SPICEY

SPICEY quantifies cell-type specificity in single-cell transcriptomic and epigenomic data, particularly scRNA-seq and scATAC-seq, by introducing entropy-based indices that enable standardized analysis of cell-type-specific regulatory programs across diverse tissues and conditions.

Key Features:

• Gene Expression Tissue Specificity Index (GETSI): Provides a continuous, interpretable entropy-based measure of cell-type specificity for gene expression data from scRNA-seq.
• Regulatory Element Tissue Specificity Index (RETSI): Provides a continuous, interpretable entropy-based measure of cell-type specificity for regulatory elements from scATAC-seq.
• Cross-modal integration: Integrates gene expression and chromatin accessibility data for unified analysis of cell-type-specific regulatory programs.

Scientific Applications:

• Cell-type specificity quantification: Measures the specificity of genes and regulatory elements across cell types in single-cell datasets.
• Regulatory program analysis: Enables standardized characterization of cell-type-specific transcriptional and epigenetic regulatory programs across diverse tissues and conditions.

Methodology:

SPICEY computes GETSI and RETSI based on entropy to provide continuous, interpretable measures of specificity.