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README.md

@@ -25,7 +25,13 @@ install.packages(c("Matrix", "data.table", "pracma", "dplyr"))
 
 ## Get Protein Prediction from sciPENN
 
-To get the protein prediction from sciPENN, run the file **./sciPENN/preprocessing_data.ipynb**. For time effiency, we chosed 8000 cells randomly instead of using the entire datasets. The gene and protein expressions are stored in the file **./scGNN/sample_Data/pmbc/Gene/original_top_expression.csv** and **./scGNN/sample_Data/pmbc/Protein/original_top_expression.csv** respectively. 
+To get the protein prediction from sciPENN, run the file **./sciPENN/preprocessing_data.ipynb**. Download the data from [Box](https://upenn.app.box.com/s/1p1f1gblge3rqgk97ztr4daagt4fsue5) and place it under the folder **./sciPENN/Data**
+
+For time effiency, we chosed 8000 cells randomly instead of using the entire datasets. The gene and protein expressions are stored in the file 
+
+**./scGNN/sample_Data/pmbc/Gene/original_top_expression.csv** and 
+
+**./scGNN/sample_Data/pmbc/Protein/original_top_expression.csv** respectively. 
 
 ## Run LTMG
 

requirements.txt

+# python == 3.8.19
+torch == 1.13.1
+scanpy == 1.9.8
+pandas == 2.0.3
+numpy == 1.23.5
+scipy == 1.10.1
+tqdm == 4.66.4
+anndata == 0.9.2
+matplotlib == 3.7.5
+# numba == 0.56.4
+umap-learn == 0.5.6
+# seaborn == 0.11.2
+similarity-index-of-label-graph == 2.0.1
+sciPENN == 0.9.5
+scikit-misc
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