Recently developed an R package, epiRomics, (https://github.com/Huising-Lab/epiRomics) designed to identify putative enhancers based on histone marks coupled with TF co-binding. It is also intended to utilize chromatin availability to help determine cell-specification of enhancers versus common, lineage enhancers. It can accept any BED data format, so methylation data, SNP data, etc. can also be included.
I'd really appreciate feedback with regards to the package: how it can be improved, what features should be added, how to make it more user friendly, and so on.
If you have a chance, please take a look and feel free to open an issue on GitHub or email me directly.
Thank you for your time and attention!