Metadata-Version: 2.4
Name: sparty
Version: 0.1.0
Summary: single-cell in-situ python package
Project-URL: Documentation, https://sparty.readthedocs.io/
Project-URL: Homepage, https://github.com/cobioda/sparty
Project-URL: Source, https://github.com/cobioda/sparty
Author: kevin lebrigand
Maintainer-email: kevin lebrigand <lebrigandk@gmail.com>
License: MIT License
        
        Copyright (c) 2023, kevin lebrigand
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
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        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
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License-File: LICENSE
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Requires-Python: >=3.11
Requires-Dist: adjusttext
Requires-Dist: anndata
Requires-Dist: decoupler
Requires-Dist: pycomplexheatmap
Requires-Dist: pydeseq2
Requires-Dist: scanpy
Requires-Dist: session-info2
Requires-Dist: sopa
Requires-Dist: spatialdata
Requires-Dist: spatialdata-io
Requires-Dist: spatialdata-plot
Requires-Dist: squidpy
Requires-Dist: statannotations
Description-Content-Type: text/markdown

<div align="center">

# **sparty**

**Spatial analysis for in-situ RNA transcripts in python**

---

<p align="center">
  <a href="https://sparty.readthedocs.io/en/latest/" target="_blank">Documentation</a> •
  <a href="https://sparty.readthedocs.io/en/latest/docs/notebooks/example.ipynb" target="_blank">Examples</a> •
  <a href="https://www.biorxiv.org/" target="_blank">Preprint</a>
</p>

[![Tests][badge-tests]][link-tests]
[![Documentation][badge-docs]][link-docs]

[badge-tests]: https://img.shields.io/github/actions/workflow/status/cobioda/sparty/test.yaml?branch=main
[link-tests]: https://github.com/cobioda/sparty/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/sparty

</div>

## Background

<p>
  A pthon package build on top of spatialdata for Single-Cell In-Situ Spatial-Omics data analysis, developped to handle Vizgen (merscope), Nanostring (cosmx) and 10xGenomics (Xenium) experiments.
</p>

<p align="center">
  <img src="https://github.com/cobioda/sparty/docs/_static/sparty.png" width="300px">
</p>

## Features

-   **Read in-situ spatial-omics assays experiments**: build on top of spatialdata package
-   **Automatic cell type annotation**: scanvi implementation
-   **Import anatomical .csv shape file from xenium explorer**: as anndata observations
-   **Automatic run pseudobulk data analysis**: using decoupler and pydeseq2 packages
-   **Compute cell type proportion in region**: integrating statistical test in case of replicates
-   **Produce high quality spatial figures**: build on top of spatialdata_plot package

## Getting started

Please refer to the [documentation][link-docs]. In particular, the

-   [API documentation][link-api].
-   [Tutorials][link-tutorial]

## Installation

1. Create a conda environment (Python >= 3.11)
2. Install sparty using pip:

```bash
conda create -n sparty python==3.11
conda activate sparty
pip install git+https://github.com/cobioda/sparty.git@main
```

## Contribution

If you found a bug or you want to propose a new feature, please use the [issue tracker][issue-tracker].

[issue-tracker]: https://github.com/cobioda/sparty/issues
[changelog]: https://sparty.readthedocs.io/en/latest/changelog.html
[link-docs]: https://sparty.readthedocs.io
[link-api]: https://sparty.readthedocs.io/en/latest/api.html
[link-tutorial]: https://sparty.readthedocs.io/en/latest/notebooks/tutorial.html
