TIVelo: RNA velocity estimation leveraging cluster-level trajectory inference

Muyang Ge, Jishuai Miao, Ji Qi, Xiaocheng Zhou and Zhixiang Lin ()
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Muyang Ge: The Chinese University of Hong Kong, Shatin
Jishuai Miao: The Chinese University of Hong Kong, Shatin
Ji Qi: The Chinese University of Hong Kong, Shatin
Xiaocheng Zhou: The Chinese University of Hong Kong, Shatin
Zhixiang Lin: The Chinese University of Hong Kong, Shatin

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract RNA velocity inference is a valuable tool for understanding cell development, differentiation, and disease progression. However, existing RNA velocity inference methods typically rely on explicit assumptions of ordinary differential equations (ODE), which prohibits them from capturing complex transcriptomic expression patterns. In this study, we introduce TIVelo, a RNA velocity estimation approach that first determines the velocity direction at the cell cluster level based on trajectory inference, before estimating velocity for individual cells. TIVelo calculates an orientation score to infer the direction at the cluster level without an explicit ODE assumption, which effectively captures complex transcriptional patterns, avoiding potential inconsistencies in velocity estimation for genes that do not follow the simple ODE assumption. We validated the effectiveness of TIVelo by its application to 16 real datasets and the comparison with six benchmarking methods.

Date: 2025
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DOI: 10.1038/s41467-025-61628-x

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