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Bioinformatics. 2018 Jul 15;34(14):2515-2517. doi: 10.1093/bioinformatics/bty124.

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC.

Li R1,2, Qu H1, Wang S1, Wei J1,3, Zhang L1,2, Ma R1,4, Lu J1,5, Zhu J6, Zhong WD5, Jia Z1,2.

Author information

1
Department of Botany and Plant Sciences.
2
Genetics, Genomics, and Bioinformatics Program, University of California, Riverside, CA, USA.
3
College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China.
4
Department of Mathematics, Bowdoin College, Brunswick, USA.
5
Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, The Second Affiliated Hospital of South China University of Technology, Guangzhou, China.
6
Department of Urology, Guizhou Provincial People's Hospital, Guizhou, China.

Abstract

Motivation:

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.

Results:

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.

Availability and implementation:

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).

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