使用R微生态包的微生物组数据统计分析和可视化工作流
Chi Liu1, Felipe R P Mansoldo2, Hankang Li3
1Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.
Nature protocols
|August 6, 2025
概括
本研究引入了用于微生物组数据分析的R包协议,涵盖了AMPLICON,元基因组学和代谢学数据. 它为统计分析和可视化提供了一个全面和可扩展的管道,简化了复杂的omics数据挑战.
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.
- 计算生物学 计算生物学
背景情况:
- 微生物组研究面临的挑战是由于复杂的实验设计和多样化的omics数据类型.
- 大型微生物组数据集的统计分析和可视化需要强大的和可适应的方法.
研究的目的:
- 以使用R微生态包进行全面的微生物组数据分析和可视化,呈现一个逐步的协议.
- 展示该协议在各种omics数据类型中的应用,包括安普利康测序,元基因组学和代谢学.
主要方法:
- 在标准化管道中使用了R微生态包.
- 包括数据预处理,规范化,多样性分析 (alpha和beta),差异丰度测试和机器学习.
- 采用参数社区模拟来评估差异丰度测试方法.
主要成果:
- 该协议有效地处理安普利康,元基因组学和代谢学数据分析.
- 演示了综合分析场景,包括差异测试,机器学习和关联分析.
- R代码是可扩展的,在标准硬件上有效运行.
结论:
- 微生态包为微生物组数据分析提供了一个全面,可扩展和高效的协议.
- 该协议解决了微生物组研究中日益增长的复杂性和数据量,促进了强大的统计分析和可视化.
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