README.md

title	author	date	package	output
Introduction to EpiSCORE and DNAm-Atlas	name affiliation Andrew E. Teschendorff CAS Key Lab of Computational Biology, PICB, SINH UCL Cancer Institute, University College London	2022-03-15	EpiSCORE	BiocStyle::html_document toc_float true

Summary

EpiSCORE is an R-package for constructing a tissue-specific DNA methylation reference matrix that can be subsequently used in conjunction with a reference-based cell-type deconvolution algorithm to (i) obtain cell-type fraction estimates in a corresponding bulk-tissue sample for which a genome-wide DNAm profile exists, and (ii) to infer cell-type specific differential DNA methylation signals in the context of a general Epigenome-Wide-Association Study. EpiScore is aimed particularly at complex solid tissues, for which experimentally generating appropriate DNAm reference matrices representing all the major cell-types within the tissue is not possible. EpiScore exploits the tissue-specific single-cell RNA-Sequencing atlases to construct corresponding tissue-specific DNA methylation references. The EpiSCORE R-package also contains a DNAm-atlas for 13 tissue-types.

Installation

To install (you will also need to install the dependency package presto):

library(devtools)
devtools::install_github("immunogenomics/presto")
devtools::install_github("aet21/EpiSCORE")

References

Teschendorff AE, Zhu T, Breeze CE, Beck S. EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data. Genome Biology 2020 Sep 4;21(1):221. doi: 10.1186/s13059-020-02126-9 .

Zhu T, Liu J, Beck S, Pan S, Capper D, Lechner M, Thirlwell C, Breeze CE, Teschendorff AE. A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution. Nat Methods 2022 Mar;19(3):296. doi: 10.1038/s41592-022-01412-7 .