Package: ssizeRNA
Type: Package
Title: Sample Size Calculation for RNA-Seq Experimental Design
Version: 1.3.3
Date: 2025-04-08
Authors@R: c(
    person("Ran", "Bi", email = "biranpier@gmail.com", role = c("aut", "cre")),
    person("Peng", "Liu", email = "pliu@iastate.edu", role = "aut"),
    person("Tim", "Triche", email = "tim.triche@gmail.com", role = "ctb"))
Maintainer: Ran Bi <biranpier@gmail.com>
Description: 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")'.
Depends: R (>= 3.2.3)
Imports: MASS, Biobase, edgeR, limma, qvalue, ssize.fdr, graphics,
        stats
VignetteBuilder: knitr
Suggests: knitr
License: GPL (>= 2)
biocViews: GeneExpression, DifferentialExpression, ExperimentalDesign,
        Sequencing, RNASeq, DNASeq, Microarray
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2025-04-08 17:36:59 UTC; Ran
Author: Ran Bi [aut, cre],
  Peng Liu [aut],
  Tim Triche [ctb]
Repository: CRAN
Date/Publication: 2025-04-08 23:30:03 UTC
Built: R 4.6.0; ; 2026-04-27 10:02:27 UTC; unix
