:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-feast' .. highlight: bash bioconductor-feast ================== .. conda:recipe:: bioconductor-feast :replaces_section_title: :noindex: FEAture SelcTion \(FEAST\) for Single\-cell clustering :homepage: https://bioconductor.org/packages/3.18/bioc/html/FEAST.html :license: GPL-2 :recipe: /`bioconductor-feast `_/`meta.yaml `_ Cell clustering is one of the most important and commonly performed tasks in single\-cell RNA sequencing \(scRNA\-seq\) data analysis. An important step in cell clustering is to select a subset of genes \(referred to as “features”\)\, whose expression patterns will then be used for downstream clustering. A good set of features should include the ones that distinguish different cell types\, and the quality of such set could have significant impact on the clustering accuracy. FEAST is an R library for selecting most representative features before performing the core of scRNA\-seq clustering. It can be used as a plug\-in for the etablished clustering algorithms such as SC3\, TSCAN\, SHARP\, SIMLR\, and Seurat. The core of FEAST algorithm includes three steps\: 1. consensus clustering\; 2. gene\-level significance inference\; 3. validation of an optimized feature set. .. conda:package:: bioconductor-feast |downloads_bioconductor-feast| |docker_bioconductor-feast| :versions: ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.6.0-0``,  ``1.2.0-2``,  ``1.2.0-1``,  ``1.2.0-0``,  ``1.0.0-0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0a0`` :depends bioconductor-sc3: ``>=1.30.0,<1.31.0`` :depends bioconductor-sc3: ``>=1.30.0,<1.31.0a0`` :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0`` :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0a0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0a0`` :depends bioconductor-tscan: ``>=1.40.0,<1.41.0`` :depends bioconductor-tscan: ``>=1.40.0,<1.41.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-irlba: :depends r-matrixstats: :depends r-mclust: :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-feast and update with:: mamba update bioconductor-feast To create a new environment, run:: mamba create --name myenvname bioconductor-feast 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-feast: (see `bioconductor-feast/tags`_ for valid values for ````) .. |downloads_bioconductor-feast| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-feast.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-feast :alt: (downloads) .. |docker_bioconductor-feast| image:: https://quay.io/repository/biocontainers/bioconductor-feast/status :target: https://quay.io/repository/biocontainers/bioconductor-feast .. _`bioconductor-feast/tags`: https://quay.io/repository/biocontainers/bioconductor-feast?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-feast/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-feast/README.html