Integrative web cloud computing and analytics using MiPair for design-based comparative analysis with paired microbiome data
Abstract Pairing (or blocking) is a design technique that is widely used in comparative microbiome studies to efficiently control for the effects of potential confounders (e.g., genetic, environmental, or behavioral factors). Some typical paired (block) designs for human microbiome studies are repea...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-11-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-25093-6 |
| _version_ | 1797985583112388608 |
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| author | Hyojung Jang Hyunwook Koh Won Gu Byungkon Kang |
| author_facet | Hyojung Jang Hyunwook Koh Won Gu Byungkon Kang |
| author_sort | Hyojung Jang |
| collection | DOAJ |
| description | Abstract Pairing (or blocking) is a design technique that is widely used in comparative microbiome studies to efficiently control for the effects of potential confounders (e.g., genetic, environmental, or behavioral factors). Some typical paired (block) designs for human microbiome studies are repeated measures designs that profile each subject’s microbiome twice (or more than twice) (1) for pre and post treatments to see the effects of a treatment on microbiome, or (2) for different organs of the body (e.g., gut, mouth, skin) to see the disparity in microbiome between (or across) body sites. Researchers have developed a sheer number of web-based tools for user-friendly microbiome data processing and analytics, though there is no web-based tool currently available for such paired microbiome studies. In this paper, we thus introduce an integrative web-based tool, named MiPair, for design-based comparative analysis with paired microbiome data. MiPair is a user-friendly web cloud service that is built with step-by-step data processing and analytic procedures for comparative analysis between (or across) groups or between baseline and other groups. MiPair employs parametric and non-parametric tests for complete or incomplete block designs to perform comparative analyses with respect to microbial ecology (alpha- and beta-diversity) and taxonomy (e.g., phylum, class, order, family, genus, species). We demonstrate its usage through an example clinical trial on the effects of antibiotics on gut microbiome. MiPair is an open-source software that can be run on our web server ( http://mipair.micloud.kr ) or on user’s computer ( https://github.com/yj7599/mipairgit ). |
| first_indexed | 2024-04-11T07:20:25Z |
| format | Article |
| id | doaj.art-e2cdf5225c904136870cdb6fe8b1d32c |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-11T07:20:25Z |
| publishDate | 2022-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-e2cdf5225c904136870cdb6fe8b1d32c2022-12-22T04:37:48ZengNature PortfolioScientific Reports2045-23222022-11-0112111410.1038/s41598-022-25093-6Integrative web cloud computing and analytics using MiPair for design-based comparative analysis with paired microbiome dataHyojung Jang0Hyunwook Koh1Won Gu2Byungkon Kang3Department of Applied Mathematics and Statistics, The State University of New York, KoreaDepartment of Applied Mathematics and Statistics, The State University of New York, KoreaDepartment of Applied Mathematics and Statistics, The State University of New York, KoreaDepartment of Computer Science, The State University of New York, KoreaAbstract Pairing (or blocking) is a design technique that is widely used in comparative microbiome studies to efficiently control for the effects of potential confounders (e.g., genetic, environmental, or behavioral factors). Some typical paired (block) designs for human microbiome studies are repeated measures designs that profile each subject’s microbiome twice (or more than twice) (1) for pre and post treatments to see the effects of a treatment on microbiome, or (2) for different organs of the body (e.g., gut, mouth, skin) to see the disparity in microbiome between (or across) body sites. Researchers have developed a sheer number of web-based tools for user-friendly microbiome data processing and analytics, though there is no web-based tool currently available for such paired microbiome studies. In this paper, we thus introduce an integrative web-based tool, named MiPair, for design-based comparative analysis with paired microbiome data. MiPair is a user-friendly web cloud service that is built with step-by-step data processing and analytic procedures for comparative analysis between (or across) groups or between baseline and other groups. MiPair employs parametric and non-parametric tests for complete or incomplete block designs to perform comparative analyses with respect to microbial ecology (alpha- and beta-diversity) and taxonomy (e.g., phylum, class, order, family, genus, species). We demonstrate its usage through an example clinical trial on the effects of antibiotics on gut microbiome. MiPair is an open-source software that can be run on our web server ( http://mipair.micloud.kr ) or on user’s computer ( https://github.com/yj7599/mipairgit ).https://doi.org/10.1038/s41598-022-25093-6 |
| spellingShingle | Hyojung Jang Hyunwook Koh Won Gu Byungkon Kang Integrative web cloud computing and analytics using MiPair for design-based comparative analysis with paired microbiome data Scientific Reports |
| title | Integrative web cloud computing and analytics using MiPair for design-based comparative analysis with paired microbiome data |
| title_full | Integrative web cloud computing and analytics using MiPair for design-based comparative analysis with paired microbiome data |
| title_fullStr | Integrative web cloud computing and analytics using MiPair for design-based comparative analysis with paired microbiome data |
| title_full_unstemmed | Integrative web cloud computing and analytics using MiPair for design-based comparative analysis with paired microbiome data |
| title_short | Integrative web cloud computing and analytics using MiPair for design-based comparative analysis with paired microbiome data |
| title_sort | integrative web cloud computing and analytics using mipair for design based comparative analysis with paired microbiome data |
| url | https://doi.org/10.1038/s41598-022-25093-6 |
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