This is the new GSEA.

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

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

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

cd GSEA.jl

julia --project

]build

Find the executable at ~/.julia/bin/gsea.

gsea --help

Run the sarcopenia example

gsea metric-rank \
  ~/Downloads \
  in/target2.tsv \
  in/data2.tsv \
  in/set2.json \
  --number-of-permutations 10 \
  --more-plots "WP_DNA_MISMATCH_REPAIR;WP_CELL_CYCLE"

See test/runtests.jl for examples.

If you have questions, issues, or suggestions, please open a GitHub issue.

Every report makes GSEA better.

Made by Kata ✅