Chromoscores

A Python package for quantitative analysis of simulated Hi-C maps, providing tools to capture, process and evaluate chromatin interaction patterns such as Topoligically Associating Domains (TADs), flames, and peaks.

Requirement 📃

• numpy

Structure of the repository

The structure of this repository follows as below:

• maputils : Required functions for processing maps such as obsdrved over expected, or piling up snippets with specific features.
• scorefunctions : functions for quantitative analysis of features.
• snipping: functions for capturing snippets containing specific features.
• analysis: notebooks and code as tutorials for analyzing simulated data.

Installation 📦

First,

git https://github.com/Fudenberg-Research-Group/chromoscores.git

then

pip install chromoscores

Usage

from chromoscores import base_function

Analysis 📊

Observable features can be quantified, including:

• Observed over expected
• TADs (Topologically Associating Domains)
• flames
• Dots (loops between barriers)

See tutorials in ./jupyter_notebooks.