Dataset Information

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 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.

SUBMITTER: Liu T

PROVIDER: S-EPMC9169257 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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Publications

phyloMDA: an R package for phylogeny-aware microbiome data analysis.

Liu Tiantian T Zhou Chao C Wang Huimin H Zhao Hongyu H Wang Tao T

BMC bioinformatics 20220606 1

<h4>Background</h4>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.<h4>Results</h4>In this paper, we describe an R package, phyloMDA, for phylogeny-aware microbiome data ana ...[more]

PMID: 35668363

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