User

Benchmarking

.. module:: nichecompass.benchmarking
.. currentmodule:: nichecompass

.. autosummary::
    :toctree: generated

    benchmarking.compute_benchmarking_metrics
    benchmarking.compute_cas
    benchmarking.compute_clisis
    benchmarking.compute_gcs
    benchmarking.compute_mlami
    benchmarking.compute_nasw

Data

.. module:: nichecompass.data
.. currentmodule:: nichecompass

.. autosummary::
    :toctree: generated

    data.load_spatial_adata_from_csv

Models

.. module:: nichecompass.models
.. currentmodule:: nichecompass

.. autosummary::
    :toctree: generated

    models.NicheCompass

Gene Program Utilities

.. module:: nichecompass.utils
.. currentmodule:: nichecompass

.. autosummary::
    :toctree: generated

    utils.add_gps_from_gp_dict_to_adata
    utils.add_multimodal_mask_to_adata
    utils.extract_gp_dict_from_collectri_tf_network
    utils.extract_gp_dict_from_nichenet_lrt_interactions
    utils.extract_gp_dict_from_mebocost_es_interactions
    utils.extract_gp_dict_from_omnipath_lr_interactions
    utils.filter_and_combine_gp_dict_gps
    utils.get_gene_annotations
    utils.generate_multimodal_mapping_dict
    utils.get_unique_genes_from_gp_dict
    utils.generate_enriched_gp_info_plots

Cell-Cell Communication Utilities

.. module:: nichecompass.utils
.. currentmodule:: nichecompass

.. autosummary::
    :toctree: generated

    utils.compute_communication_gp_network
    utils.visualize_communication_gp_network

Other Utilities

.. module:: nichecompass.utils
.. currentmodule:: nichecompass

.. autosummary::
    :toctree: generated

    utils.create_new_color_dict