Enrichment Analysis - December 2020
Section outline
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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.
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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:
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:
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"))
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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
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Exercises
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