POWSC
This is the released version of POWSC; for the devel version, see POWSC.
Simulation, power evaluation, and sample size recommendation for single cell RNA-seq
Bioconductor version: Release (3.23)
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>
citation("POWSC")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("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")| The POWSC User's Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, ImmunoOncology, SingleCell, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | GPL-2 |
| Depends | R (>= 4.1), Biobase, SingleCellExperiment, MAST |
| Imports | pheatmap, ggplot2, RColorBrewer, grDevices, SummarizedExperiment, limma |
| System Requirements | |
| URL |
See More
| Suggests | rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | POWSC_1.20.0.tar.gz |
| Windows Binary (x86_64) | POWSC_1.20.0.zip |
| macOS Binary (big-sur-x86_64) | POWSC_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | POWSC_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/POWSC |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/POWSC |
| Bioc Package Browser | https://code.bioconductor.org/browse/POWSC/ |
| Package Short Url | https://bioconductor.org/packages/POWSC/ |
| Package Downloads Report | Download Stats |