yhr91/GEARS_misc

Missing files for reproducing SI Fig 17 Horlbeck Jurkat

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jzqin commented

Hi Yusuf and Kexin,

I'm trying to reproduce SI Figure 17 of predictions for the Horlbeck dataset from this notebook: https://github.com/yhr91/GEARS_misc/blob/main/paper/SI_Fig_17_Horlbeck_Jurkat.ipynb

So far I've encountered a couple of issues.

  1. The notebook expects a dataset h5ad file for the dataset name horlbeck_gi_jurkat.
  2. The path for /dfs/user/kexinh/gears2/data/pert_genes_gi.pkl is hard-coded into pertdata.py.

Neither file is included in the repo, nor can I locate the files from the main GEARS repository. Could you help point me to where I could access these files?

Thank you!