# SpaRank

**Transferable spatial omics deconvolution.**

SpaRank turns expression profiles into rank-ordered token sequences and runs them through a Transformer encoder to predict cell-type composition at each spatial spot. Trained once on a multi-context single-cell reference, a single model deploys directly to spatial sections spanning contexts without per-slice retraining. The same pipeline handles unimodal (RNA), multimodal (RNA + ADT, …), and context-conditioned setups.

```{toctree}
:maxdepth: 2
:caption: Getting Started

installation
quickstart
```

```{toctree}
:maxdepth: 2
:caption: Tutorials

tutorials/mouse_isocortex
tutorials/human_lymphoid
tutorials/human_thymus

```

```{toctree}
:maxdepth: 1
:caption: API Reference

api
```

## Indices

* {ref}`genindex`
* {ref}`modindex`