# API

## Preprocessing

```{eval-rst}
.. module:: geneGATer.pp
.. currentmodule:: geneGATer

.. autosummary::
    :toctree: generated

    pp.pre_clustering
    pp._r_squared_linreg

```

## Tools

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

.. autosummary::
    :toctree: generated

    tl._get_quality_metric
    tl._metagene_detection
    tl._neighbour_detection
    tl._svg_detection
    tl.getComGenes
    tl.learn_model

```

## Plotting

```{eval-rst}
.. module:: geneGATer.pl
.. currentmodule:: geneGATer

.. autosummary::
    :toctree: generated

    pl.roc_auc_classification
    pl.attention_matrix
    pl.attention_pca
    pl.attention_umap
    pl.compute_saliency
    pl.get_top_k_genes
    pl.get_top_k_genes_saliency
    pl.model_pca
    pl.model_umap

```