Introduction

Massive amounts of high-throughput genomics data profiled from tumor samples were made publicly available by the Cancer Genome Atlas (TCGA).We have developed an open source software package, TCGA2STAT, to obtain the TCGA data, wrangle it, and pre-process it into a format ready for multivariate and integrated statistical analysis in the R environment. In a user-friendly format with one single function call, our package downloads and fully processes the desired TCGA data to be seamlessly integrated into a computational analysis pipeline. No further technical or biological knowledge is needed to utilize our software, thus making TCGA data easily accessible to data scientists without specific domain knowledge.TCGA2STAT is available from the https://cran.r-project.org/web/packages/TCGA2STAT/index.htmlSupplementary data are available at Bioinformatics online.zhandong.liu@bcm.edu.

Publications

  1. TCGA2STAT: simple TCGA data access for integrated statistical analysis in R.
    Cite this
    Wan YW, Allen GI, Liu Z, 2016-03-01 - Bioinformatics (Oxford, England)

Credits

  1. Ying-Wooi Wan
    Developer

    Computational and Integrative Biomedical Research Center, Department of Obstetrics and Gynecology, United States of America

  2. Genevera I Allen
    Developer

    Department of Statistics and Electrical & Computer Engineering, Rice University, United States of America

  3. Zhandong Liu
    Investigator

    Computational and Integrative Biomedical Research Center, Department of Pediatrics-Neurology, United States of America

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Summary
AccessionBT001703
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByZhandong Liu