domaincaller 0.1.0

Introduction

Domaincaller is an implementation of the original Directionality Index (DI) based TAD caller proposed by Dixon et al. [1] Instead of original separate scripts for each stage of the caller, this module provides a convenient command line interface integrating the whole pipeline, including calculating the DI track, performing HMM and post-processing. It supports the .cool matrix format, so has low memory requirements when dealing with high resolution data.

Installation

First install dependencies using conda:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda create -n domaincaller python=3.7.1 cooler=0.8.6 numpy=1.17.2 scipy=1.3.1 pomegranate=0.10.0 networkx=1.11
conda activate nholoop

Then install the domaincaller using pip:

pip install domaincaller-0.1.0-py3-none-any.whl

Usage

Check the command-line help by domaincaller [-h].

Citation