MiMultiCat: A Unified Cloud Platform for the Analysis of Microbiome Data with Multi-Categorical Responses
The field of the human microbiome is rapidly growing due to the recent advances in high-throughput sequencing technologies. Meanwhile, there have also been many new analytic pipelines, methods and/or tools developed for microbiome data preprocessing and analytics. They are usually focused on microbi...
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| Format: | Article |
| Language: | English |
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MDPI AG
2024-01-01
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| Series: | Bioengineering |
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| Online Access: | https://www.mdpi.com/2306-5354/11/1/60 |
| _version_ | 1797344626208669696 |
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| author | Jihun Kim Hyojung Jang Hyunwook Koh |
| author_facet | Jihun Kim Hyojung Jang Hyunwook Koh |
| author_sort | Jihun Kim |
| collection | DOAJ |
| description | The field of the human microbiome is rapidly growing due to the recent advances in high-throughput sequencing technologies. Meanwhile, there have also been many new analytic pipelines, methods and/or tools developed for microbiome data preprocessing and analytics. They are usually focused on microbiome data with continuous (e.g., body mass index) or binary responses (e.g., diseased vs. healthy), yet multi-categorical responses that have more than two categories are also common in reality. In this paper, we introduce a new unified cloud platform, named MiMultiCat, for the analysis of microbiome data with multi-categorical responses. The two main distinguishing features of MiMultiCat are as follows: First, MiMultiCat streamlines a long sequence of microbiome data preprocessing and analytic procedures on user-friendly web interfaces; as such, it is easy to use for many people in various disciplines (e.g., biology, medicine, public health). Second, MiMultiCat performs both association testing and prediction modeling extensively. For association testing, MiMultiCat handles both ecological (e.g., alpha and beta diversity) and taxonomical (e.g., phylum, class, order, family, genus, species) contexts through covariate-adjusted or unadjusted analysis. For prediction modeling, MiMultiCat employs the random forest and gradient boosting algorithms that are well suited to microbiome data while providing nice visual interpretations. We demonstrate its use through the reanalysis of gut microbiome data on obesity with body mass index categories. MiMultiCat is freely available on our web server. |
| first_indexed | 2024-03-08T11:05:27Z |
| format | Article |
| id | doaj.art-8b0f0fa309a3456a9edfe9adf219a37a |
| institution | Directory Open Access Journal |
| issn | 2306-5354 |
| language | English |
| last_indexed | 2024-03-08T11:05:27Z |
| publishDate | 2024-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Bioengineering |
| spelling | doaj.art-8b0f0fa309a3456a9edfe9adf219a37a2024-01-26T15:06:20ZengMDPI AGBioengineering2306-53542024-01-011116010.3390/bioengineering11010060MiMultiCat: A Unified Cloud Platform for the Analysis of Microbiome Data with Multi-Categorical ResponsesJihun Kim0Hyojung Jang1Hyunwook Koh2Department of Applied Mathematics and Statistics, The State University of New York (SUNY), Incheon 21985, Republic of KoreaDepartment of Applied Mathematics and Statistics, The State University of New York (SUNY), Incheon 21985, Republic of KoreaDepartment of Applied Mathematics and Statistics, The State University of New York (SUNY), Incheon 21985, Republic of KoreaThe field of the human microbiome is rapidly growing due to the recent advances in high-throughput sequencing technologies. Meanwhile, there have also been many new analytic pipelines, methods and/or tools developed for microbiome data preprocessing and analytics. They are usually focused on microbiome data with continuous (e.g., body mass index) or binary responses (e.g., diseased vs. healthy), yet multi-categorical responses that have more than two categories are also common in reality. In this paper, we introduce a new unified cloud platform, named MiMultiCat, for the analysis of microbiome data with multi-categorical responses. The two main distinguishing features of MiMultiCat are as follows: First, MiMultiCat streamlines a long sequence of microbiome data preprocessing and analytic procedures on user-friendly web interfaces; as such, it is easy to use for many people in various disciplines (e.g., biology, medicine, public health). Second, MiMultiCat performs both association testing and prediction modeling extensively. For association testing, MiMultiCat handles both ecological (e.g., alpha and beta diversity) and taxonomical (e.g., phylum, class, order, family, genus, species) contexts through covariate-adjusted or unadjusted analysis. For prediction modeling, MiMultiCat employs the random forest and gradient boosting algorithms that are well suited to microbiome data while providing nice visual interpretations. We demonstrate its use through the reanalysis of gut microbiome data on obesity with body mass index categories. MiMultiCat is freely available on our web server.https://www.mdpi.com/2306-5354/11/1/60microbiome data analysiscloud computinghuman microbiomemulti-categorical responsemicrobiome association testingmicrobiome prediction modeling |
| spellingShingle | Jihun Kim Hyojung Jang Hyunwook Koh MiMultiCat: A Unified Cloud Platform for the Analysis of Microbiome Data with Multi-Categorical Responses Bioengineering microbiome data analysis cloud computing human microbiome multi-categorical response microbiome association testing microbiome prediction modeling |
| title | MiMultiCat: A Unified Cloud Platform for the Analysis of Microbiome Data with Multi-Categorical Responses |
| title_full | MiMultiCat: A Unified Cloud Platform for the Analysis of Microbiome Data with Multi-Categorical Responses |
| title_fullStr | MiMultiCat: A Unified Cloud Platform for the Analysis of Microbiome Data with Multi-Categorical Responses |
| title_full_unstemmed | MiMultiCat: A Unified Cloud Platform for the Analysis of Microbiome Data with Multi-Categorical Responses |
| title_short | MiMultiCat: A Unified Cloud Platform for the Analysis of Microbiome Data with Multi-Categorical Responses |
| title_sort | mimulticat a unified cloud platform for the analysis of microbiome data with multi categorical responses |
| topic | microbiome data analysis cloud computing human microbiome multi-categorical response microbiome association testing microbiome prediction modeling |
| url | https://www.mdpi.com/2306-5354/11/1/60 |
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