BgeeDB

"BgeeDB" is an R package that is a comprehensive resource for accessing re-annotated, quality-controlled, and reprocessed expression data from the Bgee database. This database encompasses a vast collection of gene expression data from thousands of wild-type, healthy samples across multiple animal species derived from various gene expression technologies, including RNA-seq, Affymetrix microarrays, expressed sequence tags, and in situ hybridizations.

BgeeDB streamlines the integration of this extensive expression data into R, enabling researchers to quickly conduct sophisticated gene expression analyses using the suite of tools available within the Bioconductor project. A notable feature of BgeeDB is the inclusion of "TopAnat," a novel gene set enrichment test specifically designed to identify the preferred localization of gene expression within anatomical structures. This functionality complements traditional Gene Ontology enrichment analyses by offering an additional perspective for interpreting gene lists, particularly in the context of anatomical and developmental biology.