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

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

bioconductor-sincell
====================

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

   R package for the statistical assessment of cell state hierarchies from single\-cell RNA\-seq data

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

   Cell differentiation processes are achieved through a continuum of hierarchical intermediate cell\-states that might be captured by single\-cell RNA seq. Existing computational approaches for the assessment of cell\-state hierarchies from single\-cell data might be formalized under a general workflow composed of i\) a metric to assess cell\-to\-cell similarities \(combined or not with a dimensionality reduction step\)\, and ii\) a graph\-building algorithm \(optionally making use of a cells\-clustering step\). Sincell R package implements a methodological toolbox allowing flexible workflows under such framework. Furthermore\, Sincell contributes new algorithms to provide cell\-state hierarchies with statistical support while accounting for stochastic factors in single\-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies.


.. conda:package:: bioconductor-sincell

   |downloads_bioconductor-sincell| |docker_bioconductor-sincell|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.34.0-0</code>,  <code>1.32.0-0</code>,  <code>1.30.0-1</code>,  <code>1.30.0-0</code>,  <code>1.26.0-2</code>,  <code>1.26.0-1</code>,  <code>1.26.0-0</code>,  <code>1.24.0-0</code>,  <code>1.22.0-1</code>,  </span></summary>
      

      ``1.34.0-0``,  ``1.32.0-0``,  ``1.30.0-1``,  ``1.30.0-0``,  ``1.26.0-2``,  ``1.26.0-1``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-1``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-1``,  ``1.16.0-0``,  ``1.14.1-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends libblas: ``>=3.9.0,<4.0a0``
   :depends libgcc-ng: ``>=12``
   :depends liblapack: ``>=3.9.0,<4.0a0``
   :depends libstdcxx-ng: ``>=12``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-cluster: 
   :depends r-entropy: 
   :depends r-fastica: 
   :depends r-fields: 
   :depends r-ggplot2: 
   :depends r-igraph: 
   :depends r-mass: 
   :depends r-proxy: 
   :depends r-rcpp: ``>=0.11.2``
   :depends r-reshape2: 
   :depends r-rtsne: 
   :depends r-scatterplot3d: 
   :depends r-statmod: 
   :depends r-tsp: 
   :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-sincell

   and update with::

      mamba update bioconductor-sincell

  To create a new environment, run::

      mamba create --name myenvname bioconductor-sincell

  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-sincell:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-sincell";
        var versions = ["1.34.0","1.32.0","1.30.0","1.30.0","1.26.0"];
    </script>






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

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

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