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HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor

View ORCID ProfileLucas Schiffer, Rimsha Azhar, View ORCID ProfileLori Shepherd, View ORCID ProfileMarcel Ramos, View ORCID ProfileLudwig Geistlinger, View ORCID ProfileCurtis Huttenhower, View ORCID ProfileJennifer B Dowd, View ORCID ProfileNicola Segata, View ORCID ProfileLevi Waldron
doi: https://doi.org/10.1101/299115
Lucas Schiffer
1Graduate School of Public Health and Health Policy, City University of New York, New York, NY
2Institute for Implementation Science in Population Health, City University of New York, New York, NY
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Rimsha Azhar
1Graduate School of Public Health and Health Policy, City University of New York, New York, NY
2Institute for Implementation Science in Population Health, City University of New York, New York, NY
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Lori Shepherd
3Roswell Park Cancer Institute, University of Buffalo, Buffalo, NY
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Marcel Ramos
1Graduate School of Public Health and Health Policy, City University of New York, New York, NY
2Institute for Implementation Science in Population Health, City University of New York, New York, NY
3Roswell Park Cancer Institute, University of Buffalo, Buffalo, NY
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Ludwig Geistlinger
1Graduate School of Public Health and Health Policy, City University of New York, New York, NY
2Institute for Implementation Science in Population Health, City University of New York, New York, NY
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Curtis Huttenhower
4Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA
5The Broad Institute of MIT and Harvard, Cambridge, MA
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Jennifer B Dowd
1Graduate School of Public Health and Health Policy, City University of New York, New York, NY
6Department of Global Health and Social Medicine, King’s College London, London, UK
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Nicola Segata
7Centre for Integrative Biology, University of Trento, Trento, Italy
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Levi Waldron
1Graduate School of Public Health and Health Policy, City University of New York, New York, NY
2Institute for Implementation Science in Population Health, City University of New York, New York, NY
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Abstract

Phase 1 of the NIH Human Microbiome Project (HMP) investigated 18 body subsites of 239 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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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted August 29, 2018.
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HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor
Lucas Schiffer, Rimsha Azhar, Lori Shepherd, Marcel Ramos, Ludwig Geistlinger, Curtis Huttenhower, Jennifer B Dowd, Nicola Segata, Levi Waldron
bioRxiv 299115; doi: https://doi.org/10.1101/299115
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HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor
Lucas Schiffer, Rimsha Azhar, Lori Shepherd, Marcel Ramos, Ludwig Geistlinger, Curtis Huttenhower, Jennifer B Dowd, Nicola Segata, Levi Waldron
bioRxiv 299115; doi: https://doi.org/10.1101/299115

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