Metadata-Version: 2.1
Name: squidpy
Version: 1.2.3
Summary: Squidpy - Spatial Single Cell Analysis in Python
Home-page: https://github.com/scverse/squidpy
Download-URL: https://pypi.org/project/squidpy/
Author: Theislab
Author-email: giovanni.palla@helmholtz-muenchen.de, hannah.spitzer@helmholtz-muenchen.de
Maintainer: Theislab
Maintainer-email: giovanni.palla@helmholtz-muenchen.de, hannah.spitzer@helmholtz-muenchen.de
License: BSD
Project-URL: Documentation, https://squidpy.readthedocs.io/en/stable
Project-URL: Source Code, https://github.com/scverse/squidpy
Keywords: bio-informatics,image analysis,single-cell,spatial data analysis,spatial data analysis,spatial transcriptomics
Platform: Linux
Platform: MacOSX
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Typing :: Typed
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Environment :: Console
Classifier: Framework :: Jupyter
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
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License-File: LICENSE
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|PyPI| |Downloads| |CI| |Notebooks| |Docs| |Coverage| |Discourse| |Zulip|

Squidpy - Spatial Single Cell Analysis in Python
================================================

.. image:: https://raw.githubusercontent.com/scverse/squidpy/main/docs/source/_static/img/squidpy_horizontal.png
    :alt: Squidpy logo
    :width: 400px
    :align: center
    :target: https://squidpy.readthedocs.io/en/stable/

**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.

.. image:: https://raw.githubusercontent.com/scverse/squidpy/main/docs/source/_static/img/figure1.png
    :alt: Squidpy title figure
    :width: 400px
    :align: center
    :target: https://doi.org/10.1038/s41592-021-01358-2

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
--------------------------
- Build and analyze the neighborhood graph from spatial coordinates.
- Compute spatial statistics for cell-types and genes.
- Efficiently store, analyze and visualize large tissue images, leveraging `skimage`_.
- Interactively explore `anndata`_ and large tissue images in `napari`_.

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/workflow/status/scverse/squidpy/Test/main
    :target: https://github.com/scverse/squidpy/actions
    :alt: CI

.. |Pre-commit| image:: https://results.pre-commit.ci/badge/github/scverse/squidpy/main.svg
   :target: https://results.pre-commit.ci/latest/github/scverse/squidpy/main
   :alt: pre-commit.ci status

.. |Notebooks| image:: https://img.shields.io/github/workflow/status/scverse/squidpy_notebooks/CI/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

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    :alt: Discourse

.. |Zulip| image:: https://img.shields.io/badge/zulip-join_chat-%2367b08f.svg
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.. _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/
