Metadata-Version: 2.1
Name: celltraj
Version: 0.1.5
Summary: Toolset for single-cell trajectory modeling.
Author-email: Jeremy Copperman <copperma@ohsu.edu>
Project-URL: Homepage, https://github.com/jcopperm/celltraj
Project-URL: Issues, https://github.com/jcopperm/celltraj/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.5
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: h5py
Requires-Dist: matplotlib
Requires-Dist: pyemma
Requires-Dist: scipy
Requires-Dist: scikit-image
Requires-Dist: scikit-learn
Requires-Dist: pystackreg
Provides-Extra: dependencies
Requires-Dist: mahotas ; extra == 'dependencies'
Requires-Dist: umap-learn ; extra == 'dependencies'
Requires-Dist: pytorch ; extra == 'dependencies'
Requires-Dist: pandas ; extra == 'dependencies'
Requires-Dist: dask ; extra == 'dependencies'
Requires-Dist: msmtools ; extra == 'dependencies'
Requires-Dist: csaps ; extra == 'dependencies'
Requires-Dist: pygpcca ; extra == 'dependencies'
Requires-Dist: btrack ; extra == 'dependencies'
Requires-Dist: adjustText ; extra == 'dependencies'
Requires-Dist: cmapfile ; extra == 'dependencies'

========
celltraj
========


.. image:: https://img.shields.io/pypi/v/celltraj.svg
        :target: https://pypi.python.org/pypi/celltraj


A toolset for single-cell trajectory modeling.

References
----------

Copperman, Jeremy, Sean M. Gross, Young Hwan Chang, Laura M. Heiser, and Daniel M. Zuckerman. “Morphodynamical cell state description via live-cell imaging trajectory embedding.” Communications Biology 6, no. 1 (2023): 484.

Copperman, Jeremy, Ian C. Mclean, Sean M. Gross, Young Hwan Chang, Daniel M. Zuckerman, and Laura M. Heiser. “Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.” bioRxiv (2024): 2024-01.


* Free software: MIT license
* Documentation: https://jcopperm.github.io/celltraj.
* Morphodynamical Trajectory Embedding tutorial: https://github.com/jcopperm/celltraj/blob/main/tutorials/trajectory_embedding.ipynb
* MMIST: Molecular and Morphodynamics-Integrated Single-cell Trajectories tutorial (WIP)


This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
