# API

Import scMagnify as:

```
import scmagnify as scm
```

![API Flowchart](../_static/test_flowchart.svg){.inline-svg align=center}

## Models

```{eval-rst}
.. module:: scmagnify.models
.. currentmodule:: scmagnify

.. autosummary::
    :toctree: generated

    MAGNI
    MSNGC
    partial_ordering
    chromatin_constraint
    import_basalGRN

````

## Tools

```{eval-rst}
.. module:: scmagnify.tools
.. currentmodule:: scmagnify

.. autosummary::
    :toctree: generated

    tools.lineage_classifer
    tools.select_paga_path
    tools.test_association
    tools.build_metacells_SEACells
    tools.connect_peaks_genes
    tools.MotifScanner
    tools.convert_motif_format
    tools.get_network_score
    tools.RegDecomp
    tools.extract_regfactor_genes
    tools.FuncEnrich
    tools.infer_signal_pairs

````

## Plotting

```{eval-rst}
.. module:: scmagnify.plotting
.. currentmodule:: scmagnify

.. autosummary::
    :toctree: generated

    plotting.barplot
    plotting.rankplot
    plotting.circosplot
    plotting.heatmap
    plotting.trendplot
    plotting.stripplot
    plotting.distplot
    plotting.GRNVisualizer
    plotting.GenomeViewer

```

## Settings

```{eval-rst}
.. module:: scmagnify.settings
.. currentmodule:: scmagnify

.. autosummary::
    :toctree: generated

```

## Logging

```{eval-rst}
.. module:: scmagnify.logging
.. currentmodule:: scmagnify

.. autosummary::
    :toctree: generated

```

## Utils

```{eval-rst}
.. module:: scmagnify.utils
.. currentmodule:: scmagnify

.. autosummary::
    :toctree: generated

    GRNMuData

```