This page gathers information and material for “Normalization and differential analysis of RNA-seq data”, a course given during the SPS summer school “From gene expression to genomic network” given at Centre Port Royal, Saint-Lambert, July 17-22.
You will be asked to have your own R installation with a list of required packages already installed. We also advise that you install RStudio. The installation steps are described below. In case of difficulty, please, contact me (emails preferred).
RMarkdown files will be provided as well as corresponding R scripts and HTML outputs. If you want to compile the RMarkdown files, the following packages need to be installed (from CRAN):
evaluate (version 0.7.2),
formatR (version 1.1),
highr (version 0.3),
markdown (version 0.7),
yaml (version 2.1.5),
htmltools (version 0.2.4),
knitr (version 1.11),
rmarkdown (version 0.9.2). The file can then easily be compiled within RStudio by pressing the button “Knit HTML”.
For download, you have:
tar.gzarchive that must be uncompressed. Within it are two subdirectories: the first one
datawith datasets (text format) and the second one
scripts</a> with RMarkown script and resulting html and R files;