Zone Equilisation Normalisation (ZEN) is a method for normalising genomic signal bigWigs, such as ATAC-seq, ChIP-seq and TT-seq. ZEN is avaliable within the Python package ZEN-norm, which also includes modules for reversing prior bigWig normalisation and creating plots to compare performance of normalisation methods genome-wide.
Citation: T. Wilson, TA. Milne, SG. Riva and JR. Hughes, Zone Equalisation Normalisation For Improved Alignment of Epigenetic Signal, bioRvix, 2025
Contents
ZEN-norm is designed to run on Python 3.10 and above. It is installable from either Conda (recommended) or PyPI.
Conda Installation
To install the ZEN-norm package from Conda, active the conda environment you'd like to install the package into (conda activate [environment_name]) and run the command below:
conda install tommakesthings::zen-norm
If there are issues installing ZEN-norm, a conda environment with the required packages can be created with the zen_environment.yml file.
conda env create --name zen_env --file=environment/zen_environment.yml
conda activate zen_env
PyPI Installation
To install the ZEN-norm package from PyPI, run the command below:pip install ZEN-norm
Some ZEN-norm features require samtools, which is not distributed via PyPI and must be installed separately.
See the Tutorials page on GitHub for explanations of how to use ZEN-norm to:
- Normalise bigWigs with ZEN
- Reverse prior bigWig normalisation
- Compare and quanity normalisation method genome-wide alignment via Wasserstein distance
- Create plots included in the publication