ssizeRNA: Sample Size Calculation for RNA-Seq Experimental Design

We propose a procedure for sample size calculation while controlling false discovery rate for RNA-seq experimental design. Our procedure depends on the Voom method proposed for RNA-seq data analysis by Law et al. (2014) <doi:10.1186/gb-2014-15-2-r29> and the sample size calculation method proposed for microarray experiments by Liu and Hwang (2007) <doi:10.1093/bioinformatics/btl664>. We develop a set of functions that calculates appropriate sample sizes for two-sample t-test for RNA-seq experiments with fixed or varied set of parameters. The outputs also contain a plot of power versus sample size, a table of power at different sample sizes, and a table of critical test values at different sample sizes. To install this package, please use 'source("http://bioconductor.org/biocLite.R"); biocLite("ssizeRNA")'. For R version 3.5 or greater, please use 'if(!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")}; BiocManager::install("ssizeRNA")'.

Version:	1.3.2
Depends:	R (≥ 3.2.3)
Imports:	MASS, Biobase, edgeR, limma, qvalue, ssize.fdr, graphics, stats
Suggests:	knitr
Published:	2019-08-20
DOI:	10.32614/CRAN.package.ssizeRNA
Author:	Ran Bi [aut, cre], Peng Liu [aut], Tim Triche [ctb]
Maintainer:	Ran Bi <biranpier at gmail.com>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation:	no
In views:	ExperimentalDesign
CRAN checks:	ssizeRNA results

Documentation:

Reference manual:	ssizeRNA.pdf
Vignettes:	Sample Size Calculation for RNA-Seq Experimental Design

Downloads:

Package source:	ssizeRNA_1.3.2.tar.gz
Windows binaries:	r-devel: ssizeRNA_1.3.2.zip, r-release: ssizeRNA_1.3.2.zip, r-oldrel: ssizeRNA_1.3.2.zip
macOS binaries:	r-release (arm64): ssizeRNA_1.3.2.tgz, r-oldrel (arm64): ssizeRNA_1.3.2.tgz, r-release (x86_64): ssizeRNA_1.3.2.tgz, r-oldrel (x86_64): ssizeRNA_1.3.2.tgz
Old sources:	ssizeRNA archive

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