:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-clustersignificance' .. highlight: bash bioconductor-clustersignificance ================================ .. conda:recipe:: bioconductor-clustersignificance :replaces_section_title: :noindex: The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data :homepage: https://bioconductor.org/packages/3.18/bioc/html/ClusterSignificance.html :license: GPL-3 :recipe: /`bioconductor-clustersignificance `_/`meta.yaml `_ :links: biotools: :biotools:`clustersignificance`, doi: :doi:`10.1038/nmeth.3252` The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data. The term class clusters here refers to\, clusters of points representing known classes in the data. This is particularly useful to determine if a subset of the variables\, e.g. genes in a specific pathway\, alone can separate samples into these established classes. ClusterSignificance accomplishes this by\, projecting all points onto a one dimensional line. Cluster separations are then scored and the probability of the seen separation being due to chance is evaluated using a permutation method. .. conda:package:: bioconductor-clustersignificance |downloads_bioconductor-clustersignificance| |docker_bioconductor-clustersignificance| :versions: .. raw:: html
1.30.0-01.28.0-01.26.0-01.22.0-01.20.0-01.18.0-11.18.0-01.16.0-01.14.0-0 ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-1``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.2-0``,  ``1.6.0-0`` .. raw:: html
:depends r-base: ``>=4.3,<4.4.0a0`` :depends r-pracma: :depends r-princurve: ``>=2.0.5`` :depends r-rcolorbrewer: :depends r-scatterplot3d: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `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 `_ 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-clustersignificance and update with:: mamba update bioconductor-clustersignificance To create a new environment, run:: mamba create --name myenvname bioconductor-clustersignificance with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/bioconductor-clustersignificance: (see `bioconductor-clustersignificance/tags`_ for valid values for ````) .. |downloads_bioconductor-clustersignificance| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-clustersignificance.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-clustersignificance :alt: (downloads) .. |docker_bioconductor-clustersignificance| image:: https://quay.io/repository/biocontainers/bioconductor-clustersignificance/status :target: https://quay.io/repository/biocontainers/bioconductor-clustersignificance .. _`bioconductor-clustersignificance/tags`: https://quay.io/repository/biocontainers/bioconductor-clustersignificance?tab=tags .. raw:: html 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-clustersignificance/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-clustersignificance/README.html