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

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

bioconductor-scpipe
===================

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

   pipeline for single cell RNA\-seq data analysis

   :homepage: https://bioconductor.org/packages/3.14/bioc/html/scPipe.html
   :license: GPL (>= 2)
   :recipe: /`bioconductor-scpipe <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-scpipe>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-scpipe/meta.yaml>`_

   A preprocessing pipeline for single cell RNA\-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL\-seq\, MARS\-seq\, Drop\-seq\, Chromium 10x and SMART\-seq protocols.


.. conda:package:: bioconductor-scpipe

   |downloads_bioconductor-scpipe| |docker_bioconductor-scpipe|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.16.0-1</code>,  <code>1.16.0-0</code>,  <code>1.14.0-0</code>,  <code>1.12.0-1</code>,  <code>1.12.0-0</code>,  <code>1.10.0-0</code>,  <code>1.8.0-0</code>,  <code>1.6.0-1</code>,  <code>1.4.1-0</code>,  </span></summary>
      

      ``1.16.0-1``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.4.1-0``,  ``1.4.0-0``,  ``1.2.1-0``,  ``1.0.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotationdbi: ``>=1.56.0,<1.57.0``
   :depends bioconductor-biocgenerics: ``>=0.40.0,<0.41.0``
   :depends bioconductor-biomart: ``>=2.50.0,<2.51.0``
   :depends bioconductor-genomicranges: ``>=1.46.0,<1.47.0``
   :depends bioconductor-org.hs.eg.db: ``>=3.14.0,<3.15.0``
   :depends bioconductor-org.mm.eg.db: ``>=3.14.0,<3.15.0``
   :depends bioconductor-rhtslib: ``>=1.26.0,<1.27.0``
   :depends bioconductor-rtracklayer: ``>=1.54.0,<1.55.0``
   :depends bioconductor-s4vectors: ``>=0.32.0,<0.33.0``
   :depends bioconductor-scater: ``>=1.22.0,<1.23.0``
   :depends bioconductor-singlecellexperiment: ``>=1.16.0,<1.17.0``
   :depends bioconductor-summarizedexperiment: ``>=1.24.0,<1.25.0``
   :depends bioconductor-zlibbioc: ``>=1.40.0,<1.41.0``
   :depends libblas: ``>=3.8.0,<4.0a0``
   :depends libgcc-ng: ``>=10.3.0``
   :depends liblapack: ``>=3.8.0,<4.0a0``
   :depends libstdcxx-ng: ``>=10.3.0``
   :depends r-base: ``>=4.1,<4.2.0a0``
   :depends r-dplyr: 
   :depends r-ggally: 
   :depends r-ggplot2: 
   :depends r-glue: ``>=1.3.0``
   :depends r-hash: 
   :depends r-magrittr: 
   :depends r-mass: 
   :depends r-mclust: 
   :depends r-rcpp: ``>=0.11.3``
   :depends r-reshape: 
   :depends r-rlang: 
   :depends r-robustbase: 
   :depends r-scales: 
   :depends r-stringr: 
   :depends r-testthat: 
   :requirements:

   .. rubric:: Installation

   With an activated Bioconda channel (see :ref:`set-up-channels`), install with::

      conda install bioconductor-scpipe

   and update with::

      conda update bioconductor-scpipe

   or use the docker container::

      docker pull quay.io/biocontainers/bioconductor-scpipe:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-scpipe";
        var versions = ["1.16.0","1.16.0","1.14.0","1.12.0","1.12.0"];
    </script>






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-----------------

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

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