HMP16SData：通过 Bioconductor 高效访问人类微生物组计划。
HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.
机构信息
Graduate School of Public Health and Health Policy, City University of New York, New York, New York.
Institute for Implementation Science in Population Health, City University of New York, New York, New York.
出版信息
Am J Epidemiol. 2019 Jun 1;188(6):1023-1026. doi: 10.1093/aje/kwz006.
Phase 1 of the Human Microbiome Project (HMP) investigated 18 body subsites of 242 healthy American adults to produce the first comprehensive reference for the composition and variation of the "healthy" human microbiome. Publicly available data sets from amplicon sequencing of two 16S ribosomal RNA variable regions, with extensive controlled-access participant data, provide a reference for ongoing microbiome studies. However, utilization of these data sets can be hindered by the complex bioinformatic steps required to access, import, decrypt, and merge the various components in formats suitable for ecological and statistical analysis. The HMP16SData package provides count data for both 16S ribosomal RNA variable regions, integrated with phylogeny, taxonomy, public participant data, and controlled participant data for authorized researchers, using standard integrative Bioconductor data objects. By removing bioinformatic hurdles of data access and management, HMP16SData enables epidemiologists with only basic R skills to quickly analyze HMP data.
人类微生物组计划（HMP）的第一阶段研究了 242 名健康美国成年人的 18 个身体部位，以生成“健康”人类微生物组组成和变化的首个综合参考。可公开获得的两个 16S 核糖体 RNA 可变区扩增子测序的数据集，以及广泛的受控访问参与者数据，为正在进行的微生物组研究提供了参考。然而，这些数据集的利用可能会受到复杂的生物信息学步骤的阻碍，这些步骤需要访问、导入、解密和合并各种格式的组件，以适合生态和统计分析。HMP16SData 包提供了 16S 核糖体 RNA 可变区的计数数据，使用标准整合性 Bioconductor 数据对象与系统发生、分类、公共参与者数据以及授权研究人员的受控参与者数据集成。通过消除数据访问和管理的生物信息学障碍，HMP16SData 使仅具备基本 R 技能的流行病学家能够快速分析 HMP 数据。
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