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State Transition model checkpoints are meant to be used with the [Arc State](https://pypi.org/project/arc-state/) package.
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.
## Running inference from pypi
```bash
uv tool install arc-state
```
To generate predictions:
```code
state tx infer --model_dir <ST-Parse_PATH> --pert_col cytokine --adata <INPUT_ADATA>.h5ad --output <OUTPUT_DIR>
```
This will group the cells in your input AnnData by the specified `pert_col` and run inference with a pretrained ST checkpoint.
## Running from source
```bash
# Clone repo
git clone github.com:arcinstitute/state
cd state
# Initialize venv
uv venv
# Install
uv tool install -e .
```
To generate predictions:
```code
state tx infer --model_dir <ST-Parse_PATH> --pert_col cytokine --adata <INPUT_ADATA>.h5ad --output <OUTPUT_DIR>
```
For model licenses please see `MODEL_ACCEPTABLE_USE_POLICY.md`, `MODEL_LICENSE.md`, and `LICENSE.md`. |