copy-scanner 0.0.1.2

High-resolution copy number variant calling in single-cell whole-genome sequencing.

SCANNER (Single cell Allelic copy Number scanNER)

Scanner is a lightweight python package for high-resolution single-cell copy number analysis.

Content

• Installation
• Requirements
• Quick Start
• Operating System
• Documentation
• Contributing
• Support
• LICENSE

Installation

It is recommended to install scanner in a virtual environment. Here's how to create one using conda:

conda create -n scanner_env python=3.8

To install scanner, simply use pip:

pip install copy-scanner

Requirements

Scanner requires bcftools, which must be included in PATH. All other dependencies should be installed automatically with pip.

Quick Start

To get started with scanner, please refer to our tutorial. Here's a quick example:

import scanner
# define your json file path
path = "your/dir/to/json"
# preprocess
scanner.pp.preprocess(path)
# segment
scanner.tl.segment(path)
# infer copy number
scanner.tl.infer_copy_number(path)
# visualize 
scanner.pl.plot_whole_genome_track(path)

Command line interface

For advanced users interested in multi-sample segmentation (e.g., repurposing for bulk samples), Scanner provides a command line interface. In bash, simply run:

scanner-segment -i {input_file} -l {LAMBDA} -o {output_file}

For more details, please refer to our documentation.

Operating System

Scanner 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

Scanner is currently under active development. For support or questions, please open an issue on our GitHub repository.

Contributing

Contributions to scanner are welcome. Please refer to our contribution guidelines for more information.

LICENSE

Scanner is released under the MIT License, and is freely available for non-commercial use.