BgeeDB，一个用于检索经过整理的表达数据集以及进行基因列表表达定位富集测试的R软件包。

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

作者信息

Komljenovic Andrea, Roux Julien, Wollbrett Julien, Robinson-Rechavi Marc, Bastian Frederic B

机构信息

Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.

SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.

出版信息

F1000Res. 2016 Nov 23;5:2748. doi: 10.12688/f1000research.9973.2. eCollection 2016.

DOI:10.12688/f1000research.9973.2

PMID:30467516

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6113886/

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/.

摘要

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/ 。