|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 variations from scRNA-seq data with XClone <https://www.biorxiv.org/content/10.1101/2023.04.03.535352v3>`_.
.. |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
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.. |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
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