BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests

Andrea Komljenovic, Julien Roux, Marc Robinson-Rechavi, Frederic B. Bastian
2016 F1000Research  
BgeeDB is a collection of functions to import into R re-annotated, quality-controlled and reprocessed expression data available in the Bgee database. This includes data from thousands of wild-type healthy samples of multiple animal species, generated with different gene expression technologies (RNA-seq, Affymetrix microarrays, expressed sequence tags, and in situ hybridizations). BgeeDB facilitates downstream analyses, such as gene expression analyses with other Bioconductor packages. Moreover,
more » ... BgeeDB includes a new gene set enrichment test for preferred localization of expression of genes in anatomical structures ("TopAnat"). Along with the classical Gene Ontology enrichment test, this test provides a complementary way to interpret gene lists. Availability:
doi:10.12688/f1000research.9973.1 pmid:30467516 pmcid:PMC6113886 fatcat:to7kalgjwvah3mvudjv3u4suzm