Question: Clients to access TCGA data from R and Python
0
gravatar for Sean Davis
22 months ago by
Sean Davis24k
National Institutes of Health, Bethesda, MD
Sean Davis24k 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.

R

tcga R • 1.1k views
ADD COMMENTlink modified 22 months ago • written 22 months ago by Sean Davis24k

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

http://genomicsclass.github.io/book/pages/tcga.html

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 22 months ago by Vince Carey70
0
gravatar for poisonAlien
22 months ago by
poisonAlien2.5k
Asgard
poisonAlien2.5k wrote:

Friebrowser - Directly get TCGA/Firhose data into R

ADD COMMENTlink written 22 months ago by poisonAlien2.5k
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