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TCGAbiolinksGUI: A graphical user interface to analyze GDC cancer molecular and clinical data

By Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Gianluca Bontempi, Michele Ceccarelli, Benjamin P Berman, Houtan Noushmehr

Posted 08 Jun 2017
bioRxiv DOI: 10.1101/147496 (published DOI: 10.12688/f1000research.14197.1)

Background: The GDC (Genomic Data Commons) data portal provides users with data from cancer genomics studies. Recently, we developed the R/Bioconductor TCGAbiolinks package, which allows users to search, download and prepare cancer genomics data for integrative data analysis. The use of this package requires users to have advanced knowledge of R thus limiting the number of users. Results: To overcome this obstacle and improve the accessibility of the package by a wider range of users, we developed TCGAbiolinksGUI that uses shiny graphical user interface (GUI) available through the R/Bioconductor package. Conclusion: The TCGAbiolinksGUI package is freely available within the Bioconductor project at http://bioconductor.org/packages/TCGAbiolinksGUI/. Links to the GitHub repository, a demo version of the tool, a docker image and PDF/video tutorials are available at http://bit.do/TCGAbiolinksDocs.

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