Single Sample GSEA analysis
Single-sample geneset enrichment analysis (ssGSEA) is a single-sample extension of the GSEA algorithm. It calculates a separate enrichment score for each sample and gene set pairing [1].
Install the latest version
pip install single_sample_gsea
Usage
>>> from single_sample_gsea import ss_gsea
>>> gene_sets = {
"gs1": {"gene2", "gene3"},
"gs2": {"gene1", "gene4"},
}
>>> data = {
"gene": ["gene1", "gene2", "gene3", "gene4", "gene5"],
"sample-1": [1, 3, 4, 7, 32],
"sample-2": [25, 4, 6, 18, 1],
}
>>> data = pd.DataFrame(data).set_index("gene")
>>> ss_gsea(data, gene_sets)
gs1 gs2
sample-1 -1.333333 -0.962974
sample-2 -1.333333 2.543214References
[1] Barbie, D., Tamayo, P., Boehm, J. et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature 462, 108–112 (2009). https://doi.org/10.1038/nature08460
