methbiome is a pipeline for reference-based DNA methylation profiling of long-read metagenomic data, applicable to both PacBio and Oxford Nanopore sequencing.

Full details of the study are available in:

Costeira, R et al. methbiome: reference-based DNA methylation profiling of long-read metagenomic data. Manuscript submitted for publication.

The MeQTL EPIC Database reports results of meQTL analyses from Illumina Infinium MethylationEPIC array profiles in 2,358 blood samples from three UK cohorts, as well as HumanMethylation450K array profiles in 414 skin samples. The browser includes a meQTL database tab as well as a meQTL visualisation tab. Full details of the studies and datasets are available in:

Villicaña, S et al. 2023. Genetic impacts on DNA methylation help elucidate regulatory genomic processes. Genome Biol link

Shore et al. 2024. Genetic effects on the skin methylome in healthy older twins. Am J Hum Genet link

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.

Merloc performs a two-dimensional non-parametric linkage analysis using the two-locus MLS (Bell et al. 2006)

Ex-pairs performs exclusion mapping in different types of affected relative pairs (Herrera et al. 2006)

BloodXCI provides simulation models of X-chromosome inactivation and skewing in human blood cells.

KostoHal converts Kosambi cM to Haldane units for sex-averaged maps. KostoHal_ss extensions converts Kosambi cM to Haldane units for sex-specific maps.