EFORGE v2.0: Updated analysis of cell type-specific signal in epigenomic data

Charles E. Breeze*, Alex P. Reynolds, Jenny Van Dongen, Ian Dunham, John Lazar, Shane Neph, Jeff Vierstra, Guillaume Bourque, Andrew E. Teschendorff, John A. Stamatoyannopoulos, Stephan Beck

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review


The Illumina Infinium EPIC BeadChip is a new high-throughput array for DNA methylation analysis, extending the earlier 450k array by over 400 000 new sites. Previously, a method named eFORGE was developed to provide insights into cell type-specific and cell-composition effects for 450k data. Here, we present a significantly updated and improved version of eFORGE that can analyze both EPIC and 450k array data. New features include analysis of chromatin states, transcription factor motifs and DNase I footprints, providing tools for epigenome-wide association study interpretation and epigenome editing.

Original languageEnglish
Pages (from-to)4767-4769
Number of pages3
Issue number22
Publication statusPublished - 1 Nov 2019


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