dbgap2x: an R package to explore and extract data from the database of Genotypes and Phenotypes (dbGaP).
dbgap2x: an R package to explore and extract data from the database of Genotypes and Phenotypes (dbGaP).
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dbgap2x：一个 R 包，用于从基因型和表型 (dbGaP) 数据库中探索和提取数据。
DOI：
10.1093/bioinformatics/btz680
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发表时间：
2020
期刊：
影响因子：
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通讯作者：
Avillach,Paul
中科院分区：
文献类型：
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作者：
Versmée,Grégoire;Versmée,Laura;Dusenne,Mikaël;Jalali,Niloofar;Avillach,Paul
摘要根据2007年8月发布的基因组数据共享政策，美国国立卫生研究院(NIH)支持了几个存储库，如基因类型和表型数据库(DBGaP)。DBGaP是一个在线资料库，提供对包含1000多项研究的大规模遗传和表型数据集的访问。然而，浏览网站并了解研究之间的关系并不是一件容易的事情。此外，文件的解密是一个复杂的过程。在本研究中，我们提出了DBGap2x R包，它涵盖了广泛的功能，用于搜索DBGaP研究、探索研究的特征并轻松地解密来自DBGaP的文件。可用性和实现DBgap2x是一个R包，其代码可从https://github.com/gversmee/dbgap2x.获得包括包、Jupyter服务器和笔记本示例的集装箱化版本可在https://hub.docker.com/r/gversmee/dbgap2x.Supplementary信息上获得补充数据可在生物信息学在线上获得。
SummaryBased on the Genomic Data Sharing Policy issued in August 2007, the National Institutes of Health (NIH) has supported several repositories such as the database of Genotypes and Phenotypes (dbGaP). dbGaP is an online repository that provides access to large-scale genetic and phenotypic datasets with more than 1000 studies. However, navigating the website and understanding the relationship between the studies are not easy tasks. Moreover, the decryption of the files is a complex procedure. In this study we propose the dbgap2x R package that covers a broad range of functions for searching dbGaP studies, exploring the characteristics of a study and easily decrypting the files from dbGaP.Availability and implementationdbgap2x is an R package with the code available at https://github.com/gversmee/dbgap2x. A containerized version including the package, a Jupyter server and with a Notebook example is available at https://hub.docker.com/r/gversmee/dbgap2x.Supplementary informationSupplementary data are available atBioinformaticsonline.