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 and the third session on September 23-24, 2015. A fourth session will be held on May 18-19, 2017.

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 Nathalie Villa-Vialaneix.

Material

Required installation for the practical application

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

CRAN packages

  • RColorBrewer
  • mixOmics
  • VennDiagram

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

install.packages(c("RColorBrewer", "mixOmics", "VennDiagram"))

Bioconductor packages

  • edgeR
  • limma
  • HTSFilter

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

source("http://bioconductor.org/biocLite.R")
biocLite("edgeR")

(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