eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data.

ABSTRACT

SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION eFORGE v2.0 is implemented as a web tool available from https//eforge.altiusinstitute.org and https//eforge-tf.altiusinstitute.org/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.