https://github.com/theislab/ncem
Learning cell communication from spatial graphs of cells
https://github.com/theislab/ncem
cell-cell-communication cell-cell-interaction cvae encoder-decoder-model glm gnn scanpy squidpy tensorflow
Last synced: 4 months ago
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Learning cell communication from spatial graphs of cells
- Host: GitHub
- URL: https://github.com/theislab/ncem
- Owner: theislab
- License: bsd-3-clause
- Created: 2021-05-04T10:59:14.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2024-01-15T21:36:37.000Z (about 2 years ago)
- Last Synced: 2025-09-20T22:36:08.882Z (5 months ago)
- Topics: cell-cell-communication, cell-cell-interaction, cvae, encoder-decoder-model, glm, gnn, scanpy, squidpy, tensorflow
- Language: Python
- Homepage: https://ncem.readthedocs.io/
- Size: 40.8 MB
- Stars: 112
- Watchers: 5
- Forks: 13
- Open Issues: 34
-
Metadata Files:
- Readme: README.rst
- Contributing: docs/contributing.rst
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.rst
Awesome Lists containing this project
- awesome-cell-cell-communication - ncem - [python]- ncem can learn cell communication from spatial graphs of cells. (Uncategorized / Uncategorized)
README
ncem
===========================
|PyPI| |Python Version| |License| |Read the Docs| |Build| |pre-commit| |Black|
.. |PyPI| image:: https://img.shields.io/pypi/v/ncem.svg
:target: https://pypi.org/project/ncem/
:alt: PyPI
.. |Python Version| image:: https://img.shields.io/pypi/pyversions/ncem
:target: https://pypi.org/project/ncem
:alt: Python Version
.. |License| image:: https://img.shields.io/github/license/theislab/ncem
:target: https://opensource.org/licenses/BSD-3-Clause
:alt: License
.. |Read the Docs| image:: https://img.shields.io/readthedocs/ncem/latest.svg?label=Read%20the%20Docs
:target: https://ncem.readthedocs.io/
:alt: Read the documentation at https://ncem.readthedocs.io/
.. |Build| image:: https://github.com/theislab/ncem/workflows/Build%20ncem%20Package/badge.svg
:target: https://github.com/theislab/ncem/actions?workflow=Package
:alt: Build Package Status
.. |Tests| image:: https://github.com/theislab/ncem/workflows/Run%20ncem%20Tests/badge.svg
:target: https://github.com/theislab/ncem/actions?workflow=Tests
:alt: Run Tests Status
.. |Codecov| image:: https://codecov.io/gh/theislab/ncem/branch/master/graph/badge.svg
:target: https://codecov.io/gh/theislab/ncem
:alt: Codecov
.. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white
:target: https://github.com/pre-commit/pre-commit
:alt: pre-commit
.. |Black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
:target: https://github.com/psf/black
:alt: Black
.. image:: https://raw.githubusercontent.com/theislab/ncem/main/docs/_static/img/concept.png
:target: https://raw.githubusercontent.com/theislab/ncem/main/docs/_static/img/concept.png
:align: center
:alt: ncem concept
:width: 1000px
Features
--------
ncem_ is a model repository in a single python package for the manuscript *Fischer, D. S., Schaar, A. C. and Theis, F. Learning cell communication from spatial
graphs of cells. 2021.* (preprint_)
Installation
------------
You can install *ncem* via pip_ from PyPI_:
.. code:: console
$ pip install ncem
Credits
-------
This package was created with cookietemple_ using Cookiecutter_ based on Hypermodern_Python_Cookiecutter_.
.. _ncem: https://ncem.readthedocs.io
.. _cookietemple: https://cookietemple.com
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _PyPI: https://pypi.org/
.. _Hypermodern_Python_Cookiecutter: https://github.com/cjolowicz/cookiecutter-hypermodern-python
.. _pip: https://pip.pypa.io/
.. _Usage: https://ncem.readthedocs.io/en/latest/usage.html
.. _preprint: https://www.biorxiv.org/content/10.1101/2021.07.11.451750v1