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

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

bioconductor-scruff
===================

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

   Single Cell RNA\-Seq UMI Filtering Facilitator \(scruff\)

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/scruff.html
   :license: MIT + file LICENSE
   :recipe: /`bioconductor-scruff <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-scruff>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-scruff/meta.yaml>`_

   A pipeline which processes single cell RNA\-seq \(scRNA\-seq\) reads from CEL\-seq and CEL\-seq2 protocols. Demultiplex scRNA\-seq FASTQ files\, align reads to reference genome using Rsubread\, and generate UMI filtered count matrix. Also provide visualizations of read alignments and pre\- and post\-alignment QC metrics.


.. conda:package:: bioconductor-scruff

   |downloads_bioconductor-scruff| |docker_bioconductor-scruff|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.20.0-0</code>,  <code>1.18.0-0</code>,  <code>1.16.0-0</code>,  <code>1.12.0-0</code>,  <code>1.10.0-0</code>,  <code>1.8.3-0</code>,  <code>1.8.1-0</code>,  <code>1.6.0-0</code>,  <code>1.4.0-0</code>,  </span></summary>
      

      ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.3-0``,  ``1.8.1-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.4-0``,  ``1.0.1-1``,  ``1.0.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotationdbi: ``>=1.64.0,<1.65.0``
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0``
   :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0``
   :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-ggbio: ``>=1.50.0,<1.51.0``
   :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0``
   :depends bioconductor-rsubread: ``>=2.16.0,<2.17.0``
   :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-shortread: ``>=1.60.0,<1.61.0``
   :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-data.table: 
   :depends r-ggplot2: 
   :depends r-ggthemes: 
   :depends r-parallelly: 
   :depends r-plyr: 
   :depends r-scales: 
   :depends r-stringdist: 
   :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-scruff

   and update with::

      mamba update bioconductor-scruff

  To create a new environment, run::

      mamba create --name myenvname bioconductor-scruff

  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-scruff:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-scruff";
        var versions = ["1.20.0","1.18.0","1.16.0","1.12.0","1.10.0"];
    </script>






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

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

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