DALE-Eval: A comprehensive cell type-specific expression deconvolution benchmark for transcriptomics data

Abstract

Deconvolution of bulk transcriptomic data unlocks rich, cell type-specific insights from complex tissue samples. While cell type fraction deconvolution has been extensively developed and bench-marked, the next frontier--cell type-specific expression (CTSE) deconvolution--remains largely underexplored. Here, we introduce DALE-Eval, a comprehensive benchmark of CTSE methods, featuring novel evaluation metrics, identification of key drivers of performance, and practical recommendations for maximizing the value of CTSE in downstream applications.