Topic outline

  • Enrichment analysis

    streamed from Lausanne, 25 June 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 – 25.06.2021

    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(c("org.Hs.eg.db", "clusterProfiler", "pathview"))

     

     

    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(c("org.Hs.eg.db", "clusterProfiler", "pathview"))

    • 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