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ClonalGE

This in an extention of Tumoroscope model [1]. It adds one more latent variable (Bkg - average expression of gene g per one cell of clone k), one observed variable (Ysg - gene expression of gene g in spot s) and several new hyperparameters.

There are 3 main classes:

  • clonalGE.py
  • simulation.py
  • visualization.py

and additional scripts, including:

  • main_diff_config.py and run_main_diff_config.sh - for running ClonalGE on simulated data
  • generate_simulations.py and generate_simulations.sh - for generating the simulated data
  • main_real_1000.py and run_main_real_1000.sh - for running ClonalGE on the real data

The directory configs contains json files describing 3 different setups used to generate the simulations.
The directory prostate_data_configs contains files necessary for running models on the real data (prostate cancer dataset [2])

[1] Shafighi, Shadi, et al. "Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope." Nature Communications 15.1 (2024): 9343.
[2] Berglund, Emelie, et al. "Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity." Nature communications 9.1 (2018): 1-13.