BayraktarLab / cell2fate

Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.

Usage and Tutorials

Please find our documentation and tutorials here.

Publication figures

Results from all datasets in the cell2fate preprint can be reproduced with these noteobooks.

Installation

We suggest using a separate conda environment for installing cell2fate.

Create a conda environment and install the cell2fate package.

conda create -y -n cell2fate_env python=3.9

conda activate cell2fate_env
pip install git+https://github.com/BayraktarLab/cell2fate

To use this environment in a jupyter notebook, add a jupyter kernel for this environment:

conda activate cell2fate_env
pip install ipykernel
python -m ipykernel install --user --name=cell2fate_env --display-name='Environment (cell2fate_env)'

If you do not have conda please install Miniconda first:

cd /path/to/software
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
# use prefix /path/to/software/miniconda3

Before installing cell2fate and it's dependencies, it could be necessary to make sure that you are creating a fully isolated conda environment by telling python to NOT use user site for installing packages, ideally by adding this line to your ~/.bashrc file , but this would also work during a terminal session:

export PYTHONNOUSERSITE="someletters"