Preface

#> working directory clean

This manuscript was rendered from commit 0d63746fac87923e630a61276e8fb3f1cfddd74c.

This in-progress manuscript is not intended for general scientific use. It is incomplete, has not been carefully reviewed, and may contain mistakes or other inaccuracies. Please post comments or questions on the GitHub Issues page or email Mike.

This manuscript addresses the effect that the taxonomic bias inherent in microbiome measurement has on microbial differential-abundance analysis. We describe the basic problem posed by taxonomic bias for measuring changes in the abundance of particular taxa across conditions and describe new strategies for mitigating the errors it induces. Analyses of both relative and absolute abundances are considered. The manuscript is licensed under a CC BY 4.0 License. See the Zenodo record for how to cite the latest version. Supporting data analyses can be found in the accompanying [computational research notebook] (https://mikemc.github.io/differential-abundance-theory/notebook/).