Gene-set enrichment analysis workshop

Overview

This workshop will focus on performing gene-set enrichment analysis of transcriptomic data and visualising the results of enrichment analysis. We will perform single-sample gene-set enrichment using methods in the singscore package to explore molecular phenotypes in individual samples. Following this, we will perform gene-set enrichment analysis using tools from the limma and edgeR packages. Finally, we will demonstrate a graph-based approach to visualise, summarise and interpret resutls of gene-set enrichment analysis.

The workshop will be organised into two broad sections:

• Molecular phenotyping of individual samples
• Identifying and visualising higher-order phenotypes

Detailed material can be found here.

Pre-requisites

The course is aimed at PhD students, Master’s students, and third & fourth year undergraduate students. Some basic R knowledge is assumed - this is not an introduction to R course. If you are not familiar with the R statistical programming language it is compulsory that you work through an introductory R course before you attend this workshop.

R packages used

The following key R packages will be used:

• singscore
• vissE
• msigdb
• emtdata
• edgeR
• limma
• GSEABase
• igraph

Time outline

Activity	Time
Introduction & setup	10m
Part 1. Molecular phenotyping of individual samples	45m
Part 2. Identifying and visualising higher-order phenotypes	45m
Q & A	10m

Workshop goals and objectives

Learning goals

• Learn how to perform gene-set testing in R.
• Understand the results of gene-set enrichment analysis.
• Understand the importance of visualisation in bioinformatics and computational biology.

Learning objectives

• Perform a gene-set enrichment analysis and interpret the results.
• Apply vissE to identify higher-order phenotypes and to visualise the results of any gene-set enrichment analysis.

Workshop package installation

Guide

This is necessary in order to reproduce the code shown in the workshop. The workshop is designed for R 4.1 and can be installed using one of the two ways below.

Via Docker image

If you’re familiar with Docker you could use the Docker image which has all the software pre-configured to the correct versions.

docker run -e PASSWORD=password -p 8787:8787 bhuvad/genesetanalysisworkflow:latest

Once running, navigate to http://localhost:8787/ and then login with Username:rstudio and Password:password.

You should see the Rmarkdown file with all the workshop code which you can run.

Via GitHub

Alternatively, you could install the workshop using the commands below in R 4.1.

install.packages('remotes')

# Install workshop package
remotes::install_github("DavisLaboratory/GenesetAnalysisWorkflow", build_vignettes = TRUE)

# To view vignettes
library(GenesetAnalysisWorkflow)
browseVignettes("GenesetAnalysisWorkflow")