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

Abstract

<ns4:p>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<ns4:italic>in situ</ns4:italic>hybridizations). BgeeDB facilitates downstream analyses, such as gene expression analyses with other Bioconductor packages. Moreover, 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.</ns4:p><ns4:p><ns4:underline>Availability</ns4:underline>:<ns4:ext-link xmlns:ns3="http://www.w3.org/1999/xlink" ext-link-type="uri" ns3:href="http://www.bioconductor.org/packages/BgeeDB/">http://www.bioconductor.org/packages/BgeeDB/</ns4:ext-link></ns4:p>