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SPICEY

Bioc current

Calculates cell type specificity from single cell data

v1.2.0 · software · Artistic-2.0
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.22 · Oct 30, 2025

Current · Requires R 4.6

1.0 In 2 of 49 releases 3.23

Description

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.

Code

Code metrics have not been computed for this package yet.

Topics

Software › ResearchField › Transcriptomics
Software › ResearchField › Epigenetics
Software › Technology › SingleCell
Software › BiologicalQuestion › DifferentialExpression
Software › BiologicalQuestion › DifferentialPeakCalling
Software › BiologicalQuestion › GeneRegulation
Software › BiologicalQuestion › GeneTarget
Software › AssayDomain › GeneExpression
Software › AssayDomain › Transcription

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