The ✨ new ✨ Gene Set Enrichment Analysis 🧬
🚧 Under rapid development 🚧
💁 Join the bioinformatics community to get live help on GSEA (and everything bioinformatics) 🎪 ⌨️ 🔰 💡
gsea si
gsea pr
gsea st
gsea convert-gct-and-cls bad.gct output/
gsea convert-gmt bad.gmt good.json
Settings are just .json
files.
- Go to the test directory
cd test/data/sarcopenia
ls
- Make output directory
rm -rf output
mkdir output
- 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.*
- 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
- 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
git clone https://github.com/KwatMDPhD/GSEA.jl &&
cd GSEA.jl &&
julia --project --eval "using Pkg; Pkg.instantiate()"
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
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.
Start a new bash just in case.
gsea -h
🎉
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