Functional and Learnable Cell dynamicS
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.
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:
- Install the latest development version:
pip install git+https://github.com/bertinus/flecs.git@mainTo 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 .
Please refer to the documentation.