Dear authors:
Thank you for developing and releasing AlphaGenome.
We are trying to perform enhancer–gene linking using AlphaGenome input-gradient scores, however, we have been unable to locate instructions for this analysis.
Specifically, we hope to follow a similar analysis presented in Extended Data Fig. 7 of your Nature paper, which evaluates enhancer–gene linking using “input gradient scores and RNA-seq variant effect scores.” We found documentation for RNA-seq variant-effect scoring at https://www.alphagenomedocs.com/, but could not find a similar instructions or code for calculating the input-gradient scores.
Could you please let us know whether the relevant documentation or implementation is publicly available? If so, we would greatly appreciate it if you could direct us to it. If this analysis of input-gradient score is not currently documented, confirmation of that would also be very helpful.
You guidance would be extremely valuable to us. Thank you very much.