Roger-luo / GSEA.jl

The ✨ new ✨ Gene Set Enrichment Analysis 🧬

GSEA.jl

The ✨ new ✨ Gene Set Enrichment Analysis 🧬

🚧 Under rapid development 🚧

💁 Join the bioinformatics community to get live help on GSEA (and everything bioinformatics) 🎪 ⌨️ 🔰 💡

Use gsea command-line interface

Run single-sample GSEA

gsea si

Run pre-rank GSEA

gsea pr

Run standard GSEA

gsea st

Convert .gct and .cls to .tsvs

gsea convert-gct-and-cls bad.gct output/

Convert .gmt to .json

gsea convert-gmt bad.gmt good.json

Settings are just .json files.

Run test

1. Go to the test directory

cd test/data/sarcopenia

ls

2. Make output directory

rm -rf output

mkdir output

3. Convert .gct and .cls into .tsv

gsea convert-gct-and-cls gse111016_allsamplescounts_htseqcov1_sss_forgeo.sarcopenia.vs.normal_counts_collapsed_to_symbols.gct sarcopenia_binary.cls output

ls score.*

4. Convert .gmt into .json

gsea convert-gmt c2.cp.wikipathways.v7.4.symbols.gmt output/set_to_genes.json

head output/set_to_genes.json

5. Run standard GSEA

gsea run-standard-gsea ../setting/standard_gsea.json output/set_to_genes.json output/score.target_by_sample.tsv output/score.gene_by_sample.tsv output

head output/set_by_statistic.tsv

Install

1. Download

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

cd GSEA.jl &&

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

2. Build a personal or transferable binary

Personal binary

julia --project deps/build.jl

☝️ installs gsea into ~/.julia/bin.

If not already, add this bin to the path by adding 👇 to the profile (~/.zbashrc, ~/.babashrc, ...)

PATH=~/.julia/bin:$PATH

Transferable binary

julia --project deps/build.jl app tarball

☝️ makes build and gsea-application-N.N.N-julia-N.N.N-MACHINE-xNN.tar.gz.

Add build/gsea/bin to the path.

3. Test installation

Start a new bash just in case.

gsea -h

🎉

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Howdy 👋 🤠

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