diff --git a/README.md b/README.md index 1815a6b..ffc4fd6 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,11 @@ A flexible deep neural network framework for predicting the transcript distribut - numpy 1.21.6 - pandas 1.4.4 - scikit-learn 1.0.2 - +- tqdm +- logzero +- ruamel.yaml +- click +- torchvision ## Data Available The data used in our research can be downloaded from https://zenodo.org/record/8063157 @@ -24,7 +28,7 @@ mkdir saved_model 2. Run preprocess.py to generate positive samples between spatial transcriptomics. ``` -python prerocess.py -c ./configure/osmFISH_Zeisel.yaml +python preprocess.py -c ./configure/osmFISH_Zeisel.yaml ``` 3. Run main.py to train and predict the transcript distribution of the spatial transcriptomics. diff --git a/preprocess.py b/preprocess.py index 92b187b..36e2aa1 100644 --- a/preprocess.py +++ b/preprocess.py @@ -11,6 +11,8 @@ from utils import read_pkl, save_pkl +import click +import main @click.command() @click.option('-c', '--config', type=click.Path(exists=True)) @@ -53,4 +55,3 @@ def get_lasso(config): if __name__=='__main__': main() - \ No newline at end of file