TCGAbiolinks is an R package, which is licensed under the General Public License (GPLv3), and is freely available through the Bioconductor repository (21 (link)). By conforming to the strict guidelines for package submission to Bioconductor, we were able to utilize and incorporate existing R/Bioconductor packages and statistics to assist in identifying differentially altered genomic regions defined by mutation, copy number, expression or DNA methylation; to reproduce previous TCGA marker studies; and to integrate data types both within TCGA and across other data types outside of TCGA. TCGAbiolinks consists of functions that can be grouped into three main levels: Data, Analysis and Visualization. More specifically, the package provides multiple methods for the analysis of individual experimental platforms (e.g. differential expression analysis or identifying differentially methylated regions or copy number alterations) and methods for visualization (e.g. survival plots, volcano plots and starburst plots) to facilitate the development of complete analysis pipelines. In addition, TCGAbiolinks offers in-depth integrative analysis of multiple platforms, such as copy number and expression or expression and DNA methylation, as demonstrated and applied in our recent TCGA study of 1122 gliomas (6 ). These functions can be used independently or in combination to provide the user with fully comprehensible analysis pipelines applied to TCGA data. A schematic overview of the package is presented in Figure 2. We will describe each of the three main levels (Data, Analysis and Visualization) below, highlighting the importance and utility of each associated function and subfunction. We will then introduce four tumor case studies, which will help clarify the utility of TCGAbiolinks for the reader. We have also compiled an in-depth vignette, which describes every function in detail. Here, we will summarize the main functions.