RDH_mutation_analysis

• 1. Introduction
• 2. Repository Structure
• 3. Environment
• 4. Citation
• 5. License
• 6. Contact

1. Introduction

This repository contains the main datasets and scripts used in the analyses described in "Hypermutability of ultraconserved histone genes and its contribution to human disease".

2. Repository Structure

This repository is organized into two main directories:

• figures/
  Contains the data and scripts used to generate the main figures presented in the paper.

• scripts/
  Contains the primary scripts used to generate specific datasets analyzed in this study.

Detailed descriptions of the data files, scripts, and directory organization can be found in the README.md files within each corresponding folder.

3. Environment

Create and activate the tested Conda environment with:

conda env create -f environment.yml
conda activate rdhgs-mutation-analysis

The environment contains the dependencies used by all Python scripts and figure notebooks in this repository. figures/Fig2/fig2_c_d.ipynb additionally refers to external BigWig, GTF, and deepTools matrix files through machine-specific paths; replace those paths when running the notebook on another system.

Expected runtime

On the Linux server used to validate this repository:

• Creating the Conda environment takes approximately 8–12 minutes, including dependency solving and about 410 MB of package downloads. The actual time depends on network speed and whether the Conda package cache is warm.
• Running all 19 figure notebooks and smoke-loading all 7 command-line scripts takes approximately 3–5 minutes in total, provided that the external files required by fig2_c_d.ipynb are available.

The second estimate covers complete notebook execution and dependency/CLI checks for the command-line scripts. Full production runs of the command-line scripts are not included because they require user-supplied FASTA, VCF, GTF, and BigWig files, and their runtime can range from minutes to hours or longer depending on input size, CPU count, and analysis parameters.

The MuSiCal dependency used by figures/Fig2/fig2_e_f.ipynb is distributed under its own academic and non-commercial research license. The MIT license of this repository does not replace the licenses of third-party dependencies or datasets.

4. Citation

If you find this repository, data, or scripts helpful in your research, please cite:

xxx

5. License

This repository is available under the MIT License. Third-party software and datasets retain their respective licenses and terms of use.

6. Contact

If you encounter any issues with this repository or have questions beyond the scope of the provided documentation, please feel free to contact us via e-mail or open an issue on GitHub.