ZEN-norm 1.0.2

Zone Equalisation Normalisation: A Python package for bigWig scaling

Zone Equalisation Normalisation

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

1. Installation
2. Tutorials

---

1. Installation

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

Or alternatively:

conda install -c https://conda.anaconda.org/TomMakesThings zen-norm

If there are issues running either of the above, 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.

---

2. Tutorials

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