:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-powsc' .. highlight: bash bioconductor-powsc ================== .. conda:recipe:: bioconductor-powsc :replaces_section_title: :noindex: Simulation\, power evaluation\, and sample size recommendation for single cell RNA\-seq :homepage: https://bioconductor.org/packages/3.18/bioc/html/POWSC.html :license: GPL-2 :recipe: /`bioconductor-powsc `_/`meta.yaml `_ Determining the sample size for adequate power to detect statistical significance is a crucial step at the design stage for high\-throughput experiments. Even though a number of methods and tools are available for sample size calculation for microarray and RNA\-seq in the context of differential expression \(DE\)\, this topic in the field of single\-cell RNA sequencing is understudied. Moreover\, the unique data characteristics present in scRNA\-seq such as sparsity and heterogeneity increase the challenge. We propose POWSC\, a simulation\-based method\, to provide power evaluation and sample size recommendation for single\-cell RNA sequencing DE analysis. POWSC consists of a data simulator that creates realistic expression data\, and a power assessor that provides a comprehensive evaluation and visualization of the power and sample size relationship. .. conda:package:: bioconductor-powsc |downloads_bioconductor-powsc| |docker_bioconductor-powsc| :versions: ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.2.0-0``,  ``1.0.0-0`` :depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends bioconductor-mast: ``>=1.28.0,<1.29.0`` :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-ggplot2: :depends r-pheatmap: :depends r-rcolorbrewer: :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-powsc and update with:: mamba update bioconductor-powsc To create a new environment, run:: mamba create --name myenvname bioconductor-powsc 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-powsc: (see `bioconductor-powsc/tags`_ for valid values for ````) .. |downloads_bioconductor-powsc| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-powsc.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-powsc :alt: (downloads) .. |docker_bioconductor-powsc| image:: https://quay.io/repository/biocontainers/bioconductor-powsc/status :target: https://quay.io/repository/biocontainers/bioconductor-powsc .. _`bioconductor-powsc/tags`: https://quay.io/repository/biocontainers/bioconductor-powsc?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-powsc/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-powsc/README.html