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).
- Local installation
python setup.py install --prefix=${HOME}
- Global installation
sudo python setup.py install
Install with
pip install numpy scipy csb
Optional (used in only test and application scripts)
- matplotlib: download
Install with
pip install matplotlib
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.