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Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz
The rich data produced by the second phase of the Human Microbiome Project (iHMP) offers a unique opportunity to test hypotheses that interactions between microbial communities and a human host might impact an individual’s health or disease status. In this work we describe infrastructure that integr...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
F1000 Research Limited
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7366035/ https://www.ncbi.nlm.nih.gov/pubmed/32742640 http://dx.doi.org/10.12688/f1000research.24345.2 |
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author | Wagner, Justin Kancherla, Jayaram Braccia, Domenick Matsumara, James Felix, Victor Crabtree, Jonathan Mahurkar, Anup Corrada Bravo, Héctor |
author_facet | Wagner, Justin Kancherla, Jayaram Braccia, Domenick Matsumara, James Felix, Victor Crabtree, Jonathan Mahurkar, Anup Corrada Bravo, Héctor |
author_sort | Wagner, Justin |
collection | PubMed |
description | The rich data produced by the second phase of the Human Microbiome Project (iHMP) offers a unique opportunity to test hypotheses that interactions between microbial communities and a human host might impact an individual’s health or disease status. In this work we describe infrastructure that integrates Metaviz, an interactive microbiome data analysis and visualization tool, with the iHMP Data Coordination Center web portal and the HMP2Data R/Bioconductor package. We describe integrative statistical and visual analyses of two datasets from iHMP using Metaviz along with the metagenomeSeq R/Bioconductor package for statistical analysis of differential abundance analysis. These use cases demonstrate the utility of a combined approach to access and analyze data from this resource. |
format | Online Article Text |
id | pubmed-7366035 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | F1000 Research Limited |
record_format | MEDLINE/PubMed |
spelling | pubmed-73660352020-07-30 Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz Wagner, Justin Kancherla, Jayaram Braccia, Domenick Matsumara, James Felix, Victor Crabtree, Jonathan Mahurkar, Anup Corrada Bravo, Héctor F1000Res Software Tool Article The rich data produced by the second phase of the Human Microbiome Project (iHMP) offers a unique opportunity to test hypotheses that interactions between microbial communities and a human host might impact an individual’s health or disease status. In this work we describe infrastructure that integrates Metaviz, an interactive microbiome data analysis and visualization tool, with the iHMP Data Coordination Center web portal and the HMP2Data R/Bioconductor package. We describe integrative statistical and visual analyses of two datasets from iHMP using Metaviz along with the metagenomeSeq R/Bioconductor package for statistical analysis of differential abundance analysis. These use cases demonstrate the utility of a combined approach to access and analyze data from this resource. F1000 Research Limited 2021-06-21 /pmc/articles/PMC7366035/ /pubmed/32742640 http://dx.doi.org/10.12688/f1000research.24345.2 Text en Copyright: © 2021 Wagner J et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Tool Article Wagner, Justin Kancherla, Jayaram Braccia, Domenick Matsumara, James Felix, Victor Crabtree, Jonathan Mahurkar, Anup Corrada Bravo, Héctor Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz |
title | Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz |
title_full | Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz |
title_fullStr | Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz |
title_full_unstemmed | Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz |
title_short | Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz |
title_sort | interactive exploratory data analysis of integrative human microbiome project data using metaviz |
topic | Software Tool Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7366035/ https://www.ncbi.nlm.nih.gov/pubmed/32742640 http://dx.doi.org/10.12688/f1000research.24345.2 |
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