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cinema-ot's Introduction

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

image

Read our preprint on bioRxiv:

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:

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