The code to identify differential DNA methylation in non-skeletal tissues implements the algorithm described in

Yoav Mathov, Malka Nissim-Rafinia, Chen Leibson, Nir Galun, Tomas Marques-Bonet, Arye Kandel, Meir Liebergal, Eran Meshorer*, Liran Carmel* (2024). Inferring DNA methylation in non-skeletal tissues of ancient specimens. Nature Ecology and Evolution, published online.

The code is provided as a Matlab script.

RoAM is a software that computationally reconstructs premortem DNA methylation maps of ancient samples. Moreover, it can identify differentially methylated regions separating ancient samples from other ancient samples or modern samples. The algorithm is descirbed in several papers, but the full account is provided in

Yoav Mathov, Naomi Rosen, Chen Leibson, Eran Meshorer, Benjamin Yakir, Liran Carmel* (2024). RoAM: computational reconstruction of ancient methylomes and identification of differentially methylated regions. BioRxiv.

The software is written in Python and is hosted in Github.