Inference of clonal Copy Number Variation in single cells
Project description
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 full description of the algorithm and its application on published cancer datasets are described in
[full-text](link here)
The demo of XClone and results on the 3 processed cancer datasets are available at [xclone-data](https://github.com/Rongtingting/xclone-data)
Please frequently read Development and keep software up to date since XClone is being updated and improved frequently at this stage.
Installation
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
Main Module
XClone requires Python 3.7 or later. 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 installed directly from GitHub repository (for development version):
pip install git+https://github.com/single-cell-genetics/XClone
Project details
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