GSVA (Gene Set Variation Analysis)

GSVA (Gene Set Variation Analysis) is an R/Bioconductor package designed for microarray and RNA-seq data. It performs a change in coordinate systems for molecular measurements, transforming data from a gene by sample matrix into a gene-set by sample matrix.

This transformation allows for the evaluation of pathway enrichment for each individual sample. The resulting matrix of GSVA enrichment scores can be used for various downstream analytical methods, including:

• Functional enrichment
• Survival analysis
• Clustering
• CNV-pathway analysis
• Cross-tissue pathway analysis

The current repository contains the development version of GSVA, which is unstable and intended for testing new features. To install the development version, you must first have the development version of Bioconductor installed. You can then install GSVA using BiocManager.

Alternatively, you can install the development version directly from GitHub using the remotes package.

# Option 1: Via BiocManager (requires Bioconductor devel)
BiocManager::install("GSVA", version = "devel")

# Option 2: Via remotes from GitHub
install.packages("remotes")
library(remotes)
install_github("rcastelo/GSVA")

Where to report issues depends on which version of GSVA you are using:

• Release Version: Use the Bioconductor support site.
• Development Version (this repo): Use the GitHub issues tab.