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snap-stanford / UCE

UCE is a zero-shot foundation model for single-cell gene expression data
MIT License
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Human lymph node AMI figure 2d #21

Closed v-mahughes closed 7 months ago

v-mahughes commented 7 months ago

Could you point me to where I can find the human lymph node AMI data with UCE embeddings that was used to train the logisitic classifier in figure 2d ?

Yanay1 commented 7 months ago

ima_ad_lymph = ima_ad[ima_ad.obs.tissue.str.lower().str.contains("lymph")]

https://drive.google.com/drive/folders/1f63fh0ykgEhCrkd_EVvIootBw7LYDVI7 the file called ima_sample.h5ad

There is some coarse mapping of cell type information. I removed cell types that were labeled as "misc" and used the coarse labels to train the classifier.

Please let me know if you have any issues with this! Thanks

v-mahughes commented 7 months ago

Do you have a terminal command I could use to download this directly onto my virtual (Linux) system?

Yanay1 commented 7 months ago

I'm not sure exactly how to do it. This thread might help: https://stackoverflow.com/questions/25010369/wget-curl-large-file-from-google-drive

v-mahughes commented 7 months ago

Do you know what the file ids are? They dont seem to be in the share links. The IMA sample is too large to transfer onto my machine manually

Yanay1 commented 7 months ago

For ima_sample.h5ad the link is

https://drive.google.com/file/d/16UyzyZ7jK4y5Mj0PT75vqPO68i729soq/view?usp=drive_link

So I believe the file id would be 16UyzyZ7jK4y5Mj0PT75vqPO68i729soq

v-mahughes commented 7 months ago

that does not seem to work, as It downloads an html. Is there any modification from your end that allows this file to be downloaded on a remote machine? The files are too large to download then transfer manually.

v-mahughes commented 7 months ago

solved the issue by uploading them to my own drop box and downloading them from there