Topic outline

  • Transcriptomics Analysis: RNA-seq for CRCL

    08-09 February 2023

    Lyon

    For any assistance, please contact training@sib.swiss.

  • Programme

    DAY1 (9h-18h):

    • Introduction to RNA sequencing
    • RNAseq analysis pipeline
    • Differential Expression analysis

    DAY2 (9h-16h):

    • Differential Expression analysis with DESEQ2
    • Downstream analysis
    • Other topics (differential splicing, ...)


    • Software installation

      Please ensure that the following software are installed on your machine prior to the course:
      • R (https://www.r-project.org, version > 4.0)
      • latest version of R Studio

      ---------------------
      Installation of R packages for Practical 1

      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 2

      install.packages("pheatmap")

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

      BiocManager::install("clusterProfiler")
      BiocManager::install("org.Mm.eg.db")
      BiocManager::install("pathview")
      BiocManager::install("enrichplot")
      BiocManager::install("biomaRt")

      • Material

        Course material will be put online before the course.