TCGA-Assembler: open-source software for retrieving and processing TCGA data

@article{Zhu2014TCGAAssemblerOS,
  title={TCGA-Assembler: open-source software for retrieving and processing TCGA data},
  author={Yitan Zhu and Peng Qiu and Yuan Ji},
  journal={Nature Methods},
  year={2014},
  volume={11},
  pages={599-600}
}
Other big-data tools for TCGA are available4,5. In particular, level 3 TCGA data can also be obtained from Firehose at the MIT Broad Institute (https://confluence.broadinstitute.org/display/GDAC/ Home/), with one data-matrix file for each cancer type and genomics platform. Module A of TCGA-Assembler provides the same type of data matrices and also distributes R functions and associated computer programs that produce the data matrices. Users can thus control which TCGA data will be acquired… CONTINUE READING