Hi, We’re working on a tutorial notebook that will focus on a deep learning task using the TCGA-GBM (and probably LGG) cohorts, and we’re planning on having it ready soon. In the meantime, I’ve created a temporary one that can be found here . The rationale behind this notebook is to select a subse…

[image] fedorov: @david.pot is this an opportunity to explore the utility of CDA instead of relying on a CSV of unknown provenance? Yes it is. Let me introduce CDA - the “Cancer Data Aggregator” to you @giemmecci . Please take a look first at: CDA on CRDC website. . This gives you context…

Thanks! I’ll start testing the CDA for my notebook

@fedorov , Benjamin Yan ( @Interion ) just joined our lab as an intern, and since he will be working with publicly available data, we thought it could be a great opportunity to have him work on the IDC. Would it be possible to add him to our current Google Cloud project? He has already been in the la…

Sure, no worries! @Interion can you please fill out the form here , and mention in the comments that you would like to be added to Brad’s @bje project?

[image] giemmecci: addresses some of the issues encountered during data cleaning/quality control Gian Marco, thank you for sharing this. The issue you identified is something we have been thinking about earlier. It is very important to be able to identify specific kinds of series, especially …

Thanks! Yes, I did some basic data cleaning for the notebook that I can share: define imaging contrast, pre/post surgery, presence of artifacts (although is limited to the 10 exams I picked for the tutorial). What would be the best way to share this information with you? I have no experience in wo…

[image] giemmecci: What would be the best way to share this information with you? You can just share the link to the spreadsheet. Do you plan to keep working on it? [image] giemmecci: I think it could be beneficial, if feasible, to allow users to select “only earliest” or “only latest” e…

Forgot to include the issue pointer: Allow selection of the latest/earliest study when multiple studies are present · Issue #640 · ImagingDataCommons/IDC-WebApp · GitHub …

Thanks for submitting the issue! [image] fedorov: Do you plan to keep working on it? If you mean working on the notebook, yes (I’m sorry it’s taking some time, but I need to stretch it between other projects :slight_smile: ); if instead you mean working on performing quality control for the …

Great, thanks! I actually meant whether you plan to work on the curation spreadsheet. Thank you for sharing what you have. On a separate note - do you insist on the GPL license for your contribution here GitHub - giemmecci/IDC: Examples of use cases of the IDC portal ? We definitely prefer non-rest…

TCGA-GBM tutorial notebook

Support

fedorov Split this topic September 10, 2021, 8:31pm 28

7 posts were split to a new topic: Unable to re-run the notebook

Topic		Replies	Views
Using API to get images for a particular TCGA patient barcode Data	1	604	December 7, 2021
Imaging Data Commons Claude skill launched! Announcements skill	0	30	January 29, 2026
Downloading Studies (DICOMS) from IDC which is not the current one - paying customer Support	1	58	July 14, 2025
API to get patients of a collection Support	6	450	April 28, 2022
Text2Cohort: a new LLM toolkit to query IDC database using Natural Language Queries Announcements	4	750	May 27, 2023

TCGA-GBM tutorial notebook

Related topics