The official command-line program for gene-set-enrichment analysis (GSEA) 🏔️

Quick Start

1. Go to example directory

cd example/sarcopenia

ls -l

2. Make an output directory

mkdir ~/Downloads/gsea

3. Run GSEA

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

4. Look at the results

cd ~/Downloads/gsea

ls -l

head -3 *.tsv

open *.html

Use gsea command-line interface

Run metric-rank (standard) GSEA

gsea metric-rank

Run user-rank (pre-rank) GSEA

gsea user-rank

Run data-rank (single-sample) GSEA

gsea data-rank

Convert .cls and .gct to .tsvs

gsea convert-cls-gct

Convert one or more .gmts to a .json

gsea convert-gmt

Use in julia

]add

]add https://github.com/KwatMDPhD/GSEA.jl

Use

Each command-line-interface command has a corresponding function. Options and flags are keyword arguments.

Reproduce Quick Start in julia

using GSEA

const DI = joinpath("example", "sarcopenia")

GSEA.metric_rank(
    mkpath(joinpath(homedir(), "Downloads", "gsea")),
    joinpath(DI, "target_x_sample_x_number.tsv"),
    joinpath(DI, "feature_x_sample_x_number.tsv"),
    joinpath(DI, "set_features.json"),
    number_of_permutations = 10,
    more_sets_to_plot = ["WP_DNA_MISMATCH_REPAIR", "WP_CELL_CYCLE", "ALIEN"],
)

Install

1. Download the latest release and extract it.

2. Path

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

3. Use

We plan to sign the app soon. Meanwhile, enable 3rd-party apps on your macOS.

gsea --help

🎉

Build

If installation is unavailable or fails, try building.

1. Download

git clone https://github.com/KwatMDPhD/GSEA.jl

2. Instantiate

cd GSEA.jl &&

julia --project --eval "using Pkg; Pkg.instantiate()"

3. Build

julia --project deps/build.jl app tarball

4. Path

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

5. Use

gsea --help

🎊

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