# User

## Benchmarking

```{eval-rst}

.. 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

```{eval-rst}

.. module:: nichecompass.data

.. currentmodule:: nichecompass

.. autosummary::

    :toctree: generated

    data.load_spatial_adata_from_csv

```

## Models

```{eval-rst}

.. module:: nichecompass.models

.. currentmodule:: nichecompass

.. autosummary::

    :toctree: generated

    models.NicheCompass

```

## Gene Program Utilities

```{eval-rst}

.. 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

```{eval-rst}

.. module:: nichecompass.utils

.. currentmodule:: nichecompass

.. autosummary::

    :toctree: generated

    utils.compute_communication_gp_network

    utils.visualize_communication_gp_network

```

## Other Utilities

```{eval-rst}

.. module:: nichecompass.utils

.. currentmodule:: nichecompass

.. autosummary::

    :toctree: generated

    utils.create_new_color_dict

```