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

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

bioconductor-ccimpute
=====================

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

   ccImpute\: an accurate and scalable consensus clustering based approach to impute dropout events in the single\-cell RNA\-seq data \(https\:\/\/doi.org\/10.1186\/s12859\-022\-04814\-8\)

   :homepage: https://bioconductor.org/packages/3.20/bioc/html/ccImpute.html
   :license: GPL-3
   :recipe: /`bioconductor-ccimpute <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-ccimpute>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-ccimpute/meta.yaml>`_

   Dropout events make the lowly expressed genes indistinguishable from true zero expression and different than the low expression present in cells of the same type. This issue makes any subsequent downstream analysis difficult. ccImpute is an imputation algorithm that uses cell similarity established by consensus clustering to impute the most probable dropout events in the scRNA\-seq datasets. ccImpute demonstrated performance which exceeds the performance of existing imputation approaches while introducing the least amount of new noise as measured by clustering performance characteristics on datasets with known cell identities.


.. conda:package:: bioconductor-ccimpute

   |downloads_bioconductor-ccimpute| |docker_bioconductor-ccimpute|

   :versions:
      
      

      ``1.12.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.1-0``,  ``1.0.0-1``,  ``1.0.0-0``

      

   
   :depends on bioconductor-biocparallel: ``>=1.44.0,<1.45.0``
   :depends on bioconductor-biocparallel: ``>=1.44.0,<1.45.0a0``
   :depends on bioconductor-singlecellexperiment: ``>=1.32.0,<1.33.0``
   :depends on bioconductor-singlecellexperiment: ``>=1.32.0,<1.33.0a0``
   :depends on bioconductor-sparsematrixstats: ``>=1.22.0,<1.23.0``
   :depends on bioconductor-sparsematrixstats: ``>=1.22.0,<1.23.0a0``
   :depends on bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0``
   :depends on bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0a0``
   :depends on libblas: ``>=3.9.0,<4.0a0``
   :depends on libgcc: ``>=14``
   :depends on liblapack: ``>=3.9.0,<4.0a0``
   :depends on liblzma: ``>=5.8.2,<6.0a0``
   :depends on libstdcxx: ``>=14``
   :depends on libzlib: ``>=1.3.1,<2.0a0``
   :depends on r-base: ``>=4.5,<4.6.0a0``
   :depends on r-irlba: 
   :depends on r-matrix: 
   :depends on r-rcpp: 
   :depends on r-rcppeigen: 

   :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-ccimpute

to add into an existing workspace instead, run::

    pixi add bioconductor-ccimpute

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-ccimpute

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

    conda create -n envname bioconductor-ccimpute

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-ccimpute:<tag>

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


.. raw:: html

    <script>
        var package = "bioconductor-ccimpute";
        var versions = ["1.12.0","1.8.0","1.4.0","1.2.1","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::

   [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ccimpute/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-ccimpute/README.html