bioconductor-synapsis| |docker_bioconductor-synapsis|

   :versions:
      
      

      ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.0.0-0``

      

   
   :depends bioconductor-ebimage: ``>=4.44.0,<4.45.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :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-synapsis

   and update with::

      mamba update bioconductor-synapsis

  To create a new environment, run::

      mamba create --name myenvname bioconductor-synapsis

  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-synapsis:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-synapsis";
        var versions = ["1.8.0","1.6.0","1.4.0","1.0.0"];
    </script>






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

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