Gene set enrichment analysis (GSEA) 🏔️

This is the new GSEA.

We reimplemented the S0 and S0a algorithms.
They run 1,000 times faster, reproduce all results, and create prettier plots.

We also implemented a new D2 algorithm.
It uses information theory to deliver the most accurate, interpretable, and robust gene-set scores.

Install

Download the latest release, extract it, and find the executable at gsea/bin/gsea.

Or clone this repository and build

git clone https://github.com/GSEA-MSigDB/GSEA.jl

cd GSEA.jl

julia --project deps/build.jl app tarball

# Find the executable at `build/gsea/bin/gsea`.

Get started

gsea --help

Run the sarcopenia example

gsea metric-rank \
  ~/Downloads \
  in/ex.target.tsv \
  in/ex.data.tsv \
  in/ex.set.json \
  --number-of-permutations 10 \
  --more-plots "WP_DNA_MISMATCH_REPAIR;WP_CELL_CYCLE"

Contact us

If you have any questions, issues, or concerns, feel free to open a GitHub issue.

Every report helps make GSEA better.

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Made by Kata ✅