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HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor

By Lucas Schiffer, Rimsha Azhar, Lori Shepherd, Marcel Ramos, Ludwig Geistlinger, Curtis Huttenhower, Jennifer Beam Dowd, Nicola Segata, Levi D Waldron

Posted 17 Apr 2018
bioRxiv DOI: 10.1101/299115 (published DOI: 10.1093/aje/kwz006)

Phase 1 of the NIH Human Microbiome Project (HMP) investigated 18 body subsites of 235 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 rRNA 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 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.

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