Hi AlphaGenome team,
Thank you for developing this amazing tool.
I’m currently using it to predict histone modifications for a list of peak regions of interest. As we know, histone modifications always act in combination to regulate chromatin accessibility. I would like to identify which histone-mark combinations are significantly enriched or characteristic for each peak set.
Given that the predicted histone-signal matrix resembles a pseudo-read-count matrix, where each value can be interpreted as a depth-like signal for a specific peak and histone mark. I’m wondering whether you have suggestions or recommended approaches for identifying meaningful or significant histone-modification combinations from this matrix.
Any guidance on analytical strategies or best practices would be greatly appreciated.
Thank you very much!
Xiaohuan