HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.
Bioconductor
Human Microbiome Project
bioinformatics
databases
metagenomics
microbiome
statistical software
Journal
American journal of epidemiology
ISSN: 1476-6256
Titre abrégé: Am J Epidemiol
Pays: United States
ID NLM: 7910653
Informations de publication
Date de publication:
01 06 2019
01 06 2019
Historique:
received:
14
06
2018
revised:
08
10
2018
accepted:
11
10
2018
pubmed:
17
1
2019
medline:
11
2
2020
entrez:
17
1
2019
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 30649166
pii: 5288094
doi: 10.1093/aje/kwz006
pmc: PMC6545282
doi:
Substances chimiques
RNA, Ribosomal, 16S
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
1023-1026Subventions
Organisme : NIAID NIH HHS
ID : R21 AI121784
Pays : United States
Commentaires et corrections
Type : CommentIn
Type : CommentIn
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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