A self-supervised deep learning method for reference-free deconvolution.
Project description
SURF
A self-supervised deep learning method for reference-free deconvolution. The overall approach is detailed in the official paper out in xxx.
Data input
df_expr: (n_spots * n_genes), dataframe, with column names (gene names)
df_pos: (n_spots * 2), dataframe, with column names [‘x’, ‘y’]
barcodes: (n_spots,), a numpy array
Data output
‘pred.csv’: The predicted cell types proportions in each spot.
‘beta.csv’: The deconvolved gene expressions of each cell type.
‘last.pkl’: The saved trained model.
Installation
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