Section outline

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    Enrichment analysis

    streamed from Lausanne, 03 December 2021

    This page is addressed to registered participants. To access course description and application form, please click here.

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

  • R and RStudio

    Preparation of R for enrichment analysis tool – 03.12.2021

    Two options are available to perform the exercises of the enrichment analysis course.

    1. Local installation of R and RStudio:

    Install R:

    https://cran.r-project.org/

     

    Install RStudio (free version is fine)

    https://rstudio.com/products/rstudio/download/

     

    Once R and RStudio are installed, open RStudio only (no need to open R, RStudio connects automatically to your installation of R).

     

    Install the necessary packages using the following commands:

    install.packages("BiocManager")
    BiocManager::install("clusterProfiler")
    BiocManager::install("org.Hs.eg.db")
    BiocManager::install("pathview")
    BiocManager::install("enrichplot")
    install.packages("ggplot2")
    install.packages("ggrepel")

     

     

    2. Another option is to create an R session on the RStudio cloud:

    https://rstudio.cloud/

    Create a free account.  Then, go to “Workspace” and create a new project by clicking on “New project”. Once the new project has been deployed, install the necessary packages using the following commands:

    install.packages("BiocManager")
    BiocManager::install("clusterProfiler")
    BiocManager::install("org.Hs.eg.db")
    BiocManager::install("pathview")
    BiocManager::install("enrichplot")
    install.packages("ggplot2")
    install.packages("ggrepel")

  • Schedule

    9:00  - 10:30    

    Recall:

    a. Differential expression

    b. Statistical tests

    Exercise

    10:30  - 10:45    coffee break

    10:45  - 12:30    

    Method of gene set enrichment analysis

    Exercise

    12:30  - 13:30  lunch

    13:30  - 15:30   

    Ontologies and sources of gene sets

    Exercise

    15:30  - 15:45  coffee break

    15:45  - 17:00  

    Visualization of enrichment results

    Exercise

    17:00    end of day