Question: Clients to access TCGA data from R and Python
gravatar for Sean Davis
2.7 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

This is a little survey question meant to result in a list of client software to access TCGA data from R, python, or any other language. Please consider adding more to the list or to comment on your experiences with each.


tcga R • 1.9k views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Sean Davis25k

There is a very brief tutorial on the use of RTCGAToolbox (plain, not the linkNY enhanced version) at

The layout is somewhat clumsy, but approaches to use of survival, stage, mutation, expression, and methylation data are all illustrated. The conclusion of the tutorial includes the remarks:

TCGA is an obvious candidate for infrastructure development to support multiomic analysis. We have seen some of the challenges that arise when even a nicely developed tool like RTCGAToolbox is used to acquire the data: we must be alert to mismatched sample identifier labels, missing data, inadequate documentation of sample provenance and assay conduct, and so on. Human effort is invariably required; standards for data quality must go beyond numerical accuracy and address transparency and usability.

ADD REPLYlink written 2.7 years ago by Vince Carey70
gravatar for poisonAlien
2.7 years ago by
poisonAlien2.6k wrote:

Friebrowser - Directly get TCGA/Firhose data into R

ADD COMMENTlink written 2.7 years ago by poisonAlien2.6k
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