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Fix typo and add missing dependencies #1

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920e16c
Fix typo and add missing dependencies
molecules Nov 30, 2023
8b89316
Fix typo
molecules Nov 30, 2023
eab8614
Add missing imports
ChristopherBottomsOMRF Nov 30, 2023
c3b1819
Add missing dependencies
molecules Nov 30, 2023
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8 changes: 6 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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.
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3 changes: 2 additions & 1 deletion preprocess.py
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Expand Up @@ -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))
Expand Down Expand Up @@ -53,4 +55,3 @@ def get_lasso(config):

if __name__=='__main__':
main()