ZicoSeq is now integrated into the CRAN GUniFrac package (https://cran.r-project.org/web/packages/GUniFrac/index.html). Please use the CRAN version.

ZicoSeq is a permutation-based framework for differential abundance analysis of Zero-inflated Compositional Sequencing data such as microbiome data. Currently, it has the following components:

Winsorization to decrease the influence of outliers

Posterior sampling to impute zeros based on a beta mixture prior

Multiple-stage normalization to address compositional effects

An omnibus test to address diverse taxa-covariate relationships

Permutation-based FDR control to address taxa correlations and multiple testing