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

====== XClone

Inference of Clonal Copy Number Variation 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 (recommend 3.7 for stable performance). We recommend to use Anaconda environment for version control and to avoid potential conflicts::

conda create -n xclone python=3.7
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/10.1101/2023.04.03.535352v2>_.

.. |Compatible| image:: https://img.shields.io/badge/python-3.7-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