Python package for Copy-Number Variation calling
Project description
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)
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