============
Installation
============

Main Module XClone
==================

XClone requires Python 3.9 or later (Python 3.7 for XClone v0.3.4 & v0.3.5). 
We recommend to use Anaconda_ environment for version control and to avoid potential conflicts ::

    conda create -n xclone python=3.9
    conda activate xclone

We strongly recommend users install xclone in Python 3.9 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, :ref:`Tool installation <xcltk installation>`.

Dependencies
=============

Most required dependencies are automatically installed, e.g.

- `scanpy <https://scanpy-tutorials.readthedocs.io/>`_ for a few pre- and post-processing analysis
- `statsmodels <https://www.statsmodels.org/stable/index.html>`_ for GLM fitting
- `jupyter <https://jupyter.org/>`_ 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_.

.. _Anaconda: https://www.anaconda.com/
.. _xcltk: https://pypi.org/project/xcltk/
.. _GitHub: https://github.com/single-cell-genetics/XClone
.. _FAQ: https://xclone-cnv.readthedocs.io/en/latest/FAQ.html#python-environment
.. _`Getting Started`: getting_started
.. _`Prepare data and preprocessing`: preprocessing