Metadata-Version: 2.4
Name: hmmCNV
Version: 1.1.7
Summary: Python package for Copy-Number Variation calling
License: GPL-2.0-or-later
License-File: LICENSE.md
Keywords: variant,CNV,copy,number
Author: Kyle S. Smith
Author-email: kyle.smith@stjude.org
Maintainer: Kyle S. Smith
Maintainer-email: kyle.smith@stjude.org
Requires-Python: >=3.10
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Cython
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Dist: ailist (>=2.1.7)
Requires-Dist: cython (>=3.0.0,<4.0.0)
Requires-Dist: intervalframe (>=1.1.11)
Requires-Dist: linear_segment (>=1.2.1)
Requires-Dist: numpy (>=1.23.5)
Requires-Dist: pandas (>=2.0.0,<3.0.0)
Project-URL: Documentation, https://www.biosciencestack.com/static/hmmCNV/docs/index.html
Project-URL: Repository, https://github.com/kylessmith/hmmCNV
Description-Content-Type: text/markdown

# HMM copy number variation calling

[![Build Status](https://travis-ci.org/kylessmith/hmmCNV.svg?branch=master)](https://travis-ci.org/kylessmith/hmmCNV) [![PyPI version](https://badge.fury.io/py/hmmCNV.svg)](https://badge.fury.io/py/hmmCNV)
[![Coffee](https://img.shields.io/badge/-buy_me_a%C2%A0coffee-gray?logo=buy-me-a-coffee&color=ff69b4)](https://www.buymeacoffee.com/kylessmith)

This is a Python package for Copy Number Variation
detection using an HMM as implemented in [ichorCNA][code].

All citations should reference to [original paper][paper].

## Install

If you dont already have numpy and scipy installed, it is best to download
`Anaconda`, a python distribution that has them included.  
```
    https://continuum.io/downloads
```

Dependencies can be installed by:

```
    pip install -r requirements.txt
```

PyPI install, presuming you have all its requirements installed:
```
	pip install hmmCNV
```

## Usage

```python
from hmmCNV import hmmCNV

# Call CNVs for bin data
loglik, hmm_results = hmmCNV.hmmCNV(tumour_copy, verbose=True)
```

[code]: https://github.com/broadinstitute/ichorCNA
[paper]: https://www.nature.com/articles/s41467-017-00965-y
