If you do not have a working Python 3.5 or 3.6 installation, consider installing Miniconda (see Installing Miniconda). Then run:

conda install seaborn scikit-learn statsmodels numba
conda install -c conda-forge python-igraph louvain
conda create -n scanpy python=3.6 scanpy

Finally, run:

conda install -c annadanese episcanpy

Pull epiScanpy from PyPI (consider using pip3 to access Python 3):

pip install episcanpy


you can also install epiScanpy directly from Github:

pip install git+