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

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

bioconductor-pmscanr
====================

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

   Protein motifs analysis and visualisation

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

   Provides tools for large\-scale protein motif analysis and visualization in R. PMScanR facilitates the identification of motifs using external tools like PROSITE\'s ps\_scan \(handling necessary file downloads and execution\) and enables downstream analysis of results. Key features include parsing scan outputs\, converting formats \(e.g.\, to GFF\-like structures\)\, generating motif occurrence matrices\, and creating informative visualizations such as heatmaps\, sequence logos \(via seqLogo\/ggseqlogo\). The package also offers an optional Shiny\-based graphical user interface for interactive analysis\, aiming to streamline the process of exploring motif patterns across multiple protein sequences.


.. conda:package:: bioconductor-pmscanr

   |downloads_bioconductor-pmscanr| |docker_bioconductor-pmscanr|

   :versions:
      
      

      ``1.0.1-0``

      

   
   :depends on bioconductor-biocfilecache: ``>=3.0.0,<3.1.0``
   :depends on bioconductor-rtracklayer: ``>=1.70.0,<1.71.0``
   :depends on perl: ``>=5.32.1,<6.0a0 *_perl5``
   :depends on perl: ``>=5.6.0``
   :depends on r-base: ``>=4.5,<4.6.0a0``
   :depends on r-bslib: 
   :depends on r-dplyr: ``>=1.1.0``
   :depends on r-ggplot2: 
   :depends on r-ggseqlogo: 
   :depends on r-magrittr: 
   :depends on r-plotly: 
   :depends on r-reshape2: 
   :depends on r-rlang: 
   :depends on r-seqinr: 
   :depends on r-shiny: 
   :depends on r-shinyfiles: 
   :depends on r-stringr: 

   :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-pmscanr

to add into an existing workspace instead, run::

    pixi add bioconductor-pmscanr

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-pmscanr

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

    conda create -n envname bioconductor-pmscanr

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-pmscanr:<tag>

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


.. raw:: html

    <script>
        var package = "bioconductor-pmscanr";
        var versions = ["1.0.1"];
    </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-pmscanr/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-pmscanr/README.html