• 1 Detailed explanation: Get GDC data menu
  • 2 Sub-menu: Molecular data
    • 2.1 Useful information
    • 2.2 Advanced search box
    • 2.3 Download & Prepare box
  • 3 Sub-menu: Subtype data
  • 4 Sub-menu: Clinical data
    • 4.1 Useful information
    • 4.2 Clinical data inconsistencies
    • 4.3 Tutorial Video
  • 5 Sub-menu: Mutation data
    • 5.1 Mutation data search box
  • 6 Menu: Manage summarized Experiment object
  • 7 Detailed explanation: Manage SummarizedExperiment menu
  • 8 Menu: Processing raw data
    • 8.1 Sub-menu: DNA methylation
  • References

1 Detailed explanation: Get GDC data menu

For a detailed manual for this section please access this link:

  1. Data menu manual

7 Detailed explanation: Manage SummarizedExperiment menu

For a detailed manual for this section please access this link: Manage SummarizedExperiment

References

Aryee, Martin J, Andrew E Jaffe, Hector Corrada-Bravo, Christine Ladd-Acosta, Andrew P Feinberg, Kasper D Hansen, and Rafael A Irizarry. 2014. “Minfi: A Flexible and Comprehensive Bioconductor Package for the Analysis of Infinium Dna Methylation Microarrays.” Bioinformatics 30 (10). Oxford University Press:1363–9.

Huber, Wolfgang, Vincent J Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S Carvalho, Hector Corrada Bravo, et al. 2015. “Orchestrating High-Throughput Genomic Analysis with Bioconductor.” Nature Methods 12 (2). Nature Publishing Group:115–21.

Morris, Tiffany J, and Stephan Beck. 2015. “Analysis Pipelines and Packages for Infinium Humanmethylation450 Beadchip (450k) Data.” Methods 72. Elsevier:3–8.

Zhou, Wanding, Peter W Laird, and Hui Shen. 2016. “Comprehensive Characterization, Annotation and Innovative Use of Infinium Dna Methylation Beadchip Probes.” Nucleic Acids Research. Oxford Univ Press, gkw967.