Metadata-Version: 2.1
Name: CNVpytor
Version: 1.2.1
Summary: Python extension of CNVnator
Home-page: https://github.com/abyzovlab/CNVpytor
Author: Milovan Suvakov, Abyzov Lab, Mayo Clinic
Author-email: suvakov@gmail.com
License: UNKNOWN
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
License-File: LICENSE

![CNVpytor Logo](https://raw.githubusercontent.com/abyzovlab/CNVpytor/master/cnvpytor/imgs/cnvpytor_w_640.png)

[3D printable CNVpytor logo (stl file)](https://github.com/abyzovlab/CNVpytor/blob/master/imgs/CNVpytor.stl)

# CNVpytor - a python extension of CNVnator

CNVpytor is a Python package and command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads developed in Abyzov Lab, Mayo Clinic.

Follow [CNVpytor Twitter account](https://twitter.com/cnvpytor).


### Citing CNVpytor

CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing
<br />Milovan Suvakov, Arijit Panda, Colin Diesh, Ian Holmes, Alexej Abyzov, GigaScience, Volume 10, Issue 11, November 2021, giab074
[https://doi.org/10.1093/gigascience/giab074](https://doi.org/10.1093/gigascience/giab074)

## Learn how to use CNVpytor in 10 minutes

* [Geting started](GettingStarted.md) with command line interface
* [Jupyter notebook](examples/PythonLibraryGuide.ipynb): How to use CNVpytor from Python
* [Google Colab](examples/Colab.ipynb): With CEPH trio example dataset
* [Video Tutorial](https://www.youtube.com/watch?v=RJMQtrD0SuE): 3-minute YT demo

## Gallery

| | |
|---|---|
| Manhattan plot ([see example](examples/manhattan.md))| Circular plot ([see example](examples/circular.md))|
|<img src="https://raw.githubusercontent.com/abyzovlab/CNVpytor/master/imgs/manhattan.png" width="512px">|<img src="https://raw.githubusercontent.com/abyzovlab/CNVpytor/master/imgs/circular.png" width="512px">|
| Region plot ([see example](examples/region.md))| Compare regions ([see example](examples/compare.md))|
|<img src="https://raw.githubusercontent.com/abyzovlab/CNVpytor/master/imgs/region.png" width="512px">|<img src="https://raw.githubusercontent.com/abyzovlab/CNVpytor/master/imgs/compare.png" width="512px">|
| Merging and annotating calls ([see example](examples/merging.md))|Call somatic CNAs ([see example](examples/JointCaller.md))|
|<img src="https://raw.githubusercontent.com/abyzovlab/CNVpytor/master/imgs/merging.png" width="512px">|<img src="https://raw.githubusercontent.com/abyzovlab/CNVpytor/master/imgs/joint_caller.png" width="512px">


## Install

```
> pip install cnvpytor
> cnvpytor -download
```

## Using

Check [CNVpytor github page](https://github.com/abyzovlab/CNVpytor).

## License

Released under MIT licence.


