dreampy: Pseudobulk mixed-model differential expression for single-cell RNA-seq in Python

Abstract dreampy is a Python implementation of the R dreamlet framework for pseudobulk differential expression analysis of single-cell RNA-seq data. dreamlet combines voom precision-weighted linear mixed models with empirical Bayes moderation to handle batch effects, repeated measures, and other hierarchical structure in multi-donor studies, but exists entirely within the R/Bioconductor ecosystem. dreampy reproduces this pipeline natively in Python, integrating with AnnData and the scverse ecosystem. Competing Interest Statement The authors have declared no competing interest. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.