CCC-RISE

Contents:

  • Tutorial for CCC-RISE: Cell-Cell Communication Analysis
    • Installation
    • Preprocessing the Dataset
      • Input Requirements
      • Ligand-Receptor Pairs
      • Import and Prepare the Dataset
    • Choosing the Rank
      • RISE Rank Selection
      • CPD Rank Selection
    • Running the Factorization
    • Visualizing the Factors
    • Interpreting a Component
  • API Reference
    • Core Functions
      • Preprocessing
        • prepare_dataset()
        • import_ligand_receptor_pairs()
        • add_cond_idxs()
      • Factorization
        • run_ccc_rise_workflow()
        • calculate_interaction_tensor()
        • run_fms_r2x_analysis()
    • Visualization Functions
      • Rank Selection
        • plot_fms_r2x_diff_ranks()
      • Factor Plotting
        • plot_condition_factors()
        • plot_eigenstate_factors()
        • plot_lr_factors()
        • plot_lr_factors_partial()
      • PaCMAP Visualization
        • plot_labels_pacmap()
        • plot_wc_pacmap()
      • Analysis Functions
        • expression_product_matrix()
        • average_product_matrix_ccc()
  • References
    • CCC-RISE Paper
    • RISE Paper
    • Tensor Decomposition Methods
CCC-RISE
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© Copyright 2025, Andrew Ramirez, Aaron Meyer.

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