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

Hu, M.; Chikina, M.; Zhang, M. J.

doi:10.1101/2025.07.31.667984

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bioRxiv · 10.1101/2025.07.31.667984

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

Hu, M.·Chikina, M.·Zhang, M. J.

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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.

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Hu, M., Chikina, M., Zhang, M. J.. 2025-08-02. DALE-Eval: A comprehensive cell type-specific expression deconvolution benchmark for transcriptomics data. https://doi.org/10.1101/2025.07.31.667984

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