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 X\_laevis\_2\_probe\_tab.

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 Xenopus\_laevis\_probe\_tab.

Multi-level model for cross-study detection of differential gene expression.

Affymetrix Affymetrix YG_S98 Array annotation data (chip ygs98) assembled using data from public repositories.

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 YG-S98\_probe\_tab.

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 Yeast\_2\_probe\_tab.

This package provides a package containing an environment representing the Ye6100subB.CDF file.

This package provides a selection of RNA-Seq data from a yeast transcriptome experiment.

This package provides a package containing an environment representing the Yeast_2.cdf file.

The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools.

Affymetrix Affymetrix Yeast_2 Array annotation data (chip yeast2) assembled using data from public repositories.

This package provides a package containing an environment representing the Ye6100subA.CDF file.

This package provides a package containing an environment representing the YG_S98.cdf file.

Base annotation databases for yeast, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment.

This package provides a package containing an environment representing the Ye6100subC.CDF file.

This package provides a collection of so-called gold (and other) standard data sets.

This package provides a package containing an environment representing the Ye6100subD.CDF file.

This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.

This package provides a collection of different sets of experimental data from yeast.

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.

Base annotation databases for zebrafish, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

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.

The ZygosityPredictor allows to predict how many copies of a gene are affected by small variants. In addition to the basic calculations of the affected copy number of a variant, the Zygosity-Predictor can integrate the influence of several variants on a gene and ultimately make a statement if and how many wild-type copies of the gene are left. This information proves to be of particular use in the context of translational medicine. For example, in cancer genomes, the Zygosity-Predictor can address whether unmutated copies of tumor-suppressor genes are present. Beyond this, it is possible to make this statement for all genes of an organism. The Zygosity-Predictor was primarily developed to handle SNVs and INDELs (later addressed as small-variants) of somatic and germline origin. In order not to overlook severe effects outside of the small-variant context, it has been extended with the assessment of large scale deletions, which cause losses of whole genes or parts of them.