From 920e16c4393e93a2b4d06974eb21aa8f7d55c064 Mon Sep 17 00:00:00 2001 From: Christopher Bottoms Date: Thu, 30 Nov 2023 12:11:05 -0600 Subject: [PATCH 1/4] Fix typo and add missing dependencies --- README.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 1815a6b..14faadb 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,10 @@ 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 ## Data Available The data used in our research can be downloaded from https://zenodo.org/record/8063157 @@ -24,7 +27,7 @@ mkdir saved_model 2. Run preprocess.py to generate positive samples between spatial transcriptomics. ``` -python prerocess.py -c ./configure/osmFISH_Zeisel.yaml +python prerpocess.py -c ./configure/osmFISH_Zeisel.yaml ``` 3. Run main.py to train and predict the transcript distribution of the spatial transcriptomics. From 8b89316e32523713c05017b240d14adea9df46e9 Mon Sep 17 00:00:00 2001 From: Christopher Bottoms Date: Thu, 30 Nov 2023 12:13:35 -0600 Subject: [PATCH 2/4] Fix typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 14faadb..cd51608 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,7 @@ mkdir saved_model 2. Run preprocess.py to generate positive samples between spatial transcriptomics. ``` -python prerpocess.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. From eab8614f059119c483506dc02e22b0bc6a03deab Mon Sep 17 00:00:00 2001 From: "Christopher Bottoms, PhD" Date: Thu, 30 Nov 2023 18:22:00 +0000 Subject: [PATCH 3/4] Add missing imports --- preprocess.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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 From c3b181978557c1a92e4afbaab0278b97a2670f34 Mon Sep 17 00:00:00 2001 From: Christopher Bottoms Date: Thu, 30 Nov 2023 12:24:42 -0600 Subject: [PATCH 4/4] Add missing dependencies --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index cd51608..ffc4fd6 100644 --- a/README.md +++ b/README.md @@ -12,6 +12,7 @@ A flexible deep neural network framework for predicting the transcript distribut - logzero - ruamel.yaml - click +- torchvision ## Data Available The data used in our research can be downloaded from https://zenodo.org/record/8063157