scHierarchy: A toolking for cell type hierarchies

Installation

git clone [email protected]:vitkl/scHierarchy.git
cd scHierarchy

Linux installation

export PYTHONNOUSERSITE="aaaaa"
conda create -y -n test_schierarchy python=3.9
conda activate test_schierarchy
pip install git+https://github.com/BayraktarLab/cell2location.git#egg=cell2location[tutorials]
pip uninstall -y cell2location
pip install git+https://github.com/BayraktarLab/cell2location.git@cell2location_hierachical_guide
pip install .[dev,docs,tutorials]
conda activate test_schierarchy
python -m ipykernel install --user --name=test_schierarchy --display-name='Environment (test_schierarchy)'

Mac installation

export PYTHONNOUSERSITE="aaaaa"
conda create -y -n test_schierarchy python=3.8
conda activate test_schierarchy
pip install git+https://github.com/pyro-ppl/pyro.git@dev
conda install -y -c anaconda hdf5 pytables netcdf4
pip install git+https://github.com/BayraktarLab/cell2location.git#egg=cell2location[tutorials]
pip uninstall -y cell2location
pip install git+https://github.com/BayraktarLab/cell2location.git@cell2location_hierachical_guide
pip install .[dev,docs,tutorials]
conda activate test_schierarchy
python -m ipykernel install --user --name=test_schierarchy --display-name='Environment (test_schierarchy)'