phyloMDA: an R package for phylogeny-aware microbiome data analysis
Abstract Background Modern sequencing technologies have generated low-cost microbiome survey datasets, across sample sites, conditions, and treatments, on an unprecedented scale and throughput. These datasets often come with a phylogenetic tree that provides a unique opportunity to examine how share...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-06-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-022-04744-5 |
| _version_ | 1818469601822900224 |
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| author | Tiantian Liu Chao Zhou Huimin Wang Hongyu Zhao Tao Wang |
| author_facet | Tiantian Liu Chao Zhou Huimin Wang Hongyu Zhao Tao Wang |
| author_sort | Tiantian Liu |
| collection | DOAJ |
| description | Abstract Background Modern sequencing technologies have generated low-cost microbiome survey datasets, across sample sites, conditions, and treatments, on an unprecedented scale and throughput. These datasets often come with a phylogenetic tree that provides a unique opportunity to examine how shared evolutionary history affects the different patterns in host-associated microbial communities. Results In this paper, we describe an R package, phyloMDA, for phylogeny-aware microbiome data analysis. It includes the Dirichlet-tree multinomial model for multivariate abundance data, tree-guided empirical Bayes estimation of microbial compositions, and tree-based multiscale regression methods with relative abundances as predictors. Conclusion phyloMDA is a versatile and user-friendly tool to analyze microbiome data while incorporating the phylogenetic information and addressing some of the challenges posed by the data. |
| first_indexed | 2024-04-13T21:25:49Z |
| format | Article |
| id | doaj.art-41e63c64abe44ac69e527e065ec03f11 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-13T21:25:49Z |
| publishDate | 2022-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-41e63c64abe44ac69e527e065ec03f112022-12-22T02:29:19ZengBMCBMC Bioinformatics1471-21052022-06-012311610.1186/s12859-022-04744-5phyloMDA: an R package for phylogeny-aware microbiome data analysisTiantian Liu0Chao Zhou1Huimin Wang2Hongyu Zhao3Tao Wang4SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong UniversitySJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong UniversityDepartment of Biostatistics and Bioinformatics, Duke University School of MedicineSJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong UniversitySJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong UniversityAbstract Background Modern sequencing technologies have generated low-cost microbiome survey datasets, across sample sites, conditions, and treatments, on an unprecedented scale and throughput. These datasets often come with a phylogenetic tree that provides a unique opportunity to examine how shared evolutionary history affects the different patterns in host-associated microbial communities. Results In this paper, we describe an R package, phyloMDA, for phylogeny-aware microbiome data analysis. It includes the Dirichlet-tree multinomial model for multivariate abundance data, tree-guided empirical Bayes estimation of microbial compositions, and tree-based multiscale regression methods with relative abundances as predictors. Conclusion phyloMDA is a versatile and user-friendly tool to analyze microbiome data while incorporating the phylogenetic information and addressing some of the challenges posed by the data.https://doi.org/10.1186/s12859-022-04744-5Phylogeny-aware analysisRelative abundancesMultivariate model |
| spellingShingle | Tiantian Liu Chao Zhou Huimin Wang Hongyu Zhao Tao Wang phyloMDA: an R package for phylogeny-aware microbiome data analysis BMC Bioinformatics Phylogeny-aware analysis Relative abundances Multivariate model |
| title | phyloMDA: an R package for phylogeny-aware microbiome data analysis |
| title_full | phyloMDA: an R package for phylogeny-aware microbiome data analysis |
| title_fullStr | phyloMDA: an R package for phylogeny-aware microbiome data analysis |
| title_full_unstemmed | phyloMDA: an R package for phylogeny-aware microbiome data analysis |
| title_short | phyloMDA: an R package for phylogeny-aware microbiome data analysis |
| title_sort | phylomda an r package for phylogeny aware microbiome data analysis |
| topic | Phylogeny-aware analysis Relative abundances Multivariate model |
| url | https://doi.org/10.1186/s12859-022-04744-5 |
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