Gene set enrichment analysis 🏔️

The Julia implementation of the next-generation GSEA is hundreds of times faster and incorporates new information-theoretic algorithms.

Check out CLSGCTGMT.jl.

Julia

using GSEA

GSEA.metric_rank(
    joinpath(homedir(), "Downloads"),
    joinpath("example", "sarcopenia", "target_x_sample_x_number.tsv"),
    joinpath("example", "sarcopenia", "feature_x_sample_x_number.tsv"),
    joinpath("example", "sarcopenia", "set_features.json");
    number_of_permutations = 10,
    more_sets_to_plot = ["WP_DNA_MISMATCH_REPAIR", "WP_CELL_CYCLE"],
)

Command Line Interface

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

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

julia --project deps/build.jl

PATH=~/.julia/bin:$PATH

Contact Us

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

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Made by Kata 🥋