2 Setting the Enviroment

2.1 Required libraries

This chunk shows how to install the required libraries. The libraries should be installed just once. So, you dont need to run this chunk again each time when you run a new analysis. The required packages will install many dependancies. Importantly, BiocManager may require R version 3.6 or above.

install.packages("dplyr") # for data wrangling
install.packages("RColorBrewer") # for plotting heatmaps
install.packages("pheatmap") # for plotting heatmaps
install.packages("VennDiagram") # for plotting Venn diagram

install.packages("BiocManager") # for installing Bioconductor packages
BiocManager::install("rtracklayer") # for reading GTF file
BiocManager::install("DESeq2") # for differential expression analysis

2.2 Base folder etc

Record the analysis start time, clean-up environment, customise options and set the base folder

# Start time
Sys.time()

## [1] "2020-04-08 16:18:34 BST"

# Intial clean-up
rm(list=ls())
graphics.off()

# Customised options
options(stringsAsFactors = F)

# Base folder
base_folder="/Users/alexey/OneDrive/Documents/Teaching/Lecturing/rna-seq-ebi-2020-tutorial"