subSeq Installation

Dependencies

Please first install the package’s dependencies with BioConductor (subSeq will be submitted to Bioconductor when the paper is published, at which point this process will be automatic when installed):

source("http://bioconductor.org/biocLite.R")
biocLite(c("limma", "edgeR", "DESeq2", "DEXSeq", "pasilla"))

Installing subSeq

Please download and install both of these R packages (install qvalue first):

• qvalue_1.99.0.tar.gz
• subSeq_0.99.0.tar.gz

Alternatively, you can install the devtools package, and use it to install qvalue and subSeq from their GitHub repositories:

install.packages("devtools")
library(devtools)
install_github("qvalue", "jdstorey")
install_github("subSeq", "StoreyLab")

Vignette

Once subSeq is installed, the vignette may be accessed by typing:

library(subSeq)
vignette("subSeq")

Alternatively, you may download the vignette directly here: subSeq.pdf.