Metadata-Version: 2.4
Name: hmmCNV
Version: 1.1.9
Summary: Python package for Copy-Number Variation calling
Author-email: "Kyle S. Smith" <kyle.smith@stjude.org>
Maintainer-email: "Kyle S. Smith" <kyle.smith@stjude.org>
License-Expression: GPL-2.0-or-later
Project-URL: Homepage, https://github.com/kylessmith/hmmCNV
Project-URL: Repository, https://github.com/kylessmith/hmmCNV
Project-URL: Documentation, https://www.biosciencestack.com/static/hmmCNV/docs/index.html
Project-URL: Issues, https://github.com/kylessmith/hmmCNV/issues
Keywords: variant,CNV,copy,number
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
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: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE.md
Requires-Dist: numpy>=2.0.0
Requires-Dist: pandas<3,>=2.0.0
Requires-Dist: ailist<3,>=2.2.1
Requires-Dist: linear_segment>=1.2.3
Requires-Dist: intervalframe>=1.2.2
Provides-Extra: dev
Requires-Dist: pytest>=7.0; extra == "dev"
Requires-Dist: cython-lint; extra == "dev"
Dynamic: license-file

# 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)
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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
