Breeze, CE;
Reynolds, AP;
van Dongen, J;
Dunham, I;
Lazar, J;
Neph, S;
Vierstra, J;
... Beck, S; + view all
(2019)
eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data.
Bioinformatics
10.1093/bioinformatics/btz456.
(In press).
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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 analyse both EPIC and 450k array data. New features include analysis of chromatin states, TF motifs and DNase I footprints, providing tools for EWAS interpretation and epigenome editing. AVAILABILITY: 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.
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