POWSC

DOI: 10.18129/B9.bioc.POWSC    

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

Bioconductor version: Release (3.13)

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.

Author: Kenong Su [aut, cre], Hao Wu [aut]

Maintainer: Kenong Su <kenong.su at emory.edu>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("POWSC")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("POWSC")

 

HTML	R Script	The POWSC User's Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, ImmunoOncology, SingleCell, Software
Version	1.0.0
In Bioconductor since	BioC 3.13 (R-4.1) (< 6 months)
License	GPL-2
Depends	R (>= 4.1), Biobase, SingleCellExperiment, MAST
Imports	pheatmap, ggplot2, RColorBrewer, grDevices, SummarizedExperiment, limma
LinkingTo
Suggests	rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	POWSC_1.0.0.tar.gz
Windows Binary	POWSC_1.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	POWSC_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/POWSC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/POWSC
Package Short Url	https://bioconductor.org/packages/POWSC/
Package Downloads Report	Download Stats