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

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

bioconductor-ccfindr
====================

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

   Cancer Clone Finder

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/ccfindR.html
   :license: GPL (>= 2)
   :recipe: /`bioconductor-ccfindr <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-ccfindr>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-ccfindr/meta.yaml>`_

   A collection of tools for cancer genomic data clustering analyses\, including those for single cell RNA\-seq. Cell clustering and feature gene selection analysis employ Bayesian \(and maximum likelihood\) non\-negative matrix factorization \(NMF\) algorithm. Input data set consists of RNA count matrix\, gene\, and cell bar code annotations.  Analysis outputs are factor matrices for multiple ranks and marginal likelihood values for each rank. The package includes utilities for downstream analyses\, including meta\-gene identification\, visualization\, and construction of rank\-based trees for clusters.


.. conda:package:: bioconductor-ccfindr

   |downloads_bioconductor-ccfindr| |docker_bioconductor-ccfindr|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.22.0-0</code>,  <code>1.20.0-0</code>,  <code>1.18.0-1</code>,  <code>1.18.0-0</code>,  <code>1.14.0-2</code>,  <code>1.14.0-1</code>,  <code>1.14.0-0</code>,  <code>1.12.0-0</code>,  <code>1.10.0-1</code>,  </span></summary>
      

      ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-1``,  ``1.18.0-0``,  ``1.14.0-2``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-1``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.2-0``,  ``1.2.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-s4vectors: ``>=0.40.2,<0.41.0a0``
   :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0``
   :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0a0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0a0``
   :depends gsl: ``>=2.7,<2.8.0a0``
   :depends libblas: ``>=3.9.0,<4.0a0``
   :depends libgcc-ng: ``>=12``
   :depends liblapack: ``>=3.9.0,<4.0a0``
   :depends libstdcxx-ng: ``>=12``
   :depends r-ape: 
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-gtools: 
   :depends r-irlba: 
   :depends r-matrix: 
   :depends r-rcolorbrewer: 
   :depends r-rcpp: 
   :depends r-rcppeigen: 
   :depends r-rdpack: ``>=0.7``
   :depends r-rmpi: 
   :depends r-rtsne: 
   :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-ccfindr

   and update with::

      mamba update bioconductor-ccfindr

  To create a new environment, run::

      mamba create --name myenvname bioconductor-ccfindr

  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-ccfindr:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-ccfindr";
        var versions = ["1.22.0","1.20.0","1.18.0","1.18.0","1.14.0"];
    </script>






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

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

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