Define a relatively light class for managing Xenium data using Bioconductor. Address use of parquet for coordinates, SpatialExperiment for assay and sample data. Address serialization and use of cloud storage.

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\_tropicalis\_probe\_tab.

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

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

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

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

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

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

This package provides a package containing an environment representing the YG_S98.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 Ye6100subB.CDF file.

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 Ye6100subC.CDF file.

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

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

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

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

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

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

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().

Affymetrix Affymetrix Zebrafish Array annotation data (chip zebrafish) 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 Zebrafish\_probe\_tab.

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.