escape.gene.sets: Built-In Gene Sets for escape

In ncborcherding/escape: Easy single cell analysis platform for enrichment

Built-In Gene Sets for escape

Description

'escape.gene.sets' ships with **escape** and provides a convenient set of cell-type and pathway signatures from the scRNA-seq tumor micro-environment study by Azizi *et al.* (2018, Cell \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.cell.2018.06.021")}). These signatures capture major immune and stromal populations observed across breast-cancer samples and serve as a lightweight default for quick testing or exploratory analyses.

Usage

data("escape.gene.sets")

Details

The original paper defined cell-type signatures as the top differentially expressed genes per cluster (Azizi *et al.*, Supplementary Table S3).

Source

Supplementary Table S3 in Azizi *et al.* (2018) <https://pubmed.ncbi.nlm.nih.gov/29961579/>

References

Azizi E, *et al.* **Single-cell map of diverse immune phenotypes in the breast tumor microenvironment.** *Cell* 173(5):1293-1308 (2018).

See Also

[runEscape()], [escape.matrix()], [getGeneSets()]

ncborcherding/escape documentation built on June 12, 2025, 1 p.m.