vandijklab/CINEMA-OT

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:

• Getting Started with CINEMA-OT

Download the data used for the tutorial here:

• Ex vivo stimulation of human peripheral blood mononuclear cells (PBMC) with interferon