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

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

bioconductor-batchelor
======================

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

   Single\-Cell Batch Correction Methods

   :homepage: https://bioconductor.org/packages/3.20/bioc/html/batchelor.html
   :license: GPL-3
   :recipe: /`bioconductor-batchelor <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-batchelor>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-batchelor/meta.yaml>`_
   :links: biotools: :biotools:`batchelor`

   Implements a variety of methods for batch correction of single\-cell \(RNA sequencing\) data. This includes methods based on detecting mutually nearest neighbors\, as well as several efficient variants of linear regression of the log\-expression values. Functions are also provided to perform global rescaling to remove differences in depth between batches\, and to perform a principal components analysis that is robust to differences in the numbers of cells across batches.


.. conda:package:: bioconductor-batchelor

   |downloads_bioconductor-batchelor| |docker_bioconductor-batchelor|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.22.0-0</code>,  <code>1.18.0-1</code>,  <code>1.18.0-0</code>,  <code>1.16.0-0</code>,  <code>1.14.0-1</code>,  <code>1.14.0-0</code>,  <code>1.10.0-2</code>,  <code>1.10.0-1</code>,  <code>1.10.0-0</code>,  </span></summary>
      

      ``1.22.0-0``,  ``1.18.0-1``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.10.0-2``,  ``1.10.0-1``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.2-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.1-0``,  ``1.0.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-beachmat: ``>=2.22.0,<2.23.0``
   :depends bioconductor-beachmat: ``>=2.22.0,<2.23.0a0``
   :depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0``
   :depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0a0``
   :depends bioconductor-biocneighbors: ``>=2.0.0,<2.1.0``
   :depends bioconductor-biocneighbors: ``>=2.0.0,<2.1.0a0``
   :depends bioconductor-biocparallel: ``>=1.40.0,<1.41.0``
   :depends bioconductor-biocparallel: ``>=1.40.0,<1.41.0a0``
   :depends bioconductor-biocsingular: ``>=1.22.0,<1.23.0``
   :depends bioconductor-biocsingular: ``>=1.22.0,<1.23.0a0``
   :depends bioconductor-delayedarray: ``>=0.32.0,<0.33.0``
   :depends bioconductor-delayedarray: ``>=0.32.0,<0.33.0a0``
   :depends bioconductor-delayedmatrixstats: ``>=1.28.0,<1.29.0``
   :depends bioconductor-delayedmatrixstats: ``>=1.28.0,<1.29.0a0``
   :depends bioconductor-residualmatrix: ``>=1.16.0,<1.17.0``
   :depends bioconductor-residualmatrix: ``>=1.16.0,<1.17.0a0``
   :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0``
   :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0a0``
   :depends bioconductor-scaledmatrix: ``>=1.14.0,<1.15.0``
   :depends bioconductor-scaledmatrix: ``>=1.14.0,<1.15.0a0``
   :depends bioconductor-scuttle: ``>=1.16.0,<1.17.0``
   :depends bioconductor-scuttle: ``>=1.16.0,<1.17.0a0``
   :depends bioconductor-singlecellexperiment: ``>=1.28.0,<1.29.0``
   :depends bioconductor-singlecellexperiment: ``>=1.28.0,<1.29.0a0``
   :depends bioconductor-sparsearray: ``>=1.6.0,<1.7.0``
   :depends bioconductor-sparsearray: ``>=1.6.0,<1.7.0a0``
   :depends bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0``
   :depends bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0a0``
   :depends libblas: ``>=3.9.0,<4.0a0``
   :depends libgcc: ``>=13``
   :depends liblapack: ``>=3.9.0,<4.0a0``
   :depends libstdcxx: ``>=13``
   :depends r-base: ``>=4.4,<4.5.0a0``
   :depends r-igraph: 
   :depends r-matrix: 
   :depends r-rcpp: 
   :requirements:

   :additional platforms:
      
      .. raw:: html

         <span class="additional-platforms"><code>linux-aarch64</code></span>
      

   .. 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-batchelor

   and update with::

      mamba update bioconductor-batchelor

  To create a new environment, run::

      mamba create --name myenvname bioconductor-batchelor

  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-batchelor:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-batchelor";
        var versions = ["1.22.0","1.18.0","1.18.0","1.16.0","1.14.0"];
    </script>






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

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

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