escape

escape facilitates gene set enrichment analysis (GSEA) in the context of single-cell RNA sequencing by enabling ssGSEA, GSVA, AUCell, UCell, and rank-based GSEA calculations across individual cells using raw count information, Seurat objects, or SingleCellExperiment format.

Key Features:

• Multiple enrichment algorithms: Supports ssGSEA, GSVA, AUCell, and UCell-based enrichment calculations across individual cells.
• Rank-based GSEA integration: Supports rank-based GSEA using differential gene expression via fgsea.
• Flexible input formats: Accepts raw count information, Seurat objects, or SingleCellExperiment format.
• Visualization capabilities: Enables visualization of enrichment calculations.

Scientific Applications:

• Single-cell gene set enrichment analysis: Performs GSEA in the context of single-cell RNA sequencing data.
• Differential expression-based enrichment: Applies rank-based GSEA to differential gene expression results.

Methodology:

The package functions as a bridging R package that integrates multiple established GSEA algorithms for single-cell analysis.