Comments (3)
Richarizardd
commented on May 27, 2024
Hi @bryanwong17 - I perhaps saved the CSV files in an unconventional way (saved previously for storing the count matrices / RNA-seq abundances for all 20K-ish genes). You can open the dataset CSV files via pandas.
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bryanwong17
commented on May 27, 2024
Hi @Richarizardd,
Thanks for your fast reply. I was able to open the dataset CSV files and see all slide_ids. Moreover, I found CSV files for the 10 splits. If I want to download WSI files, should I manually download them one by one? Is there a better way?
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Richarizardd
commented on May 27, 2024
I think the best way to download is via https://portal.gdc.cancer.gov. I would query by the cancer type, get a "manifest" of all diagnostic WSIs for that cancer type, and then download slides from the manifest. Then, afterwards, one can align the downloaded WSIs with the slide_id column.
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