API Reference

The CardamomOT API is organised into three sub-packages:

Sub-package	Description
CardamomOT.model	Core NetworkModel class — parameters, fitting, simulation
CardamomOT.inference	Kinetics, network inference, trajectory algorithms
CardamomOT.tools	Visualisation and analysis utilities

The full auto-generated reference is available below.

• CardamomOT
  • Key Features
  • Author
  • License
  • Submodules
    • CardamomOT.config
    • CardamomOT.inference
    • CardamomOT.model
    • CardamomOT.tools

Top-level imports

The most commonly used objects are re-exported at package level:

from CardamomOT import (
    NetworkModel,                  # core model class
    kon_ref_vector,                # burst kinetics fitting
    extract_degradation_rates,
    select_DEgenes,
    # --- marginals & UMAP ---
    plot_data_distrib,
    plot_data_pmf_temporal,
    plot_data_umap_toref,
    compare_marginals,
    # --- cell-type analysis ---
    train_classifier,
    predict_cell_types,
    check_cell_types_full,
    check_cell_types_mixture,
    # --- result comparison ---
    plot_results_rna_mixture,
    plot_results_rna_clean,
    plot_results_prot,
    # --- KO/OV perturbations ---
    plot_results_sim_kov,
    compare_cell_types,
    # --- network visualisation ---
    analyse_reseau,
    reseau_top_regulateurs,
    plot_network,
)