Journal
BIOINFORMATICS
Volume 34, Issue 14, Pages 2515-2517Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/bty124
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Funding
- Faculty Start-up Fund
- UC Academic Senate Regents Faculty Fellowship
- National Key Basic Research Program of China [2015CB553706]
- Fundamental Research Funds for the Central Universities [2017PY023]
- Projects of Guizhou Province [QKHW-G [2014]7004]
- National Natural Science Foundation of China [81571427, 81641102, 81660426, 81360119]
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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.
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