hiclib

Notice 6/14/19

This repository is not actively maintained.

Please see cooler (https://github.com/mirnylab/cooler/), cooltools (https://github.com/mirnylab/cooltools), and distiller (https://github.com/mirnylab/distiller-nf) for actively maintained & developed Hi-C analysis tools.

Read the documentation.

Installation

The easiest way is to use pip.

First, install mirnylib, e.g:

$ pip install https://bitbucket.org/mirnylab/mirnylib/get/tip.tar.gz

Then install hiclib:

$ pip install https://bitbucket.org/mirnylab/hiclib/get/tip.tar.gz

Or clone the repo and install from there. Alternatively, there is a install script that doesn't use pip (Linux only).

Installation requirements

Python dependencies

Python 2.7/3.3+

Getting the basic Scientific Python stack can be trickier on some platforms than others. For more details, see the instructions on scipy.org. You should already have these dependencies installed and running correctly before attempting to install this package.

numpy (1.6+)
scipy
matplotlib
h5py
cython
numexpr
statsmodels

We highly recommend using the conda package/environment manager if you have trouble building the core scientific Python packages.

$ conda install numpy scipy matplotlib h5py cython ...

Other deps:

biopython
pysam

Optional:

Sphinx (to generate documentation)

Non-python dependencies