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Article
Open AccessMultigroup analysis of compositions of microbiomes with covariate adjustments and repeated measures
Microbiome differential abundance analysis methods for two groups are well-established in the literature. However, many microbiome studies involve more than two groups, sometimes even ordered groups such as st...
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Chapter
Multiple Imputation for Compositional Data (MICoDa) Adjusting for Covariates
In many applications, researchers are interested in multivariate outcomes that are compositional. However, for various reasons, including the method of collection of data, sometimes not all variables are measu...
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Article
Open AccessLinear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data
It is well-known that human gut microbiota form an ecosystem where microbes interact with each other. Due to complex underlying interactions, some microbes may correlate nonlinearly. There are no measures in t...
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Article
Open AccessAnalysis of microbial compositions: a review of normalization and differential abundance analysis
Increasingly, researchers are discovering associations between microbiome and a wide range of human diseases such as obesity, inflammatory bowel diseases, HIV, and so on. The first step towards microbiome wide...
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Article
Open AccessAnalysis of compositions of microbiomes with bias correction
Differential abundance (DA) analysis of microbiome data continues to be a challenging problem due to the complexity of the data. In this article we define the notion of “sampling fraction” and demonstrate a ma...
