Komljenovic A, Roux J, Wollbrett J, Robinson-Rechavi M, Bastian FB. BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests.
F1000Res 2016;
5:2748. [PMID:
30467516 PMCID:
PMC6113886 DOI:
10.12688/f1000research.9973.1]
[Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/11/2016] [Indexed: 09/29/2023] Open
Abstract
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, 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: http://www.bioconductor.org/packages/BgeeDB/.
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