HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor. Issue 6 (10th January 2019)

• Record Type: Journal Article
• Authors: Schiffer, Lucas; Azhar, Rimsha; Shepherd, Lori; Ramos, Marcel; Geistlinger, Ludwig; Huttenhower, Curtis; Dowd, Jennifer B; Segata, Nicola; Waldron, Levi
• Is Part Of: American journal of epidemiology. Volume 188:Issue 6(2019)
• Page Start: 1023
• Page End: 1026
• Publication Date: 2019-01-10
• Subjects: Bioconductor -- bioinformatics -- databases -- Human Microbiome Project -- metagenomics -- microbiome -- statistical software; Epidemiology -- Periodicals; Public health -- Periodicals; 614.4
• DOI: 10.1093/aje/kwz006
• Languages: English
• ISSNs: 0002-9262

Abstract

Abstract: 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.