Question: Clinical Survival data of TCGA
0
gravatar for kanwarjag
3.9 years ago by
kanwarjag890
United States
kanwarjag890 wrote:

I was wondering how  can I find out in the TCGA data   (has permission) that which patient has survived and which not? I downloaded the file which says clinical data it doe snot have that information. I want to make sure that I am not missing the information. I was able to downlaod the actual data RNA-seq methylation etc. via CGhub UCSC browser. I alos looked at published Nature paper of this Cancer and could not find any information. Any suggestion please.

 

tcga survival data • 6.3k views
ADD COMMENTlink modified 13 months ago by xushutan30 • written 3.9 years ago by kanwarjag890
4
gravatar for EagleEye
3.9 years ago by
EagleEye5.5k
Sweden
EagleEye5.5k wrote:

Use the simple script in the URL to retrieve clinical information for all cancer types in TCGA. It will download all clinical data in current folder from where you run. Let me know if yo need any help.

http://kandurilab.org/bioinformatics/biostars/files/TCGA_clinical_data.tar.gz

ADD COMMENTlink written 3.9 years ago by EagleEye5.5k

+1. Nice idea. Definetly saves a lot of clicking and thus time. An alternative is (like i did it and as i said, takes some time) is to use the TCGA data Matrix (https://tcga-data.nci.nih.gov/tcga/dataAccessMatrix.htm), select the tumor entity and "CLinical" in the data type field and download the tar-ball manually. In this tar you get all clinical metadata. 

ADD REPLYlink written 3.9 years ago by Sebastian Boegel440
1
gravatar for EagleEye
17 months ago by
EagleEye5.5k
Sweden
EagleEye5.5k wrote:

The above code does not work. Now you can download BioTab BCR data from GDC legacy archive.

ADD COMMENTlink written 17 months ago by EagleEye5.5k
0
gravatar for cying
2.4 years ago by
cying10
China
cying10 wrote:

Here(https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/) is the link of updated clinical information for all types of tumors. The follow up data is updated with the time.

ADD COMMENTlink written 2.4 years ago by cying10

Hello,

the link s broken. Is there any way we can get a updated link.

Thanks a lot!

ADD REPLYlink written 4 months ago by mangiolastefano0

The link I have mentioned above will work.

ADD REPLYlink written 4 months ago by EagleEye5.5k
0
gravatar for jmzeng1314
17 months ago by
jmzeng131480
jmzeng131480 wrote:

In fact, I do like the files that contains all of the information I need, I will parse it by my own script, but not using the web-tools. what's a pity! we can access the files by FTP, we have to search the samples from GDC .

ADD COMMENTlink written 17 months ago by jmzeng131480
0
gravatar for xushutan
13 months ago by
xushutan30
xushutan30 wrote:

Here is a link for breast cancer survial curve based on TCGA and METABRIC data http://tumorsurvival.org/

ADD COMMENTlink written 13 months ago by xushutan30
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