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

.. title:: Package Recipe 'bioconductor-looking4clusters'
.. highlight: bash

bioconductor-looking4clusters
=============================

.. conda:recipe:: bioconductor-looking4clusters
   :replaces_section_title:
   :noindex:

   Interactive Visualization of scRNA\-Seq

   :homepage: https://bioconductor.org/packages/3.22/bioc/html/looking4clusters.html
   :license: GPL-2 | GPL-3
   :recipe: /`bioconductor-looking4clusters <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-looking4clusters>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-looking4clusters/meta.yaml>`_

   Enables the interactive visualization of dimensional reduction\, clustering\, and cell properties for scRNA\-Seq results. It generates an interactive HTML page using either a numeric matrix\, SummarizedExperiment\, SingleCellExperiment or Seurat objects as input. The input data can be projected into two\-dimensional representations by applying dimensionality reduction methods such as PCA\, MDS\, t\-SNE\, UMAP\, and NMF. Displaying multiple dimensionality reduction results within the same interface\, with interconnected graphs\, provides different perspectives that facilitate accurate cell classification. The package also integrates unsupervised clustering techniques\, whose results that can be viewed interactively in the graphical interface. In addition to visualization\, this interface allows manual selection of groups\, labeling of cell entities based on processed meta\-information\, generation of new graphs displaying gene expression values for each cell\, sample identification\, and visual comparison of samples and clusters.


.. conda:package:: bioconductor-looking4clusters

   |downloads_bioconductor-looking4clusters| |docker_bioconductor-looking4clusters|

   :versions:
      
      

      ``1.0.0-0``

      

   
   :depends on bioconductor-biocbaseutils: ``>=1.12.0,<1.13.0``
   :depends on bioconductor-singlecellexperiment: ``>=1.32.0,<1.33.0``
   :depends on bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0``
   :depends on r-base: ``>=4.5,<4.6.0a0``
   :depends on r-jsonlite: 

   :additional platforms:
      

Installation
------------

You need a conda-compatible package manager
(currently either `pixi <https://pixi.sh>`__, `conda <https://docs.conda.io/projects/conda>`__, or `micromamba <https://mamba.readthedocs.io>`__)
and the Bioconda channel already activated (see :ref:`bioconda_setup`).
Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi
""""

With pixi_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`),
to install globally, run::

    pixi global install bioconductor-looking4clusters

to add into an existing workspace instead, run::

    pixi add bioconductor-looking4clusters

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace::

    pixi workspace channel add conda-forge
    pixi workspace channel add bioconda

Conda
"""""

With conda_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`), to install into an existing and activated environment, run::

    conda install bioconductor-looking4clusters

Alternatively, to install into a new environment, run::

    conda create -n envname bioconductor-looking4clusters

with ``envname`` being the name of the desired environment.

Container
"""""""""

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime.
For e.g. docker, run::

    docker pull quay.io/biocontainers/bioconductor-looking4clusters:<tag>

(see `bioconductor-looking4clusters/tags`_ for valid values for ``<tag>``).

Integrated deployment
"""""""""""""""""""""

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment.
Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency.
Check the documentation of your workflow management system to find out about the integration.

.. _conda: https://conda.io
.. _pixi: https://pixi.sh
.. |downloads_bioconductor-looking4clusters| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-looking4clusters.svg?style=flat
   :target: https://anaconda.org/bioconda/bioconductor-looking4clusters
   :alt:   (downloads)
.. |docker_bioconductor-looking4clusters| image:: https://quay.io/repository/biocontainers/bioconductor-looking4clusters/status
   :target: https://quay.io/repository/biocontainers/bioconductor-looking4clusters
.. _`bioconductor-looking4clusters/tags`: https://quay.io/repository/biocontainers/bioconductor-looking4clusters?tab=tags


.. raw:: html

    <script>
        var package = "bioconductor-looking4clusters";
        var versions = ["1.0.0"];
    </script>






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

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

Link to this page
-----------------

Render an |install-with-bioconda| badge with the following MarkDown::

   [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-looking4clusters/README.html)

.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/bioconductor-looking4clusters/README.html