PT  - JOURNAL ARTICLE
AU  - Ruidong Li
AU  - Han Qu
AU  - Shibo Wang
AU  - Julong Wei
AU  - Le Zhang
AU  - Renyuan Ma
AU  - Jianming Lu
AU  - Jianguo Zhu
AU  - Wei-De Zhong
AU  - Zhenyu Jia
TI  - <em>GDCRNATools</em>: an R/Bioconductor package for integrative analysis of lncRNA, miRNA, and mRNA data in GDC
AID  - 10.1101/229799
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 229799
4099  - http://biorxiv.org/content/early/2017/12/11/229799.short
4100  - http://biorxiv.org/content/early/2017/12/11/229799.full
AB  - 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, to facilitate downloading, organizing, and analyzing RNA data in GDC with an emphasis on deciphering the lncRNA-mRNA related competing endogenous RNAs (ceRNAs) 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 GDCRNATools is an R/Bioconductor package that is freely available at https://github.com/Jialab-UCR/GDCRNATools