AUCell

AUCell computes gene set activity in single-cell RNA sequencing (scRNA-seq) data by measuring enrichment of predefined gene sets within each cell using the Area Under the Curve (AUC).

Key Features:

• Gene Set Enrichment Analysis: Computes the AUC for each cell's expression profile against predefined gene sets to quantify per-cell gene set enrichment.
• Single-Cell Resolution: Operates at single-cell resolution to identify cells with active gene sets and dissect cellular heterogeneity.
• Integration with Regulatory Network Analysis: Complements regulatory network reconstruction methods such as SCENIC by providing per-cell gene set activity scores for integration with network inference.

Scientific Applications:

• Cellular Heterogeneity Studies: Identifies active gene sets across cells to characterize distinct cell types and states within tissues.
• Disease Mechanism Exploration: Pinpoints active biological pathways at single-cell resolution to investigate disease mechanisms, including cancer.
• Transcription Factor Activity Profiling: Aids identification of transcription factor–associated activity by scoring enrichment of gene sets regulated by specific transcription factors, especially when combined with methods like SCENIC.

Methodology:

Calculates the Area Under the Curve (AUC) for each cell's expression profile against predefined gene sets to assess whether a subset of input genes is enriched among the expressed genes in that cell.