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Single-cell-specific statistical models often report large numbers of candidate genes but can exhibit inflated false positive rates, whereas pseudobulk approaches improve false discovery control at the cost of reduced sensitivity. To overcome the noise and bias that other tools have, and allow the user to have more control of the DEG process, we present CellDEEP, which uses a cell aggregation (metacell) approach. This tool provides a framework for flexible selection of pooling strategies and parameterization for differential expression analysis. Benchmarking on simulated and real datasets, including COVID-19 and rheumatoid arthritis, shows that CellDEEP often outperforms other methods, consistently reduces false positives compared to single-cell methods and recovers more true positives than pseudobulk methods. Our work shifts the focus from selecting a single \u2018best\u2019 method to an approach that reduces cell-level noise while preserving biological signal, together with transparent validation framework, advancing more reliable differential-expression analysis in single-cell transcriptomics.<\/jats:p>","DOI":"10.1093\/nargab\/lqag128","type":"journal-article","created":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T09:04:42Z","timestamp":1792573482000},"source":"Crossref","is-referenced-by-count":0,"title":["Cell DiffErential Expression by Pooling (CellDEEP) highlights issues in differential gene expression in scRNA-seq"],"prefix":"10.1093","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-3329-6842","authenticated-orcid":false,"given":"Yiyi","family":"Cheng","sequence":"first","affiliation":[{"name":"School of Infection & Immunity, University of Glasgow , G12 8TA,Glasgow ,","place":["United Kingdom"]},{"name":"Bernhard Nocht Institute of Tropical Medicine , 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