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Base annotation databases for zebrafish, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.
This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Zebrafish\_probe\_tab.
Zenith performs gene set analysis on the result of differential expression using linear (mixed) modeling with dream by considering the correlation between gene expression traits. This package implements the camera method from the limma package proposed by Wu and Smyth (2012). Zenith is a simple extension of camera to be compatible with linear mixed models implemented in variancePartition::dream().
This package provides a package containing an environment representing the Zebrafish.cdf file.
zitools allows 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. This becomes applicable in the context of microbiome analyses, where the data is often overdispersed and zero-inflated, therefore making data analysis extremly challenging.