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

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

bioconductor-csoa
=================

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

   Calculate per\-cell gene signature scores in scRNA\-seq data using cell set overlaps

   :homepage: https://bioconductor.org/packages/3.22/bioc/html/CSOA.html
   :license: MIT + file LICENSE
   :recipe: /`bioconductor-csoa <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-csoa>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-csoa/meta.yaml>`_

   Cell Set Overlap Analysis \(CSOA\) is a tool for calculating per\-cell gene signature scores in an scRNA\-seq dataset. CSOA constructs a set for each gene in the signature\, consisting of the cells that highly express the gene. Next\, all overlaps of pairs of cell sets are computed\, ranked\, filtered and scored. The CSOA per\-cell score is calculated by summing up all products of the overlap scores and the min\-max\-normalized expression of the two involved genes. CSOA can run on a Seurat object\, a SingleCellExperiment object\, a matrix and a dgCMatrix.


.. conda:package:: bioconductor-csoa

   |downloads_bioconductor-csoa| |docker_bioconductor-csoa|

   :versions:
      
      

      ``1.0.0-0``

      

   
   :depends on bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0``
   :depends on r-base: ``>=4.5,<4.6.0a0``
   :depends on r-bayesbio: 
   :depends on r-dplyr: 
   :depends on r-ggplot2: 
   :depends on r-henna: 
   :depends on r-kerntools: 
   :depends on r-qs: 
   :depends on r-reshape2: 
   :depends on r-rlang: 
   :depends on r-seurat: 
   :depends on r-seuratobject: 
   :depends on r-sgof: 
   :depends on r-spatstat.utils: 
   :depends on r-textshape: 
   :depends on r-wesanderson: 

   :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-csoa

to add into an existing workspace instead, run::

    pixi add bioconductor-csoa

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-csoa

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

    conda create -n envname bioconductor-csoa

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-csoa:<tag>

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


.. raw:: html

    <script>
        var package = "bioconductor-csoa";
        var versions = ["1.0.0"];
    </script>






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

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

Link to this page
-----------------

Render an |install-with-bioconda| badge with the following MarkDown::

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.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/bioconductor-csoa/README.html