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Genentech / scimilarity

A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training.
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code to download data from GEO #16

Open kingwzun opened 1 month ago

kingwzun commented 1 month ago

First of all, thank you for open-sourcing the model. Have you open-sourced the code for downloading data from GEO? If so, which folder is it? I can't find it. If not, would you consider open-sourcing it?

javh commented 2 weeks ago

Hi @kingwzun, Apologies for the slow reply. This slipped through the cracks.

We haven't shared the code to download from GEO. For the current release of the model, a the data collection was only semi-automated and a lot of the metadata curation was manual.