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stana:基于临床数据的R包,用于基于临床数据的元原型分析和交互应用

Noriaki Sato¹, Kotoe Katayama², Daichi Miyaoka³

¹Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

NAR genomics and bioinformatics

|January 9, 2025

概括

一个新的R包,stana,有助于分析元基因类型化数据,以了解微生物社区的多样性和功能. 它处理遗传变异和基因拷贝数,提供对克罗恩病等人类疾病的见解.

科学领域:

微生物学微生物学
生物信息学是一种生物信息学.
基因组学就是基因组学.

背景情况:

转基因类型定型对于通过单核酸变异来解决微生物物种内部多样性的关键.
基因拷贝数分析提高了对微生物社区代谢功能的理解.
缺乏综合平台,阻碍了分析元原型化结果与相关分组数据的分析.

研究的目的:

开发一个R包,stana,用于处理和分析元基因类型化数据.
为探索元原型化结果提供一个互动的环境.
促进与人类疾病相关的肠道微生物群元原型的研究.

主要方法:

开发R包"stana",其中包含预处理,统计分析,功能分析和可视化模块.
创建一个交互式分析环境.
利用了1000多个与人类疾病相关的公开可用的元基因组样本.

主要成果:

该stana包能够全面分析元原型化数据,包括变体识别和基因拷贝数量评估.
发布了一个交互式环境,整合了1000多个与人类疾病相关的元基因组样本.
在末期病,克罗恩病和帕金森病中进行了肠道微生物组元型的分析.

结论:

该stana包有效地支持分析元原型化数据,证实以前的发现和产生新的假设.
开发的平台有助于更深入地了解微生物群落与人类疾病之间的联系.
R包和交互式环境是公开可用于研究的.

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