xclone 0.4.0
XClone: Inference of clonal Copy Number Alterations in single cells
Requires Python: <4.0,>=3.9

|DOI| |Stars| |Compatible| |PyPI| |PyPiDownloads| |Docs Status|


======
XClone
======

Inference of Clonal Copy Number Alterations in Single Cells

XClone is an algorithm to infer allele- and haplotype-specific copy numbers 
in individual cells from low-coverage and sparse single-cell RNA sequencing data 
(e.g., those generated by 10x Genomics, Smart-seq, etc.). 


The demo of XClone and results on the all processed cancer datasets are available at
`xclone-data <https://github.com/Rongtingting/xclone-data>`_.


Please frequently read the `tutorials and release history <https://xclone-cnv.readthedocs.io/en/latest/>`_ and keep software up to date since XClone is being updated 
and improved frequently at this stage.

.. image:: ./docs/image/XClone_overview_150dpi.png


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

Main Module
-----------

XClone requires Python 3.7 or Python >=3.9 (Recommend 3.9 for stable performance in latest version). 
Details of the environment requirements, see `XClone FAQs <https://xclone-cnv.readthedocs.io/en/latest/FAQ.html#python-environment>`_.

We recommend to use Anaconda environment for version control and to avoid potential conflicts::

    conda create -n xclone python=3.9
    conda activate xclone

XClone package can be conveniently (1~2mins) installed via PyPI::

    pip install xclone

or directly from GitHub repository (for development version)::

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


Preprocessing via xcltk 
-----------------------

xcltk is a toolkit for XClone preprocessing.
xcltk is avaliable through pypi. To install, type the following command line, and add -U for upgrading::

    pip install -U xcltk

Alternatively, you can install from this GitHub repository for latest (often development) version by following command line::

    pip install -U git+https://github.com/hxj5/xcltk


User Guide
==========

For a complete guide, please see `XClone Documentation <https://xclone-cnv.readthedocs.io/en/latest/>`_.


Documentation
=============

`Tutorials on demo dataset (Glioma sample, BCH869) <https://xclone-cnv.readthedocs.io/en/latest/BCH869_XClone_tutorials.html>`_

`Tutorials on demo dataset (Triple-negative breast cancer sample, TNBC1) <https://xclone-cnv.readthedocs.io/en/latest/TNBC1_XClone_tutorials.html>`_

Download the **Jupyter Notebooks** by clicking the following links:

`Notebook on demo dataset (Glioma sample, BCH869) <https://github.com/Rongtingting/xclone-data/blob/main/examples/BCH869_XClone_tutorials.ipynb>`_

`Notebook on demo dataset (Triple-negative breast cancer sample, TNBC1) <https://github.com/Rongtingting/xclone-data/blob/main/examples/TNBC1_XClone_tutorials.ipynb>`_

`Notebook on demo dataset (Anaplastic thyroid cancer sample, ATC2) <https://github.com/Rongtingting/xclone-data/blob/main/examples/ATC2_XClone_demo.ipynb>`_

`Notebook on demo dataset (Astrocytoma sample, GBM_10XsnRNA) <https://github.com/Rongtingting/xclone-data/tree/main/examples/GBM_10XsnRNA_XClone_demo.ipynb>`_

Ciatation
==========

For details of the method, please checkout our paper `Robust analysis of allele-specific copy number alterations from scRNA-seq data with XClone <https://www.nature.com/articles/s41467-024-51026-0>`_.

.. |Compatible| image:: https://img.shields.io/badge/python-3.7%203.9-blue
    :target: https://pypi.org/project/xclone
    :alt: Compatible

.. |DOI| image:: https://img.shields.io/badge/DOI-10.1101/2023.04.03.535352-orange?logo=gitbook&logoColor=FFFFFF&style=flat-square
    :target: https://doi.org/10.1101/2023.04.03.535352
    :alt: DOI

.. |Stars| image:: https://img.shields.io/github/stars/single-cell-genetics/XClone?logo=GitHub&color=yellow&style=flat-square
    :target: https://github.com/single-cell-genetics/XClone
    :alt: Stars

.. |PyPI| image:: https://img.shields.io/pypi/v/xclone?logo=PyPi&logoColor=FFFFFF&style=flat-square&color=blue
    :target: https://pypi.org/project/xclone
    :alt: PyPI

.. |PyPiDownloads| image:: https://static.pepy.tech/personalized-badge/xclone?period=total&units=international_system
    :target: https://pepy.tech/project/xclone
    :alt: PyPiDownloads

.. |Docs Status| image:: https://img.shields.io/readthedocs/xclone-cnv/latest?logo=readthedocs&logoColor=FFFFFF&style=flat-square
    :target: https://xclone-cnv.readthedocs.io/en/latest/
    :alt: Docs Status

License
=======

Licensed under the Apache License, Version 2.0 (see the LICENSE);

Copyright 2024 Rongting Huang, Yuanhua Huang, StatBiomed Lab