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README.md

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@@ -17,7 +17,7 @@ For bulk2space, the python version need is over 3.8. If you have installed Pytho
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conda create -n bulk2space python=3.8.5
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conda activate bulk2space
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cd bulk2space
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cd bulk2space-main
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pip install -r requirements.txt
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```
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@@ -26,11 +26,13 @@ pip install -r requirements.txt
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## Run the demo data
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If you choose the spatial barcoding-based data (10x Genomics, ST, or Slide-seq) as spatial reference, run the following command:
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```
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cd bulk2space
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python bulk2space.py --project_name test1 --data_path example_data/demo1 --input_sc_meta_path demo1_sc_meta.csv --input_sc_data_path demo1_sc_data.csv --input_bulk_path demo1_bulk.csv --input_st_data_path demo1_st_data.csv --input_st_meta_path demo1_st_meta.csv --BetaVAE_H --epoch 3000 --spot_data True
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```
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else, if you choose the image-based in situ hybridization data (MERFISH, SeqFISH, or STARmap) as spatial reference, run the following command:
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```
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cd bulk2space
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python bulk2space.py --project_name test2 --data_path example_data/demo2 --input_sc_meta_path demo2_sc_meta.csv --input_sc_data_path demo2_sc_data.csv --input_bulk_path demo2_bulk.csv --input_st_data_path demo2_st_data.csv --input_st_meta_path demo2_st_meta.csv --BetaVAE_H --epoch 3000 --spot_data False
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```
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