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proRate:一个R包来推断基因转录率,使用一种新的最小平方和方法

Yu Liu¹, Fadhl Alakwaa²

¹Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor 48109 MI, United States.

NAR genomics and bioinformatics

|September 8, 2025

概括

我们开发了proRate,一个R包,通过识别RNA聚合酶II (Pol II) 占用数据中的过渡点来准确测量转录延长率. 这个工具简化了复杂的转录动态分析.

科学领域:

分子生物学分子生物学
基因组学就是基因组学.
生物信息学是一种生物信息学.

背景情况:

转录延长动态对于RNA处理和出口至关重要.
目前使用Pro-seq或Gro-seq数据测量延长率的方法在识别药物诱导的过渡点方面面临挑战.
传统的隐藏马尔科夫模型 (HMM) 由于隐藏的变量和参数估计,对此分析是复杂的.

研究的目的:

开发一个新的R包,proRate,用于准确量化转录延长率.
引入一种新的最小平方和 (LSS) 方法,用于识别数据序列中的过渡点.
为全面的转录动态研究提供一个用户友好的工具.

主要方法:

开发R包"proRate"的发展.
实施一种新的最小平方和 (LSS) 方法来识别过渡点.
在Pro-seq和Gro-seq数据集上的应用和验证.

主要成果:

该proRate包准确地识别过渡点,并计算延长率.
与传统的HMM相比,LSS方法的准确性更高.
proRate包括用于转录动态分析的额外功能,例如元基因绘图和暂停索引计算.

结论:

proRate R包为量化转录延长率提供了一个更准确,更简单的方法.
这种工具有助于更深入地了解转录动态和相关的生物过程.
proRate对于研究基因表达调节的研究人员来说是一个宝贵的资源.

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