Installation

Main Module XClone

XClone requires Python 3.7 or later. We recommend to use Anaconda environment for version control and to avoid potential conflicts

conda create -n xclone python=3.7
conda activate xclone

We strongly recommend users install xclone in Python 3.7 environment, for higher version may not stable for higher version of packages dependencies.

XClone package can be conveniently installed via PyPI (for stable version)

pip install xclone

or directly from GitHub repository (for development version):

pip install git+https://github.com/single-cell-genetics/XClone

Preprocessing tool xcltk

For recommeded preprocessing tool xcltk, refer to preprocessing page, Tool installation.

Dependencies

Most required dependencies are automatically installed, e.g.

  • scanpy for a few pre- and post-processing analysis

  • statsmodels for GLM fitting

  • jupyter for running XClone CNV detection within notebooks

And we recommend users install requests pacakage before trying tutorials (Jupyter Notebook):

pip install requests

If you run into any issues or errors are raised during the installation process, please refer to FAQ or feel free to contact us at GitHub.