Inferential structure determination of chromosomes
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README.md
setup.py

README.md

isdhic

This Python package implements a minimal version of Inferential Structure Determination (ISD) and can be used to calculate structures of chromosomes from single-cell Hi-C data. More details can be found in Carstens et al. (2016).

Installation

  • Local installation
python setup.py install --prefix=${HOME}
  • Global installation
sudo python setup.py install

Dependencies

Install with

pip install numpy scipy csb

Optional (used in only test and application scripts)

Install with

pip install matplotlib

Usage

Examples for running ISD on single-cell chromosome data from Nagano et al. (2013) can be found in the scripts/ folder.

Execute the scripts run_hmc.py and analyze.py.