| Name | squidpy JSON |
| Version |
1.6.2
JSON |
| download |
| home_page | None |
| Summary | Spatial Single Cell Analysis in Python |
| upload_time | 2024-11-12 13:01:45 |
| maintainer | None |
| docs_url | None |
| author | Giovanni Palla, Michal Klein, Hannah Spitzer |
| requires_python | >=3.10 |
| license | BSD 3-Clause License Copyright (c) 2021, Theis Lab All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
bio-informatics
image analysis
single-cell
spatial data analysis
spatial transcriptomics
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
|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 <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
.. |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/
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