TIVelo:利用聚类级轨迹推断进行RNA速度估计。
TIVelo: RNA velocity estimation leveraging cluster-level trajectory inference.
作者信息
Ge Muyang, Miao Jishuai, Qi Ji, Zhou Xiaocheng, Lin Zhixiang
机构信息
Department of Statistics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
出版信息
Nat Commun. 2025 Jul 7;16(1):6258. doi: 10.1038/s41467-025-61628-x.
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.
RNA速度推断是理解细胞发育、分化和疾病进展的一项有价值的工具。然而,现有的RNA速度推断方法通常依赖于常微分方程(ODE)的明确假设,这使得它们无法捕捉复杂的转录组表达模式。在本研究中,我们引入了TIVelo,一种RNA速度估计方法,该方法首先基于轨迹推断在细胞簇水平确定速度方向,然后再估计单个细胞的速度。TIVelo计算一个方向得分以在不做明确ODE假设的情况下推断簇水平的方向,这有效地捕捉了复杂的转录模式,避免了对不遵循简单ODE假设的基因进行速度估计时可能出现的不一致性。我们通过将TIVelo应用于16个真实数据集并与六种基准方法进行比较,验证了其有效性。