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"