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Improved reconstruction of single-cell developmental potential with CytoTRACE 2
Minji Kang, Gunsagar S. Gulati, Erin L. Brown and 11 more
Nature Methods · 2025 · CC BY
Abstract
While single-cell RNA sequencing has advanced our understanding of cell fate, identifying molecular hallmarks of potency—a cell’s ability to differentiate into other cell types—remains a challenge. Here we introduce CytoTRACE 2, an interpretable deep learning framework for predicting absolute developmental potential from single-cell RNA sequencing data. Across diverse platforms and tissues, CytoTRACE 2 outperformed previous methods in predicting developmental hierarchies, enabling detailed mapping of single-cell differentiation landscapes and expanding insights into cell potency.
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