Preface

This introduction to base R course was designed for biologists with no previous programming experience. It has a focus on analysing RNA-sequencing data using the Bioconductor package limma. The F1000 paper ‘RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR’ was used as a guide for the later sessions.

It is intended to be delivered over four 2.5 hour workshops at the Walter and Eliza Hall Institute of Medical Research (WEHI).

0.1 Data files

You can download and unzip the files using the following commands

download.file("https://github.com/Shians/BaseR_Intro/raw/master/data/workshop_data.zip", "workshop_data.zip")
unzip("workshop_data.zip", exdir = "data")
unzip("data/Ses3_counts.zip", exdir = "data/counts")

0.2 R Packages

Extra packages are required for later sessions, these can be downloaded by the following commands

if (!requireNamespace("BiocManager", quietly = TRUE)) 
    install.packages("BiocManager") 
 
BiocManager::install("RNAseq123")

Acknowledgements

The source code for this page can be found on Github.