Installing R

R is not a requirement for this package but is currently needed to do differential expression analysis using the edgeR package. You will not need to use R directly at all. smallrnaseq handles pre-processing your count data according to the factors you want to compare.

Linux

Installation is via the package managers so on Ubuntu:

sudo apt install r-base

Windows/Mac

Go to https://cran.r-project.org/ and download the installers.

edgeR

This is an extra package provided as part of the bioconductor project. You can install from the command line as follows:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("edgeR")

Links

• https://www.r-project.org/about.html
• http://bioconductor.org/packages/release/bioc/html/edgeR.html