Causal INdependent Effect Module Attribution + Optimal Transport (CINEMA-OT)
CINEMA-OT is a causal framework for perturbation effect analysis to identify individual treatment effects and synergy at the single cell level.
Architecture
Read our preprint on bioRxiv:
- Dong, Mingze, et al. "Causal identification of single-cell experimental perturbation effects with CINEMA-OT". bioRxiv (2022). https://www.biorxiv.org/content/10.1101/2022.07.31.502173v3
System requirements
Hardware requirements
CINEMA-OT requires only a standard computer with enough RAM to perform in-memory computations.
OS requirements
The CINEMA-OT package is supported for all OS in principle. The package has been tested on the following systems:
- macOS: Monterey (12.4)
- Linux: RHEL Maipo (7.9), Ubantu (18.04)
Dependencies
See setup.cfg for details.
Installation
CINEMA-OT requires python version 3.7+. Install directly from pip with:
pip install cinemaot
The installation should take no more than a few minutes on a normal desktop computer.
Usage
For detailed usage, follow our step-by-step tutorial here:
Download the data used for the tutorial here:
1 maintainer
Metadata
1 maintainer
Release files for cinemaot 0.0.5
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| cinemaot-0.0.5.tar.gz | 27.1 kB | Without provenance | Details for cinemaot-0.0.5.tar.gz |
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| File | Interpreter | ABI | Platform | Actions Reset |
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| cinemaot-0.0.5-py3-none-any.whl | Python 3 | none | any | Details for cinemaot-0.0.5-py3-none-any.whl |
Total release size: 55.9 kB
Release files / cinemaot-0.0.5.tar.gz
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| Tags | Python 3 |
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