coMET is a web-based plotting tool and R-based package to visualize EWAS (epigenome-wide association scan) results in a genomic region of interest (Martin et al. 2015). coMET provides a plot of the EWAS association signal and visualisation of the methylation correlation between CpG sites (co-methylation). The coMET package also provides the option to annotate the region using functional genomic information, including both user-defined features and pre-selected features based on Encode, Roadmap, and other data. The software is designed for epigenetic data, but can be applied to functional genomic datasets in any species.
BloodXCI provides simulation models of X-chromosome inactivation and skewing in human blood cells.
eQTLbrowser from Pritchard lab.