kylessmith / hmmCNV

Copy Number Variation detection by HMM

HMM copy number variation calling

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

All citations should reference to original 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

from hmmCNV import hmmCNV

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