README.md

AcidGSEA

Install with Bioconda

Perform parameterized gene set enrichment analysis (GSEA) on multiple differential expression contrasts. 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()
    ),
    dependencies = TRUE
)

Conda method

Configure Conda to use the Bioconda channels.

# Don't install recipe into base environment.
name='r-acidgsea'
conda create --name="$name" "$name"
conda activate "$name"
R

Docker method

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


acidgenomics/acidgsea documentation built on June 29, 2022, 5:12 p.m.