Comparisons.Rmd

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title: "Community comparisons"
author: "Leo Lahti, Sudarshan Shetty et al. `r Sys.Date()`"
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## Group-wise comparisons

A number of methods for microbiota community comparisons have been proposed. For a recent benchmarking study, see [Weiss et al. (2017)](http://doi.org/10.1186/s40168-017-0237-y). For a comprehensive example workflow, see [Callahan et al. F1000 (2017)](https://f1000research.com/articles/5-1492/v2).

### Univariate comparisons

For individual taxa, diversity indicators etc.

 * [Linear mixed effect models](Mixedmodels.html) 
 * [Negative binomial test](Negativebinomial.html)

Other methods, not implemented here (see [Weiss et al. (2017)](http://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0237-y) for a recent survey):

 * [Zero-inflated Gaussians (ZIGs)](https://www.ncbi.nlm.nih.gov/pubmed/24076764/) (see [metagenomeSeq](https://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html) Bioconductor package)
 * [DESeq2](deseq2.html) and other advanced methods based on negative binomial


### Multivariate comparisons

For community-level multivariate comparisons

 * [Multivariate linear models (limma)](limma.html)
 * [PERMANOVA](PERMANOVA.html)