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

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

bioconductor-spsimseq
=====================

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

   Semi\-parametric simulation tool for bulk and single\-cell RNA sequencing data

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/SPsimSeq.html
   :license: GPL-2
   :recipe: /`bioconductor-spsimseq <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-spsimseq>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-spsimseq/meta.yaml>`_

   SPsimSeq uses a specially designed exponential family for density estimation to constructs the distribution of gene expression levels from a given real RNA sequencing data \(single\-cell or bulk\)\, and subsequently simulates a new dataset from the estimated marginal distributions using Gaussian\-copulas to retain the dependence between genes. It allows simulation of multiple groups and batches with any required sample size and library size.


.. conda:package:: bioconductor-spsimseq

   |downloads_bioconductor-spsimseq| |docker_bioconductor-spsimseq|

   :versions:
      
      

      ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-1``,  ``1.0.0-0``

      

   
   :depends bioconductor-edger: ``>=4.0.0,<4.1.0``
   :depends bioconductor-limma: ``>=3.58.0,<3.59.0``
   :depends bioconductor-phyloseq: ``>=1.46.0,<1.47.0``
   :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-fitdistrplus: 
   :depends r-hmisc: 
   :depends r-mvtnorm: 
   :depends r-wgcna: 
   :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-spsimseq

   and update with::

      mamba update bioconductor-spsimseq

  To create a new environment, run::

      mamba create --name myenvname bioconductor-spsimseq

  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-spsimseq:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-spsimseq";
        var versions = ["1.12.0","1.10.0","1.8.0","1.4.0","1.2.0"];
    </script>






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

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

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