zitools

One fundamental objective of microbiome analyses is to identify differentially abundant taxa among different experimental groups or conditions. However, microbiome data are often overdispersed and zero inflated making data analysis extremely challenging. Although there are several models considering zero inflation, none of them provides functionality for subsequent analyses. Therefore, we propose zitools, an R package allowing for zero inflated count data analysis by either using down-weighting of excess zeros or by replacing an appropriate proportion of excess zeros with NA. Through overloading frequently used statistical functions (such as mean, median, standard deviation), plotting functions (such as boxplots or heatmap) or differential abundance tests, it allows a wide range of downstream analyses for zero-inflated data in a less biased manner.

Installation

You can install the development version of zitools from GitHub with:

# install.packages("devtools")
devtools::install_github("kreutz-lab/zitools")

if(!requireNamespace("BiocManager")){
  install.packages("BiocManager")
}
BiocManager::install("zitools")

Example

This is a basic example which shows you how to solve a common problem:

library(zitools)
## basic example code