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bioRxiv · 10.64898/2026.07.06.736732

pylimma: a faithful, AnnData-native Python port of R limma for differential expression analysis

Mulvey, J.
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Abstract

pylimma is a faithful Python port of limma, intended to bring one of the most widely used tools for differential expression analysis to the developing Python ecosystem for transcriptomics and proteomics. We validated pylimma against the existing R implementation through 227 function-level comparisons and across six real world datasets spanning microarray, RNAseq, proteomics and single-cell transcriptomics. pylimma reproduces limmas numerical output to a median agreement of 13 significant figures and calls identical sets of differentially expressed features and gene sets. This supports its use as a drop-in replacement for the R implementation.

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Mulvey, J.. 2026-07-10. pylimma: a faithful, AnnData-native Python port of R limma for differential expression analysis. https://doi.org/10.64898/2026.07.06.736732

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