# Tools

## Quantification

```{eval-rst}
.. module:: troutpy.tl
.. currentmodule:: troutpy

.. autosummary::
    :toctree: generated/quanticication

    tl.colocalization_proportion
    tl.spatial_variability
    tl.create_urna_metadata
    tl.quantify_overexpression
    tl.extracellular_enrichment
    tl.spatial_colocalization
    tl.in_out_correlation
    tl.compare_intra_extra_distribution
    tl.segmentation_free_clustering
    tl.get_proportion_expressed_per_cell_type

```

## Source, target and communication

```{eval-rst}
.. autosummary::
    :toctree: generated/communication

    tl.compute_distant_cells_proportion
    tl.compute_source_cells
    tl.compute_source_score
    tl.distance_to_source_cell
    tl.calculate_target_cells
    tl.compute_target_score
    tl.define_target_by_celltype
    tl.cluster_distribution_from_source 
    tl.get_gene_interaction_strength
    tl.communication_strength
    tl.gene_specific_interactions
```

## Cell scores

```{eval-rst}
.. autosummary::
    :toctree: generated/cell_scores
    
    tl.compute_contribution_score
```

## Factor analysis

```{eval-rst}
.. autosummary::
    :toctree: generated/factors
    
    tl.factors_to_cells
    tl.latent_factor
```

## Diffusion-related

```{eval-rst}
.. autosummary::
    :toctree: generated/diffusion

    tl.assess_diffusion
    tl.compute_js_divergence
    
```

## Multimodal quantication

```{eval-rst}
.. autosummary::
    :toctree: generated/multimodal
    
    tl.image_intensities_per_transcript
```