Genome Biology (Jul 2023)

CimpleG: finding simple CpG methylation signatures

  • Tiago Maié,
  • Marco Schmidt,
  • Myriam Erz,
  • Wolfgang Wagner,
  • Ivan G. Costa

DOI
https://doi.org/10.1186/s13059-023-03000-0
Journal volume & issue
Vol. 24, no. 1
pp. 1 – 28

Abstract

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Abstract DNA methylation signatures are usually based on multivariate approaches that require hundreds of sites for predictions. Here, we propose a computational framework named CimpleG for the detection of small CpG methylation signatures used for cell-type classification and deconvolution. We show that CimpleG is both time efficient and performs as well as top performing methods for cell-type classification of blood cells and other somatic cells, while basing its prediction on a single DNA methylation site per cell type. Altogether, CimpleG provides a complete computational framework for the delineation of DNAm signatures and cellular deconvolution.

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