Ruidong Li1,2, Han Qu1, Shibo Wang1, Julong Wei1,3, Le Zhang1,2, Renyuan Ma1,4, Jianming Lu1,5, Jianguo Zhu6, Wei-De Zhong5, Zhenyu Jia1,2. 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).
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).
Authors: Lucas Maciel Vieira; Natasha Andressa Nogueira Jorge; João Batista de Sousa; João Carlos Setubal; Peter F Stadler; Maria Emília Machado Telles Walter Journal: Front Oncol Date: 2021-06-10 Impact factor: 6.244
Authors: Mairah T Khan; Joely J Irlam-Jones; Ronnie Rodrigues Pereira; Brian Lane; Helen R Valentine; Kai Aragaki; Lars Dyrskjøt; David J McConkey; Peter J Hoskin; Ananya Choudhury; Catharine M L West Journal: Br J Cancer Date: 2021-04-12 Impact factor: 7.640