: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 multi\-omic data pre\-processing

   :homepage: https://bioconductor.org/packages/3.18/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\/ATAC\-seq data that starts from the fastq files and produces a feature 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>2.2.0-0</code>,  <code>2.0.0-0</code>,  <code>1.19.0-1</code>,  <code>1.19.0-0</code>,  <code>1.16.1-0</code>,  <code>1.16.0-1</code>,  <code>1.16.0-0</code>,  <code>1.14.0-0</code>,  <code>1.12.0-1</code>,  </span></summary>
      

      ``2.2.0-0``,  ``2.0.0-0``,  ``1.19.0-1``,  ``1.19.0-0``,  ``1.16.1-0``,  ``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: ``>=1.64.0,<1.65.0``
   :depends bioconductor-annotationdbi: ``>=1.64.1,<1.65.0a0``
   :depends bioconductor-basilisk: ``>=1.14.0,<1.15.0``
   :depends bioconductor-basilisk: ``>=1.14.1,<1.15.0a0``
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-biocgenerics: ``>=0.48.1,<0.49.0a0``
   :depends bioconductor-biomart: ``>=2.58.0,<2.59.0``
   :depends bioconductor-biomart: ``>=2.58.0,<2.59.0a0``
   :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0``
   :depends bioconductor-biostrings: ``>=2.70.1,<2.71.0a0``
   :depends bioconductor-dropletutils: ``>=1.22.0,<1.23.0``
   :depends bioconductor-dropletutils: ``>=1.22.0,<1.23.0a0``
   :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0a0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-genomicranges: ``>=1.54.1,<1.55.0a0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0``
   :depends bioconductor-multiassayexperiment: ``>=1.28.0,<1.29.0``
   :depends bioconductor-multiassayexperiment: ``>=1.28.0,<1.29.0a0``
   :depends bioconductor-org.hs.eg.db: ``>=3.18.0,<3.19.0``
   :depends bioconductor-org.hs.eg.db: ``>=3.18.0,<3.19.0a0``
   :depends bioconductor-org.mm.eg.db: ``>=3.18.0,<3.19.0``
   :depends bioconductor-org.mm.eg.db: ``>=3.18.0,<3.19.0a0``
   :depends bioconductor-rhtslib: ``>=2.4.0,<2.5.0``
   :depends bioconductor-rhtslib: ``>=2.4.0,<2.5.0a0``
   :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0``
   :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0a0``
   :depends bioconductor-rsubread: ``>=2.16.0,<2.17.0``
   :depends bioconductor-rsubread: ``>=2.16.0,<2.17.0a0``
   :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0``
   :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0a0``
   :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 bioconductor-zlibbioc: ``>=1.48.0,<1.49.0``
   :depends bioconductor-zlibbioc: ``>=1.48.0,<1.49.0a0``
   :depends libblas: ``>=3.9.0,<4.0a0``
   :depends libgcc-ng: ``>=12``
   :depends liblapack: ``>=3.9.0,<4.0a0``
   :depends libstdcxx-ng: ``>=12``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-data.table: 
   :depends r-dplyr: 
   :depends r-flexmix: 
   :depends r-ggally: 
   :depends r-ggplot2: 
   :depends r-glue: ``>=1.3.0``
   :depends r-hash: 
   :depends r-magrittr: 
   :depends r-mass: 
   :depends r-matrix: ``>=1.5.0``
   :depends r-mclust: 
   :depends r-purrr: 
   :depends r-rcpp: ``>=0.11.3``
   :depends r-reshape: 
   :depends r-reticulate: 
   :depends r-rlang: 
   :depends r-robustbase: 
   :depends r-scales: 
   :depends r-stringr: 
   :depends r-testthat: 
   :depends r-tibble: 
   :depends r-tidyr: 
   :depends r-vctrs: ``>=0.5.2``
   :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-scpipe

   and update with::

      mamba update bioconductor-scpipe

  To create a new environment, run::

      mamba create --name myenvname bioconductor-scpipe

  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-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 = ["2.2.0","2.0.0","1.19.0","1.19.0","1.16.1"];
    </script>






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

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

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