多批空间转录组学数据的RNA速度推断

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Wenxin Long, Tianyu Liu, Lingzhou Xue, Hongyu Zhao
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引用次数: 0

摘要

RNA速度已经成为解释转录动力学和从快照数据集推断轨迹的强大工具。然而,目前的方法无法利用空间转录组学固有的空间信息,并且在多批数据集中缺乏可扩展性。在这里,我们介绍spVelo,一个可扩展的框架,用于多批空间转录组学数据的RNA速度推断。spVelo支持多种下游应用,包括不确定性量化、复杂轨迹模式发现、驱动标记识别、基因调控网络推断和时间细胞-细胞通信推断。spVelo有潜力提供对复杂组织组织的更深入的了解,并强调基于空间解析模式的生物机制。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
spVelo: RNA velocity inference for multi-batch spatial transcriptomics data
RNA velocity has emerged as a powerful tool to interpret transcriptional dynamics and infer trajectory from snapshot datasets. However, current methods fail to utilize the spatial information inherent in spatial transcriptomics and lack scalability in multi-batch datasets. Here, we introduce spVelo, a scalable framework for RNA velocity inference of multi-batch spatial transcriptomics data. spVelo supports several downstream applications, including uncertainty quantification, complex trajectory pattern discovery, driver marker identification, gene regulatory network inference, and temporal cell-cell communication inference. spVelo has the potential to provide deeper insights into complex tissue organization and underscore biological mechanisms based on spatially resolved patterns.
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来源期刊
Genome Biology
Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍: Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.
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