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Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.

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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.

Please frequently read the tutorials and release history and keep software up to date since XClone is being updated and improved frequently at this stage.

./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.

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.

Documentation

Tutorials on demo dataset (Glioma sample, BCH869)

Tutorials on demo dataset (Triple-negative breast cancer sample, TNBC1)

Download the Jupyter Notebooks by clicking the following links:

Notebook on demo dataset (Glioma sample, BCH869)

Notebook on demo dataset (Triple-negative breast cancer sample, TNBC1)

Notebook on demo dataset (Anaplastic thyroid cancer sample, ATC2)

Notebook on demo dataset (Astrocytoma sample, GBM_10XsnRNA)

Ciatation

For details of the method, please checkout our paper Robust analysis of allele-specific copy number alterations from scRNA-seq data with XClone.

License

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

Copyright 2024 Rongting Huang, Yuanhua Huang, StatBiomed Lab