Chapter 11 Bioinformatics Workshop
In this special chapter, bioinformatician Dr. Bastienne Vriesendorp will show you a real analysis of high-dimensional transcriptomics data (RNAseq). We will use various techniques that you have learned throughout the course, including PCA and multiple testing correction.
11.1 Preparation
This workshop requires packages from a specialized repository for bioinformatics. Since this is prone to installation problems, please try installing the following packages before the workshop. We are happy to help you with any installation issues.
install.packages(c('ggplot2','plyr','dplyr','mvdalab', 'ggfortify', 'stringr'))
# The last package is not installed from CRAN (the usual place we install from),
# but from a specialized repository for bioinformatics called Bioconductor:
install.packages("BiocManager")
BiocManager::install("DESeq2")11.3 Exercises
Download the R markdown file and the both data sets (raw counts and meta data). Save all three files in the same location, then open the R markdown file. This file contains all instructions required for the workshop.