Contributors

This ChIP-seq Analysis Tutorial series was developed and is maintained by:

Raja Ishaq Nabi Khan Epigenetics Researcher Research Focus: RNA Modifications & Epigenetics

GitHub

Acknowledgments

This tutorial is informed by experimental standards and analytical guidelines established by the ENCODE Consortium and makes extensive use of established open-source tools, including MACS3, HOMER, deepTools, and IDR. Publicly available ChIP-seq datasets (including SRP115709) were used for demonstration, benchmarking, and validation. Special mention to Waseem Akram Malla for reviewing the tutorial and providing valuable feedback

Contributing

Contributions are welcome. To contribute:

  1. Fork the repository
  2. Create a feature branch
  3. Submit a pull request with a clear description of the changes

Bug fixes, corrections, and documentation improvements are particularly encouraged.

AI Usage Disclosure

AI tools were used in a limited, assistive capacity for script troubleshooting, installation guidance, and documentation consistency.

Citation

If you use this tutorial in research or teaching, please cite the archived version:

Khan, R. I. N. (2025). ChIP-seq Analysis Tutorial: A Practical Guide to Chromatin Immunoprecipitation Sequencing Data Analysis (Version 1.0) [Software]. Zenodo. https://doi.org/10.5281/zenodo.XXXXXXX

Last updated: December 2025 Version: 1.0