Predicting whole-transcriptome expression of spatial transcriptomics data through integration with scRNA-seq data.

pip install git+https://github.com/liuzaoqu/SpaGE.git

import SpaGE
import pandas as pd

# Load your data
spatial_data = pd.read_csv("spatial.csv", index_col=0)  # cells x genes
scrna_data = pd.read_csv("scrna.csv", index_col=0)      # cells x genes

# Run SpaGE
predicted_genes = SpaGE.SpaGE(
    Spatial_data=spatial_data,
    RNA_data=scrna_data,
    n_pv=20
)

• Spatial_data: Normalized spatial transcriptomics data (cells × genes)
• RNA_data: Normalized scRNA-seq data (cells × genes)
• n_pv: Number of principal vectors to use
• genes_to_predict: Genes to predict (default: genes in RNA but not in spatial)

Abdelaal T, Mourragui S, Mahfouz A, Reinders MJT. SpaGE: Spatial Gene Enhancement using scRNA-seq. Nucleic Acids Research. 2020;48(18):e107. doi:10.1093/nar/gkaa740

This is a refactored version for easier installation. Original code: https://github.com/tabdelaal/SpaGE