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

Détails

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Etat: Public
Version: Final published version
Licence: CC BY 4.0
ID Serval
serval:BIB_0AA1ED033ECE
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests.
Périodique
F1000Research
Auteur(s)
Komljenovic A., Roux J., Wollbrett J., Robinson-Rechavi M., Bastian F.B.
ISSN
2046-1402 (Electronic)
ISSN-L
2046-1402
Statut éditorial
Publié
Date de publication
2018
Peer-reviewed
Oui
Volume
5
Pages
2748
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: epublish
Résumé
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/.
Mots-clé
Bioconductor, Collective Data Access, Gene Enrichment Analysis, Gene expression, R Package
Pubmed
Open Access
Oui
Création de la notice
07/02/2017 10:47
Dernière modification de la notice
20/08/2019 13:32
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