FLeCS

Functional and Learnable Cell dynamicS

Overview

We introduce FLeCS, a functional and learnable model of cell dynamics that incorporates gene network structure into coupled differential equations and:

• accurately infers cell dynamics at scale
• provides improved functional insights into transcriptional mechanisms
• simulates single-cell trajectories

For a quick overview, please refer to notebooks/Overview.ipynb and notebooks/SingleCellExample.ipynb.

Installation

Pip

You need to have Python 3.8 or newer installed on your system. If you don't have Python installed, we recommend installing Mambaforge.

There are several alternative options to install flecs:

1. Install the latest development version:

pip install git+https://github.com/bertinus/flecs.git@main

Conda

To install the conda environment on GPU, please run

conda env create -f environment_gpu.yml
conda activate flecs
pip install -e .

To install the conda environment on CPU, please run

conda env create -f environment_cpu.yml
conda activate flecs
pip install -e .

Documentation

Please refer to the documentation.