Komljenovic Andrea, Roux Julien, Wollbrett Julien, Robinson-Rechavi Marc, Bastian Frederic B
Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
F1000Res. 2016 Nov 23;5:2748. doi: 10.12688/f1000research.9973.2. eCollection 2016.
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/.
BgeeDB是一组函数，用于将Bgee数据库中重新注释、质量控制和重新处理的表达数据导入R。这包括来自多种动物物种数千个野生型健康样本的数据，这些数据是使用不同的基因表达技术（RNA测序、Affymetrix微阵列、表达序列标签和原位杂交）生成的。BgeeDB便于进行下游分析，例如与其他Bioconductor软件包进行基因表达分析。此外，BgeeDB包括一种新的基因集富集测试，用于分析基因在解剖结构中的优先表达定位（“TopAnat”）。与经典的基因本体富集测试一起，该测试提供了一种补充方式来解释基因列表。获取方式：https://www.bioconductor.org/packages/BgeeDB/ 。
