I’m not sure if it contains information that can be useful for the portal, but there has been a dataset cleaning effort performed on the TCGA-GBM/LGG cohorts described here Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features - PubMed
Differentiation of pre vs. post-surgery cases was one of the aims; some metadata are included here and they point to a separate TCIA cohort that contains only the pre-surgery sub-cohort here
@giemmecci yes, I am aware of that publication, and we were looking at it.
For some reason, I can’t edit the original message, so a brief update on the Colab version:
@fedorov pointed out that Docker is not supported in Colab, and the segmentation tool used in the notebook needs Docker. So I’ll try to find a way around this issue.
Thanks!
Hi, I’ve been trying accessing my VM for a while, but I keep receiving this error message
How can I solve this issue?
EDIT: now it seems to be working; in the past, I had the same issue but it resolved in 5-10 minutes; this time it took way longer; what causes this difference?
Thanks!
Thanks for your work with the CDA.
Unfortunately, I wasn’t able to retrieve the information I’m looking for.
What I’d like to achieve is: given a cohort (i.e. TCGA-GBM), I’d like the list of all the subjects that show a mutation in a specific gene (i.e. IDH1).
The same search using the GDP platform gives back this:
None of the fields available in cdapython seem to report this information. Am I missing something? Thanks!
I ran into this myself in the past, and usually after some time the resources become available. You can also try changing the zone for your VM, as discussed in this post.
Thanks for giving CDA a try! I will let @david.pot respond as to whether this behavior is expected, and if there are plans to revise it in the future.
Good morning @giemmecci . You are not missing anything as this functionality is not in CDA at this time. We will be looking into it, as this data comes from parsing and indexing open access MAF (mutation) files, rather than the APIs available from GDC. Your use case is very valuable to CDA and thank you for your efforts using it! Do you have other suggestions/issues using CDA, as you have exactly the background and research needs that CDA is trying to serve. David.
7 posts were split to a new topic: Unable to re-run the notebook
