| Name | hiscanner JSON |
| Version |
0.2a0
JSON |
| download |
| home_page | None |
| Summary | High-resolution copy number variant calling in single-cell whole-genome sequencing. |
| upload_time | 2024-04-11 15:38:05 |
| maintainer | None |
| docs_url | None |
| author | Yifan Zhao |
| requires_python | >=3.8 |
| license | MIT |
| keywords |
genomics
cnv
cna
single cell
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
<img src="image.png" alt="Logo generated by DALLE-3" width="80" height="90" style="float: right;"/>
# HiScanner (HIgh-resolution Single-Cell Allelic copy Number callER)
[](https://badge.fury.io/py/hiscanner)
[](https://opensource.org/licenses/MIT)
HiScanner is a lightweight python package for high-resolution single-cell copy number analysis.
## Content
- [Installation](#installation)
- [Requirements](#requirements)
- [Quick Start](#quick-start)
- [Operating System](#operating-system)
- [Documentation](#documentation)
- [Contributing](#contributing)
- [Support](#support)
- [LICENSE](#license)
## Installation
It is recommended to install HiScanner in a virtual environment. Here's how to create one using conda:
```bash
conda create -n hiscanner_env python=3.8
conda activate hiscanner_env
```
To install HiScanner, simply use pip:
```bash
pip install hiscanner
```
## Requirements
HiScanner requires [`bcftools`](https://samtools.github.io/bcftools/bcftools.html), 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](https://github.com/parklab/hiscanner/blob/main/image.png). Here's a quick example:
```python
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:
```bash
hiscanner-segment -i {input_file} -l {LAMBDA} -o {output_file}
```
For more details, please refer to our [documentation](https://github.com/parklab/hiscanner/tree/main/docs).
## Required input
### 1) JSON
HiScanner requires a json file as input. Here's an example:
```
{
"bin_path": "/Users/yifan/dev/scanner_tutorial/tests/data/bins",
"phase_file": "/Users/yifan/dev/scanner_tutorial/tests/data/hsnps/samplename_phased_hsnps.vcf",
"germline": "bulkname",
"gatk_vcf": "/Users/yifan/dev/scanner_tutorial/tests/data/hsnps/samplename_gatk.vcf",
"stem": "/Users/yifan/dev/scanner_tutorial/tests/data/output/",
"j": 20,
"singlecell":"cellA,cellB",
"MAX_WGD": 1,
"LAMBDA":200
}
```
### 2) BAM
The BAM file should be indexed and sorted.
### 3) Unphased VCF
output from GATK or SCAN-SNV;
The VCF file should be indexed and sorted.
### 4) Phased VCF
output from Eagle or other phasing tools;
### 5) Bins
The bins file should be a bed file (output from BIC-seq2)
## 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](https://github.com/parklab/hiscanner/tree/main/docs).
## Support
HiScanner is currently under active development. For support or questions, please open an issue on our [GitHub repository](github.com/parklab/hiscanner).
## Contributing
Contributions to HiScanner are welcome. Please refer to our [contribution guidelines](https://github.com/parklab/hiscanner/tree/main/docs/contribution_guidelines.md) for more information.
## LICENSE
HiScanner is released under the MIT License, and is freely available for non-commercial use.
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"description": "<img src=\"image.png\" alt=\"Logo generated by DALLE-3\" width=\"80\" height=\"90\" style=\"float: right;\"/>\n\n# HiScanner (HIgh-resolution Single-Cell Allelic copy Number callER)\n[](https://badge.fury.io/py/hiscanner)\n[](https://opensource.org/licenses/MIT)\n\nHiScanner is a lightweight python package for high-resolution single-cell copy number analysis.\n\n## Content\n- [Installation](#installation)\n- [Requirements](#requirements)\n- [Quick Start](#quick-start)\n- [Operating System](#operating-system)\n- [Documentation](#documentation)\n- [Contributing](#contributing)\n- [Support](#support)\n- [LICENSE](#license)\n\n## Installation\n\nIt is recommended to install HiScanner in a virtual environment. Here's how to create one using conda:\n```bash\nconda create -n hiscanner_env python=3.8\nconda activate hiscanner_env\n```\nTo install HiScanner, simply use pip:\n```bash\npip install hiscanner\n```\n## Requirements\nHiScanner requires [`bcftools`](https://samtools.github.io/bcftools/bcftools.html), which must be included in `PATH`. All other dependencies should be installed automatically with pip.\n\n\n## Quick Start\nTo get started with HiScanner, please refer to our [tutorial](https://github.com/parklab/hiscanner/blob/main/image.png). Here's a quick example:\n```python\nimport hiscanner\n# define your json file path\npath = \"your/dir/to/json\"\n# preprocess\nhiscanner.pp.preprocess(path)\n# segment\nhiscanner.tl.segment(path)\n# infer copy number\nhiscanner.tl.infer_copy_number(path)\n# visualize \nhiscanner.pl.plot_whole_genome_track(path)\n```\n\n## Command line interface\nFor advanced users interested in multi-sample segmentation (e.g., repurposing for bulk samples), HiScanner provides a command line interface. In bash, simply run:\n```bash\nhiscanner-segment -i {input_file} -l {LAMBDA} -o {output_file}\n```\nFor more details, please refer to our [documentation](https://github.com/parklab/hiscanner/tree/main/docs).\n\n## Required input\n### 1) JSON \nHiScanner requires a json file as input. Here's an example:\n```\n{\n \"bin_path\": \"/Users/yifan/dev/scanner_tutorial/tests/data/bins\",\n \"phase_file\": \"/Users/yifan/dev/scanner_tutorial/tests/data/hsnps/samplename_phased_hsnps.vcf\",\n \"germline\": \"bulkname\",\n \"gatk_vcf\": \"/Users/yifan/dev/scanner_tutorial/tests/data/hsnps/samplename_gatk.vcf\",\n \"stem\": \"/Users/yifan/dev/scanner_tutorial/tests/data/output/\",\n \"j\": 20,\n \"singlecell\":\"cellA,cellB\",\n \"MAX_WGD\": 1,\n \"LAMBDA\":200\n}\n\n```\n### 2) BAM\nThe BAM file should be indexed and sorted.\n### 3) Unphased VCF \noutput from GATK or SCAN-SNV;\nThe VCF file should be indexed and sorted.\n### 4) Phased VCF \noutput from Eagle or other phasing tools;\n### 5) Bins\nThe bins file should be a bed file (output from BIC-seq2)\n\n\n\n## Operating System\nHiScanner was tested in the following operating systems:\n- macOS Ventura 13.5.2\n- CentOS Linux 7.9\n- Windows 11\n\n## Documentation\nFor more detailed information and advanced usage, please refer to our [documentation](https://github.com/parklab/hiscanner/tree/main/docs).\n\n## Support\nHiScanner is currently under active development. For support or questions, please open an issue on our [GitHub repository](github.com/parklab/hiscanner).\n\n## Contributing\nContributions to HiScanner are welcome. Please refer to our [contribution guidelines](https://github.com/parklab/hiscanner/tree/main/docs/contribution_guidelines.md) for more information.\n\n## LICENSE\nHiScanner is released under the MIT License, and is freely available for non-commercial use.\n",
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