Biostatistics analysis of RNA-Seq data

Biostatistics analysis of RNA-Seq data

This course is part of the INRA training session about “bioinformatics and biostatistics analysis of RNA-seq data” and of the Biostatistics platform “Initiation à LA statistique, niveau 4”. The first session was held in Toulouse on November 18-21, 2014, the second session on April 2-3, 2015, the third session on September 23-24, 2015 and the fourth session on May 18-19, 2017. The next session will be held on February 11-12, 2019.

The material provided on the present webpage is related to the biostatistics part and covers the following topics:

  • R and RStudio
  • design of experiments
  • variability
  • count data normalization
  • differential analysis

The material has been prepared by Ignacio Gonzales, Annick Moisan and myself. The class will be taught by Gaëlle Lefort and myself.

Material

Required installation for the practical application

R is needed for the practical application, as well as the following packages:

CRAN packages

  • ggplot2
  • gridExtra
  • reshape2
  • RColorBrewer
  • VennDiagram
  • devtools

These packages can be installed using the following command line in an R console:

install.packages(c("ggplot2"))

(and similarly for the other packages).

Bioconductor packages

  • mixOmics
  • edgeR

These packages can be installed using the following command lines in an R console (after the CRAN package BiocManager has been installed as above:

BiocManager::install("mixOmics")

(and similarly for the other packages).

The precise versions of R and of the packages used in the practical application is given at the end (session information) of the solution of the analysis (this HTML file).

Additional (older and not updated) material

How to install R and RStudio?

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, screenshots welcome).

   

Install R

R can be downloaded for free on the official repository website. Choose the version depending of your OS (Windows, Linux or Mac). Mac users should also probably install tcltk which is available in the section called tools. Some linux users might also found R in their distribution repositories (this is the case for Ubuntu and Debian users; further details are provided on this page).
   

Install RStudio

RStudio (Desktop version) can be downloaded for free at this link. Choose the version ("Installers" prefer) depending of your OS (Windows, Linux or Mac). Ubuntu users can install the .deb file with
sudo dpkg -i rstudio-VERSION.deb
sudo apt-get install -f