Section outline

  • 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")