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

Wells, S. B.; Shahnawaz, H.; Jones, J. L.

2026-03-24 bioinformatics
10.64898/2026.03.21.713408 bioRxiv
Show 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.

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