recipe bioconductor-powsc

Simulation, power evaluation, and sample size recommendation for single cell RNA-seq

Homepage

https://bioconductor.org/packages/3.14/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.

package bioconductor-powsc

Versions

1.2.0-0,  1.0.0-0

Depends

• bioconductor-biobase >=2.54.0,<2.55.0

• bioconductor-limma >=3.50.0,<3.51.0

• bioconductor-mast >=1.20.0,<1.21.0

• bioconductor-singlecellexperiment >=1.16.0,<1.17.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• r-base >=4.1,<4.2.0a0

• r-ggplot2

• r-pheatmap

• r-rcolorbrewer

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-powsc

and update with:

conda update bioconductor-powsc

or use the docker container:

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

(see bioconductor-powsc/tags for valid values for <tag>)

Download stats

Link to this page

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