### TCGAbiolinksGUI uses the following Biocondutor packages:

TCGAbiolinks

Article | Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, Sabedot T, Malta TM, Pagnotta SM, Castiglioni I, Ceccarelli M, Bontempi G and Noushmehr H. "TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data." Nucleic acids research (2015): gkv1507.
Article | Silva TC, Colaprico A, Olsen C et al. TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 1; referees: 1 approved, 1 approved with reservations]. F1000Research 2016, 5:1542 (doi: 10.12688/f1000research.8923.1)
Used in menu | All
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ELMER

Article | Yao, L., Shen, H., Laird, P. W., Farnham, P. J., & Berman, B. P. "Inferring regulatory element landscapes and transcription factor networks from cancer methylomes." Genome Biol 16 (2015): 105.
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Article | Yao, Lijing, Benjamin P. Berman, and Peggy J. Farnham. "Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes." Critical reviews in biochemistry and molecular biology 50.6 (2015): 550-573.
Used in menu | ELMER

ComplexHeatmap

Article | Gu, Zuguang, Roland Eils, and Matthias Schlesner. "Complex heatmaps reveal patterns and correlations in multidimensional genomic data." Bioinformatics (2016): btw313.
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Used in menu | OncoPrint plot and Heatmap Plot

Pathview

Article | Luo, Weijun, Brouwer and Cory (2013). “Pathview: an R/Bioconductor package for pathway-based data integration and visualization.” Bioinformatics, 29(14), pp. 1830-1831.
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Used in menu | Differential expression analysis: Pathway Graphs box