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

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State: Public
Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_0AA1ED033ECE
Type
Article: article from journal or magazin.
Collection
Publications
Title
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests.
Journal
F1000Research
Author(s)
Komljenovic A., Roux J., Wollbrett J., Robinson-Rechavi M., Bastian F.B.
ISSN
2046-1402 (Electronic)
ISSN-L
2046-1402
Publication state
Published
Issued date
2018
Peer-reviewed
Oui
Volume
5
Pages
2748
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
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/.
Keywords
Bioconductor, Collective Data Access, Gene Enrichment Analysis, Gene expression, R Package
Pubmed
Open Access
Yes
Create date
07/02/2017 10:47
Last modification date
20/08/2019 13:32
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