Metadata-Version: 2.1
Name: hmmCNV
Version: 1.0.0
Summary: Python package for Copy-Number Variation calling
Home-page: https://github.com/kylessmtih/hmmCNV
Author: Kyle S. Smith
Author-email: kyle.smith@stjude.org
License: GPL2
Description: # 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
Keywords: next generation sequencing CNV copy number hmm
Platform: Linux
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Cython
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Provides: hmmCNV
Description-Content-Type: text/markdown
