Gene set enrichment analysis 🏔️

Julia implementation of next-generation Gene Set Enrichment Analysis (GSEA), featuring 200X faster original algorithms and new information-theoretic algorithms for enhanced analysis.

Julia

using GSEA

GSEA.metric_rank(
    joinpath(homedir(), "Downloads"),
    joinpath("example", "sarcopenia", "target.tsv"),
    joinpath("example", "sarcopenia", "data.tsv"),
    joinpath("example", "sarcopenia", "set.json");
    number_of_permutations = 10,
    more_sets_to_plot = "WP_DNA_MISMATCH_REPAIR WP_CELL_CYCLE",
)

GSEA.read_cls(joinpath("data", "a.cls"))

GSEA.read_gct(joinpath("data", "b.gct"))

GSEA.read_gmt(joinpath("data", "c.gmt"))

Command Line Interface

gsea metric-rank \
    ~/Downloads \
    example/sarcopenia/target.tsv \
    example/sarcopenia/data.tsv \
    example/sarcopenia/set.json \
    --number-of-permutations 10 \
    --more-sets-to-plot "WP_DNA_MISMATCH_REPAIR WP_CELL_CYCLE"

gsea cls ~/Downloads/a.tsv data/a.cls

gsea gct ~/Downloads/b.tsv data/b.gct

gsea gmt ~/Downloads/cd.json data/c.gmt data/d.gmt

Install

We plan to sign this app for macOS soon. In the meantime, please enable third-party apps.

Download and extract the latest release.

PATH=$(pwd)/gsea/bin:$PATH

Build

]build

PATH=~/.julia/bin:$PATH

Contact Us

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

---

Made by Kata 🥋