Topic outline

  • Enrichment analysis

    streamed from Lausanne, 4 December 2020

    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 – 4.12.2020

    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

  • Course material