时间序列生物医学数据的非负张量分解工作流程
Koki Tsuyuzaki1, Naoki Yoshida2, Tetsuo Ishikawa3
1Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama 351-0198, Japan; Japan Science and Technology Agency, PRESTO, 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan.
STAR protocols
|July 8, 2023
概括
本研究介绍了TensorLyCV,这是生物医学数据分析中非负张量分解 (NTF) 的简化协议. 它简化了复杂的NTF方法,使潜伏组件提取更容易获得和可重复.
科学领域:
- 生物医学数据分析
- 计算生物学 计算生物学
- 生物信息学是一种生物信息学.
背景情况:
- 非负张量分解 (NTF) 对于从高维生物医学数据中提取潜在组件非常有价值.
- 传统的NTF所涉及的复杂性和众多步骤构成了重大实施障碍.
研究的目的:
- 介绍TensorLyCV,一个可访问和可重复的NTF分析协议.
- 为生物医学研究人员简化NTF的实施.
主要方法:
- 使用了Snakemake工作流管理系统和Docker容器化以实现可重复性.
- 开发了一个管道,包括数据处理,张量分解,最佳排名估计和可视化.
- 将协议应用于疫苗不良反应数据的演示.
主要成果:
- 成功展示了一个简化和可重复的NTF分析管道.
- 从复杂的生物医学数据中提取和可视化潜伏组件.
- 使用真实世界的疫苗不良反应数据验证了该协议的实用性.
结论:
- TensorLyCV显著降低了在生物医学研究中实施NTF的障碍.
- 该协议增强了从高维数据中提取隐藏组件的可访问性和可重复性.
- 这项工作为研究人员分析复杂的生物医学数据集提供了实用工具.
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