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

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/.

SUBMITTER: Komljenovic A

PROVIDER: S-EPMC6113886 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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

Komljenovic Andrea A Roux Julien J Wollbrett Julien J Robinson-Rechavi Marc M Bastian Frederic B FB

F1000Research 20161123

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, ...[more]

PMID: 30467516

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