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

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

bioconductor-islify
===================

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

   Automatic scoring and classification of cell\-based assay images

   :homepage: https://bioconductor.org/packages/3.22/bioc/html/islify.html
   :license: GPL-3
   :recipe: /`bioconductor-islify <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-islify>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-islify/meta.yaml>`_

   This software is meant to be used for classification of images of cell\-based assays for neuronal surface autoantibody detection or similar techniques. It takes imaging files as input and creates a composite score from these\, that for example can be used to classify samples as negative or positive for a certain antibody\-specificity. The reason for its name is that I during its creation have thought about the individual picture as an archielago where we with different filters control the water level as well as ground characteristica\, thereby finding islands of interest.


.. conda:package:: bioconductor-islify

   |downloads_bioconductor-islify| |docker_bioconductor-islify|

   :versions:
      
      

      ``1.2.0-0``

      

   
   :depends on bioconductor-rbioformats: ``>=1.10.0,<1.11.0``
   :depends on r-abind: ``>=1.4.8``
   :depends on r-autothresholdr: ``>=1.4.2``
   :depends on r-base: ``>=4.5,<4.6.0a0``
   :depends on r-dbscan: ``>=1.1.12``
   :depends on r-matrix: ``>=1.6.1``
   :depends on r-png: ``>=0.1.8``
   :depends on r-tiff: ``>=0.1.12``

   :additional platforms:
      

Installation
------------

You need a conda-compatible package manager
(currently either `pixi <https://pixi.sh>`__, `conda <https://docs.conda.io/projects/conda>`__, or `micromamba <https://mamba.readthedocs.io>`__)
and the Bioconda channel already activated (see :ref:`bioconda_setup`).
Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi
""""

With pixi_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`),
to install globally, run::

    pixi global install bioconductor-islify

to add into an existing workspace instead, run::

    pixi add bioconductor-islify

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace::

    pixi workspace channel add conda-forge
    pixi workspace channel add bioconda

Conda
"""""

With conda_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`), to install into an existing and activated environment, run::

    conda install bioconductor-islify

Alternatively, to install into a new environment, run::

    conda create -n envname bioconductor-islify

with ``envname`` being the name of the desired environment.

Container
"""""""""

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime.
For e.g. docker, run::

    docker pull quay.io/biocontainers/bioconductor-islify:<tag>

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

Integrated deployment
"""""""""""""""""""""

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment.
Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency.
Check the documentation of your workflow management system to find out about the integration.

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


.. raw:: html

    <script>
        var package = "bioconductor-islify";
        var versions = ["1.2.0"];
    </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-islify/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-islify/README.html