transcriptformer_embedding/embedding_generation/README.md

## Step 1 - Download TranscriptFormer
git clone https://github.com/czi-ai/transcriptformer.git

## Step 2 - Create a local folder structure
Disease-atlas/
|-- fl
|   `-- fixed.h5ad
|-- ra
|   |-- e04346ba-cdc5-418b-81e6-2f896696e3dd.h5ad
|   `-- fixed.h5ad
|-- ss
|   |-- 4e6c8033-87d5-45e6-a240-10281074d440.h5ad
|   `-- fixed.h5ad
`-- t1dm
    |-- 5378ac26-e216-41e8-b171-a7f4d819a9ff.h5ad
    `-- fixed.h5ad
    
## Step 3 - Download and Check the Disease Atlas
python preprocess_adata.py /root/Disease-atlas/t1dm/5378ac26-e216-41e8-b171-a7f4d819a9ff.h5ad /root/Disease-atlas
/t1dm/fixed.h5ad

## Step 4 - Run Inference
python celltype_disease_cge_inference.py /root/Disease-atlas/t1dm/fixed.h5ad t1dm_cge_embeddings.h5ad ~/transcriptformer/checkpoints/tf_sapiens/ 1000 100 1