Community comparisons

Group-wise comparisons

A number of methods for microbiota community comparisons have been proposed. For a recent benchmarking study, see Weiss et al. (2017). For a comprehensive example workflow, see Callahan et al. F1000 (2017).

Univariate comparisons

For individual taxa, diversity indicators etc.

• Linear mixed effect models
• Negative binomial test
• post-hoc testing For Kruskal-Wallis

Other methods, not implemented here (see Weiss et al. (2017) for a recent survey):

• Zero-inflated Gaussians (ZIGs) (see metagenomeSeq Bioconductor package)
• DESeq2 and other advanced methods based on negative binomial

Multivariate comparisons

For community-level multivariate comparisons

• Multivariate linear models (limma)
• PERMANOVA