Abstract
BgeeDB is a collection of functions to import into R re-annotated, quality-controlled and re-processed 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: https://www.bioconductor.org/packages/BgeeDB/.
Highlights
Gene expression levels influence the behavior of cells, the functionality of tissues, and a wide range of processes from development and aging to physiology or behavior
Until 2016 the Bgee database lacked a programmatic access to data through a R package, a shortcoming that we have addressed with the release of the BgeeDB Bioconductor package, available at https://www.bioconductor.org/packages/BgeeDB/
In summary, the BgeeDB package serves as a bridge between curated data from the Bgee database and the R/Bioconductor environment, facilitating the access to high-quality curated and re-analyzed gene expression datasets, and significantly reducing time for downstream analyses of the datasets
Summary
We have updated considerably the Bgee database, and the corresponding documentation. This addresses the comments made by the reviewers about a lack of transparency of our data processing steps. We have added information about the processing of gene expression data performed at the Bgee database. We have updated the examples and results based on the use of the latest Bgee release and BgeeDB package version. We have added an author, Julien Wollbrett, to the author list Since this manuscript was first submitted, Julien Wollbrett made significant contributions to the development of the package described in this paper, and notably towards the aim of submitting this revised manuscript.
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