CycleVI: Isolating cell cycle variation with an interpretable deep generative model.

Abstract

Cell cycle progression is a dominant source of variation in single-cell RNA sequencing (scRNA-seq) data, often obscuring other transcriptional signals of interest. Several methods have been developed to infer continuous cell cycle phase from transcriptomic data, but their estimates tend to be unstable when proliferation is intertwined with other biological processes or technical sources of heterogeneity. We present CycleVI, a deep generative model that disentangles cell cycle-driven variation from other signals in scRNA-seq data using a partitioned latent representation with a dedicated circular subspace. CycleVI accurately infers a continuous cell cycle phase, validated against orthogonal protein-level measurements, and yields a residual latent space free of cell cycle artefacts. This disentangled representation helps resolve biological processes intertwined with the cell cycle, clarifying hematopoietic differentiation and preserving drug-response signals better than standard cell cycle regression. By isolating cell cycle-related variation rather than removing it, CycleVI provides a principled framework for analysing cellular heterogeneity in proliferating systems. CycleVI is available at www.github.com/jeuken/CycleVI, or through the 'cyclevi' Python package. Supplementary data are available at Bioinformatics online.