SPICEY

Calculates cell type specificity from single cell data

Bioconductor version: 3.23 · Package version: 1.2.0

SPICEY (SPecificity Index for Coding and Epigenetic activitY) is an R package designed to quantify cell-type specificity in single-cell transcriptomic and epigenomic data, particularly scRNA-seq and scATAC-seq. It introduces two complementary indices: the Gene Expression Tissue Specificity Index (GETSI) and the Regulatory Element Tissue Specificity Index (RETSI), both based on entropy to provide continuous, interpretable measures of specificity. By integrating gene expression and chromatin accessibility, SPICEY enables standardized analysis of cell-type-specific regulatory programs across diverse tissues and conditions.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SPICEY")