TCGAbiolinksGUI: a graphical user interface (GUI) for integrative analysis of TCGA data.

### Description of the menus

Step 1 Data

> Get GDC Data | Download GDC data (molecular, mutation, clinical, subtype information) that will be used in the analysis steps.
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Step 2 Analysis

> Clinical analysis | Perform a survival analysis.
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> Epigenetic analysis | Perform differentially methylated regions (DMR) analysis.The result can be seen through a volcano plot, a heatmap plot.
> Transcriptomic analysis | Perform differential expression analysis (DEA). The result can be viewed through a volcano plot and a heatmap plot. Also, for the genes that were identified as upregulated or downregulated an enrichment analysis can be done.
> Genomic analysis | Visualize mutation status through a oncoprint using a Mutation Annotation Format (MAF) file.

Step 3 Integrative analysis

> Starburst plot | Integrate the epigenetic analysis and transcriptomic analysis results using a starburstplot (correlates the DNA methylation level and nearest gene expression level)
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> ELMER | Identify candidate regulatory elements in the non-coding regions of the genome associated with cancer using the R/Bioconductor ELMER pacakge.