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Tutorials for Squidpy
https://squidpy.readthedocs.io/en/stable/
MIT License
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Squidpy - Spatial Single Cell Analysis in Python

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<p align="center">
    <a href="https://squidpy.readthedocs.io/en/stable/">
        <img src="https://raw.githubusercontent.com/scverse/squidpy/main/docs/source/_static/img/squidpy_horizontal.png"
         width="400px" alt="Squidpy logo">
    </a>
</p>

Squidpy is a tool for the analysis and visualization of spatial molecular data. It builds on top of scanpy and anndata, from which it inherits modularity and scalability. It provides analysis tools that leverages the spatial coordinates of the data, as well as tissue images if available.

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<p align="center">
    <a href="https://doi.org/10.1038/s41592-021-01358-2">
        <img src="https://raw.githubusercontent.com/scverse/squidpy/main/docs/source/_static/img/figure1.png"
         width="400px" alt="Squidpy title figure">
    </a>
</p>

Visit our documentation_ for installation, tutorials, examples and more.

Manuscript

Please see our manuscript Palla, Spitzer et al. (2022)_ in Nature Methods to learn more.

Squidpy's key applications

Installation

Install Squidpy via PyPI by running::

pip install squidpy
# or with napari included
pip install 'squidpy[interactive]'

or via Conda as::

conda install -c conda-forge squidpy

Contributing to Squidpy

We are happy about any contributions! Before you start, check out our contributing guide <CONTRIBUTING.rst>_.

.. |PyPI| image:: https://img.shields.io/pypi/v/squidpy.svg :target: https://pypi.org/project/squidpy/ :alt: PyPI

.. |CI| image:: https://img.shields.io/github/actions/workflow/status/scverse/squidpy/test.yml?branch=main :target: https://github.com/scverse/squidpy/actions :alt: CI

.. |Notebooks| image:: https://img.shields.io/github/actions/workflow/status/scverse/squidpy_notebooks/ci.yml?branch=main&label=notebooks :target: https://github.com/scverse/squidpy_notebooks/actions :alt: Notebooks CI

.. |Docs| image:: https://img.shields.io/readthedocs/squidpy :target: https://squidpy.readthedocs.io/en/stable/ :alt: Documentation

.. |Coverage| image:: https://codecov.io/gh/scverse/squidpy/branch/main/graph/badge.svg :target: https://codecov.io/gh/scverse/squidpy :alt: Coverage

.. |Downloads| image:: https://pepy.tech/badge/squidpy :target: https://pepy.tech/project/squidpy :alt: Downloads

.. |Discourse| image:: https://img.shields.io/discourse/posts?color=yellow&logo=discourse&server=https%3A%2F%2Fdiscourse.scverse.org :target: https://discourse.scverse.org/ :alt: Discourse

.. |Zulip| image:: https://img.shields.io/badge/zulip-join_chat-%2367b08f.svg :target: https://scverse.zulipchat.com :alt: Zulip

.. _Palla, Spitzer et al. (2022): https://doi.org/10.1038/s41592-021-01358-2 .. _scanpy: https://scanpy.readthedocs.io/en/stable/ .. _anndata: https://anndata.readthedocs.io/en/stable/ .. _napari: https://napari.org/ .. _skimage: https://scikit-image.org/ .. _documentation: https://squidpy.readthedocs.io/en/stable/