Please ensure that the following software are installed on your machine PRIOR to the course:
• FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
• QualiMap (http://qualimap.bioinfo.cipf.es/)
• R (https://www.r-project.org, version > 4.0)
• latest version of R Studio
---------------------
Installation of R packages for Practical 1
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("NOISeq")
BiocManager::install("Repitools")
BiocManager::install("Rsamtools")
BiocManager::install("Rsubread")
BiocManager::install("rtracklayer")
---------------------
Installation of R packages for Practical 2
install.packages("devtools")
install.packages("ggplot2")
install.packages("gridExtra")
install.packages("RColorBrewer")
install.packages("reshape2")
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")
BiocManager::install("edgeR")
BiocManager::install("mixOmics")
---------------------
Installation of R packages for Practical 3
install.packages("pheatmap")
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("clusterProfiler")
BiocManager::install("org.Mm.eg.db")
BiocManager::install("enrichplot")
