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 download the actual data RNA-seq methylation etc. via CGhub UCSC browser. I also looked at published Nature paper of this Cancer and could not find any information. Any suggestion please.
4 answers
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
The above code does not work. Now you can download BioTab BCR data from GDC legacy archive.
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.
Hello,
the link s broken. Is there any way we can get a updated link.
Thanks a lot!
Here is a link for breast cancer survial curve based on TCGA and METABRIC data http://tumorsurvival.org/
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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 .