TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data [version 1; peer review: 1 approved, 1 approved with reservations]

Tiago Chedraoui Silva, Antonio Colaprico, Catharina Olsen, Tathiane M. Malta, Gianluca Bontempi, Michele Ceccarelli, Benjamin P. Berman, Houtan Noushmehr

Research output: Contribution to journalArticlepeer-review

Abstract

The GDC (Genomic Data Commons) data portal provides users with data from cancer genomics studies. Recently, we developed the R/Bioconductor TCGAbiolinks package, which allows users to search, download and prepare cancer genomics data for integrative data analysis. The use of this package requires users to have advanced knowledge of R thus limiting the number of users. To overcome this obstacle and improve the accessibility of the package by a wider range of users, we developed a graphical user interface (GUI) using Shiny available through the package TCGAbiolinksGUI. The TCGAbiolinksGUI package is freely available within the Bioconductor project at http://bioconductor.org/packages/TCGAbiolinksGUI/. Links to the GitHub repository, a demo version of the tool, a docker image and PDF/video tutorials are available from the TCGAbiolinksGUI site.

Original languageAmerican English
Article number439
JournalF1000Research
Volume7
DOIs
StatePublished - 2018
Externally publishedYes

Keywords

  • Bioinformatics
  • Cancer
  • Epigenomics
  • Genomics
  • TCGA

All Science Journal Classification (ASJC) codes

  • General Immunology and Microbiology
  • General Biochemistry,Genetics and Molecular Biology
  • Pharmacology, Toxicology and Pharmaceutics(all)

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