Pathway-centric analyses of omics data with GSVA

Quick-install 

BiocManager::install(
    "functionalgenomics/GSVAEuroBioC2024", dependencies=TRUE, build_vignettes=TRUE
)

Instructor names and contact information

Axel Klenk, Robert Castelo

Dept. of Medicine and Life Sciences

Universitat Pompeu Fabra

Barcelona

Workshop description

This workshop demonstrates how to use GSVA to conduct pathway-centric analyses of omics data. It uses the current development version of GSVA available at the time of EuroBioC2024, which contains a number of new features that will become part of the next version of GSVA 2.0 in the next release of Bioconductor on October 2024. Some of the features illustrated in this workshop may change until GSVA 2.0 is released, and others that are currently missing may still become part of that version.

Keywords: pathway analysis, transcriptomics, proteomics

Pre-requisites

  • Basic knowledge of R syntax.
  • Familiarity with the SummarizedExperiment and the SingleCellExperiment classes.

Time outline

40 minutes total

Activity Time
Import gene set annotations 10m
Analysis of bulk RNA-seq data 15m
Analysis of single-cell RNA-seq data 15m

Docker commands for this workshop

The Docker image for this workshop is available on the GitHub Container Registry. Pull (download) the image with the following command:

docker pull ghcr.io/functionalgenomics/gsvaeurobioc2024:latest

Run the workshop with Docker by first using the following command:

docker run -d -e PASSWORD=bioc -p 8787:8787 ghcr.io/functionalgenomics/gsvaeurobioc2024:latest

Second, open the url localhost:8787 in a new tab of your web browser.

Workshop goals and objectives

Learning goals

  • Import gene sets from GMT files.

  • Obtain pathway enrichment scores using GSVA.

  • Use the resulting pathway enrichment scores in downstream analyses.

Questions & Comments

For questions, comments, or bug reports, please use the Bioconductor support site or create an issue on the GSVA Github repo.