Perform parameterized gene set enrichment analysis (GSEA) on multiple differential expression contrasts.

AcidGSEA currently extends the functionality of fgsea.

Installation

R method

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
install.packages(
    pkgs = "AcidGSEA",
    repos = c(
        "https://r.acidgenomics.com",
        BiocManager::repositories()
    )
)

Docker method

image="acidgenomics/r-acidgsea"
workdir="/mnt/work"
docker pull "$image"
docker run -it \
    --volume="${PWD}:${workdir}" \
    --workdir="$workdir" \
    "$image" \
    R