Abstract
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. To overcome this obstacle and improve the accessibility of the package by a wider range of users, we developed a graphical user interface (GUI) using Shiny available through the package TCGAbiolinksGUI. 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 from the TCGAbiolinksGUI site.
Highlights
The National Cancer Institute’s (NCI) Genomic Data Commons (GDC), a data sharing platform that promotes precision medicine in oncology, provides a rich resource of molecular and clinical data
For raw DNA methylation data obtained in the form of Intensity Data (IDAT) files, we provide a pipeline using the R/Bioconductor minfi package to prepare the data for subsequent bioinformatics analysis12 performing a background and dye-bias correction with the preprocessnoob function followed by a detection P-value quality masking13 and probes overlapping repeats or single nucleotide polymorphisms masking14 (Figure 3)
With TCGAbiolinksGUI, we developed the platform so that the user can define the sample groups based on their mutation spectrum, perform supervised analysis that can define differentially expressed or methylated gene list and this can be directly ported into pathway analysis
Summary
Any reports and responses or comments on the article can be found at the end of the article. This article is included in the Bioconductor gateway. This article is included in the RPackage gateway. This article is included in the International Society for Computational Biology Community Journal gateway
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
