Credits

License

This project is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) license.

This means you are free to: - Share — copy and redistribute the material in any medium or format - Adapt — remix, transform, and build upon the material

Under the following terms: - Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made - NonCommercial — You may not use the material for commercial purposes without explicit permission - ShareAlike — If you remix, transform, or build upon the material, you must distribute your contributions under the same license

For commercial use, please contact the author for permission.

See the License file for full details.

Citation

Until it is published under this name, if you use the Epigenetic Button in your research, please cite:

Cahn, J., Regulski, M., Lynn, J. et al. MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication. Nat Commun 15, 10854 (2024). https://doi.org/10.1038/s41467-024-55195-w

Contributing

Contributions are welcome! Please feel free to submit a Pull Request to the epigenetic button github

References

This pipeline is only a combination of great tools developped by others. A non-exhaustive list of packages used are listed below. Please refer to them for more details:

• AnnotationForge

• bedtools

• Bismark

• Bowtie2

• ComplexUpset

• Conda

• Cutadapt

• deepTools

• DMRcaller

• edgeR

• FastQC

• ggplot2

• Gviz

• IDR

• MACS2

• Python

• R

• Samtools

• ShortStack

• Snakemake

• SRA-Toolkit

• STAR

• The MEME suite

Acknowledgements

In addition to all the contributors to the development of the pipeline, special thanks to the members of the Martienssen lab for their support and help, to Thomas Dahl for the EPICC logo, and to Howard Hughes Medical Institute and Cold Spring Harbor Laboratory for funding and computational resources.