Section outline

  • Collapse all Expand all

    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")