Skip to content
master
Go to file
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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.

About

Inferential structure determination of chromosomes

Resources

License

Releases

No releases published

Packages

No packages published