Toolset for single-cell trajectory modeling.
Project description
A toolset for the modeling and analysis of single-cell trajectories.
Key Features
Single-Cell Trajectory Analysis: Leverages time-lapse imaging data to construct detailed trajectories of single-cell behavior, capturing changes in morphology and motility.
Morphodynamical State Decomposition: Utilizes data-driven methods to define and analyze cell states based on dynamic cellular features, providing insights into cell state transitions.
Dynamical Modeling: Implements MSMs and Koopman operator-based approaches to kinetically characterize cell state transitions and generate embeddings for visualizing cell dynamics.
Integration with Molecular Data: Maps live-cell imaging data to gene expression profiles, enabling predictions of RNA transcript levels based on cell state dynamics.
Tutorials: Includes jupyter-notebooks with links to Zenodo repositories with downloadable data to guide users through the process of trajectory embedding and MMIST (Molecular and Morphodynamics-Integrated Single-cell Trajectories).
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.
License
Free software: MIT license
Documentation
Tutorials
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for celltraj-0.1.53-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | c1c951a72d0014dce8b86f8bc1ebd201e1d9fa5ef697d1359ed49a902b70a7c4 |
|
MD5 | db27ad24abadf48bc41b38c2faf87b3e |
|
BLAKE2b-256 | e08dedff3d7b446bc8181c903c45b8079e641afc4502a537bcb7365f97cf8539 |