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https://github.com/scverse/squidpy

Spatial Single Cell Analysis in Python
https://github.com/scverse/squidpy

data-visualization image-analysis single-cell-genomics single-cell-rna-seq spatial-analysis spatial-transcriptomics squidpy

Last synced: about 2 months ago
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Spatial Single Cell Analysis in Python

Host: GitHub
URL: https://github.com/scverse/squidpy
Owner: scverse
License: bsd-3-clause
Created: 2020-08-21T15:46:28.000Z (over 4 years ago)
Default Branch: main
Last Pushed: 2024-10-29T20:01:22.000Z (2 months ago)
Last Synced: 2024-10-29T22:39:59.556Z (2 months ago)
Topics: data-visualization, image-analysis, single-cell-genomics, single-cell-rna-seq, spatial-analysis, spatial-transcriptomics, squidpy
Language: Python
Homepage: https://squidpy.readthedocs.io/en/stable/
Size: 9.86 MB
Stars: 434
Watchers: 9
Forks: 79
Open Issues: 66
Metadata Files:
- Readme: README.rst
- Contributing: CONTRIBUTING.rst
- License: LICENSE

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awesome-biological-image-analysis - Squidpy - Python framework that brings together tools from omics and image analysis to enable scalable description of spatial molecular data, such as transcriptome or multivariate proteins. (Image processing and segmentation)
top-life-sciences - **scverse/squidpy** - visualization`, `image-analysis`, `single-cell-genomics`, `single-cell-rna-seq`, `spatial-analysis`, `spatial-transcriptomics`, `squidpy`<br><img src='https://github.com/HubTou/topgh/blob/main/icons/gstars.png'> 399 <img src='https://github.com/HubTou/topgh/blob/main/icons/forks.png'> 71 <img src='https://github.com/HubTou/topgh/blob/main/icons/code.png'> Python <img src='https://github.com/HubTou/topgh/blob/main/icons/license.png'> BSD 3-Clause "New" or "Revised" License <img src='https://github.com/HubTou/topgh/blob/main/icons/last.png'> 2024-06-08 21:22:47 | (Ranked by starred repositories)

README

        |PyPI| |Downloads| |CI| |Docs| |Coverage| |Discourse| |Zulip| |NumFOCUS|

Squidpy - Spatial Single Cell Analysis in Python

================================================

**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.

Visit our `documentation`_ for installation, tutorials, examples and more.

Squidpy is part of the scverse project (`website`_, `governance`_) and is fiscally sponsored by `NumFOCUS`_.

Please consider making a tax-deductible `donation`_ to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

|NumFOCUS logo|

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 `_.

.. |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

.. |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

.. |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

.. |NumFOCUS| image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A

    :target: http://numfocus.org

    :alt: NumFOCUS

.. |NumFOCUS logo| image:: https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png

    :target: https://numfocus.org/project/scverse

    :width: 200

.. _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/

.. _website: https://scverse.org/

.. _governance: https://scverse.org/about/roles/

.. _NumFOCUS: https://numfocus.org/

.. _donation: https://numfocus.org/donate-to-scverse/