Request: demo notebook for `scanpy`/matmul aspect of Methods 3.1

[jamesbraza]

In the paper's Methods section 3.1, paragraph 2, it talks about using scanpy and then doing matrix multiplication with embeddings.

Any chance you'd be willing to add an IPython notebook showing how scanpy and the matrix multiplication logic were implemented?

It really helps me to read Python code at the same time as reading the Methods section. Thank you in advance

[yiqunchen]

Thanks for your great question! We have now updated the aorta_data_analysis notebook to show how we can get GenePT-w embeddings from a simple numpy matrix multiplication (to reproduce the example w/o having the compute the gene embeddings yourself, one can use the precomputed pkl files deposited at https://zenodo.org/records/10030426).

Please let me know if you have additional questions!

[jamesbraza]

Thank you @yiqunchen ! Going to close this out, will reopen another issue if I encounter something else. Cheers!