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  Transcriptomics Analysis: RNA-seq for CRCL
  

  08-09 February 2023

  Lyon

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

  • Select activity Feedback form (Open from 09 Feb 15:00)

    

    Feedback form (Open from 09 Feb 15:00) URL
• Select section Programme

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  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, ...)

  
  

  
  
• Select section Software installation

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  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")
  
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  Material

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