# API

## Preprocessing

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

.. autosummary::
    :toctree: generated

    pp.load_vcf
    pp.annotate_contexts
    pp.add_vaf_layer
    pp.filter_variants
    pp.filter_cells
    pp.filter_by_coverage
    pp.filter_to_snps
```

## Tools

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

.. autosummary::
    :toctree: generated

    tl.compute_spectrum
    tl.compute_callable_sites
    tl.normalize_spectrum
    tl.private_mutations
```

## Plotting

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

.. autosummary::
    :toctree: generated

    pl.spectrum
    pl.spectrum_from_df
    pl.compare_spectra
```