Create README.md
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README.md
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State Transition model checkpoints are meant to be used with the [Arc State](https://pypi.org/project/arc-state/) package.
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State is distributed via [`uv`](https://docs.astral.sh/uv). To train models on your own AnnDatas, please see the [repository](https://github.com/ArcInstitute/state) README.
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## Running inference from pypi
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```bash
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uv tool install arc-state
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```
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To
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```code
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state tx infer --model_dir <ST-Parse_PATH> --pert_col cytokine --adata <INPUT_ADATA>.h5ad --output <OUTPUT_DIR>
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```
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## Running from source
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```bash
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# Clone repo
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git clone github.com:arcinstitute/state
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cd state
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# Initialize venv
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uv venv
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# Install
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uv tool install -e .
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```
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To generate embeddings given an AnnData:
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```code
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state tx infer --model_dir <ST-Parse_PATH> --pert_col cytokine --adata <INPUT_ADATA>.h5ad --output <OUTPUT_DIR>
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```
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For model licenses please see `MODEL_ACCEPTABLE_USE_POLICY.md`, `MODEL_LICENSE.md`, and `LICENSE.md`.
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