eFORGE 40K (mammalian array version)

Description

   ▸ eFORGE is the epigenetic equivalent of FORGE, using EWAS rather than GWAS data.

▸ eFORGE identifies tissue or cell type-specific signal by analysing a minimum set of 5 differentially methylated positions (DMPs) for overlap with DNase I hypersensitive sites (DHSs) compared to matched background DMPs and provides both graphical and tabulated outputs.

▸ eFORGE can now analyse Illumina Horvath 40K array data.
 		   

Data

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Credits
Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PÉ, Bourque G, Bergmann AK, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JH, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S (2016). eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Reports 17(8):2137-2150. doi: 10.1016/j.celrep.2016.10.059
Breeze CE, Reynolds AP, van Dongen J, Dunham I, Lazar J, Neph S, Vierstra J, Bourque G, Teschendorff AE, Stamatoyannopoulos JA, Beck S (2019). eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data. Bioinformatics doi: 10.1093/bioinformatics/btz456
Breeze, CE (2022). Cell Type-Specific Signal Analysis in Epigenome-Wide Association Studies. in Epigenome-Wide Association Studies: Methods and Protocols (ed. Guan, W.) 57-71 (Springer US). doi:10.1007/978-1-0716-1994-0_5 (bioRxiv preprint available at doi:10.1101/2021.05.21.445209)