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satijalab / azimuth-references

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Question about generating Azimuth reference files from new lung tumor cell atlas #21

Closed ghost closed 7 months ago

ghost commented 8 months ago

Hi!

I would like to generate Azimuth reference files for this lung tumor cell atlas:

https://datasets.cellxgene.cziscience.com/6e5e887d-96f7-40af-908c-9b4fc5057ef9.rds

Is it possible to use this Seurat v5 object for that or do I need some other files? I looked at the code that you used for generating the "human lung cell atlas v2" reference files and I am not sure if I can just use SCTransform on the atlas Seurat object and go from there?

Any help would be greatly appreciated. Thank you!

Gesmira commented 7 months ago

You can use seurat v5 objects for creating Azimuth reference files. If you run into any problems, please open an issue in the azimuth repo as we don't monitor this one often.