epispot is an R package for molecular QTL mapping that integrates large-scale epigenetic annotations to enhance the detection and interpretation of cis- and trans- acting QTLs, including hotspots. It employs a Bayesian variational expectation-maximisation approach to jointly analyse thousands of molecular phenotypes (e.g., gene, protein or metabolite levels) and genetic variants while incorporating epigenetic marks as candidate auxiliary data on the potential of genetic variants to control traits.
H. Ruffieux, B. Fairfax, I. Nassiri, E. Vigorito, C. Wallace, S. Richardson, L. Bottolo. EPISPOT : An epigenome-driven approach for detecting and interpreting hotspots in molecular QTL studies, The American Journal of Human Genetics, 108:1-18, 10.1016/j.ajhg.2021.04.010, 2021.
To install, run the following commands in R:
if(!require(remotes)) install.packages("remotes")
remotes::install_github("hruffieux/epispot")This software uses the GPL v3 license, see LICENSE. Authors and copyright are provided in DESCRIPTION.
To report an issue, please use the epispot issue tracker at github.com.