Department of Botany and Plant Sciences.
Genetics, Genomics, and Bioinformatics Program, University of California, Riverside, CA, USA.
Bioinformatics. 2018 Jul 15;34(14):2515-2517. doi: 10.1093/bioinformatics/bty124.
The large-scale multidimensional omics data in the Genomic Data Commons (GDC) provides opportunities to investigate the crosstalk among different RNA species and their regulatory mechanisms in cancers. Easy-to-use bioinformatics pipelines are needed to facilitate such studies.
We have developed a user-friendly R/Bioconductor package, named GDCRNATools, for downloading, organizing and analyzing RNA data in GDC with an emphasis on deciphering the lncRNA-mRNA related competing endogenous RNAs regulatory network in cancers. Many widely used bioinformatics tools and databases are utilized in our package. Users can easily pack preferred downstream analysis pipelines or integrate their own pipelines into the workflow. Interactive shiny web apps built in GDCRNATools greatly improve visualization of results from the analysis.
GDCRNATools is an R/Bioconductor package that is freely available at Bioconductor (http://bioconductor.org/packages/devel/bioc/html/GDCRNATools.html). Detailed instructions, manual and example code are also available in Github (https://github.com/Jialab-UCR/GDCRNATools).
基因组数据共享库（GDC）中的大规模多维组学数据为研究癌症中不同 RNA 物种之间的相互作用及其调控机制提供了机会。需要易于使用的生物信息学管道来促进此类研究。
我们开发了一个用户友好的 R/Bioconductor 包，名为 GDCRNATools，用于在 GDC 中下载、组织和分析 RNA 数据，重点是破译癌症中 lncRNA-mRNA 相关竞争内源性 RNA 调控网络。我们的包中使用了许多广泛使用的生物信息学工具和数据库。用户可以轻松地将首选的下游分析管道打包或将自己的管道集成到工作流程中。GDCRNATools 中构建的交互式 shiny web apps 极大地改善了分析结果的可视化。
GDCRNATools 是一个 R/Bioconductor 包，可在 Bioconductor（http://bioconductor.org/packages/devel/bioc/html/GDCRNATools.html）上免费获得。详细的说明、手册和示例代码也可在 Github（https://github.com/Jialab-UCR/GDCRNATools）上获得。
