High-resolution copy number variant calling in single-cell whole-genome sequencing.
Project description
HiScanner (High-resolutionSingle cell Allelic copy Number callER)
HiScanner is a lightweight python package for high-resolution single-cell copy number analysis.
Content
Installation
It is recommended to install HiScanner in a virtual environment. Here's how to create one using conda:
conda create -n hiscanner_env python=3.8
To install HiScanner, simply use pip:
pip install hiscanner
Requirements
HiScanner requires bcftools
, which must be included in PATH
. All other dependencies should be installed automatically with pip.
Quick Start
To get started with HiScanner, please refer to our tutorial. Here's a quick example:
import hiscanner
# define your json file path
path = "your/dir/to/json"
# preprocess
hiscanner.pp.preprocess(path)
# segment
hiscanner.tl.segment(path)
# infer copy number
hiscanner.tl.infer_copy_number(path)
# visualize
hiscanner.pl.plot_whole_genome_track(path)
Command line interface
For advanced users interested in multi-sample segmentation (e.g., repurposing for bulk samples), HiScanner provides a command line interface. In bash, simply run:
hiscanner-segment -i {input_file} -l {LAMBDA} -o {output_file}
For more details, please refer to our documentation.
Operating System
HiScanner was tested in the following operating systems:
- macOS Ventura 13.5.2
- CentOS Linux 7.9
- Windows 11
Documentation
For more detailed information and advanced usage, please refer to our documentation.
Support
HiScanner is currently under active development. For support or questions, please open an issue on our GitHub repository.
Contributing
Contributions to HiScanner are welcome. Please refer to our contribution guidelines for more information.
LICENSE
HiScanner is released under the MIT License, and is freely available for non-commercial use.
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