Individual skill
dna-methylation-analysis
DNA methylation analysis — array and bisulfite-seq processing, DMP/DMR calling, and epigenetic clocks.
skills/dna-methylation-analysis/SKILL.md
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## Overview
dna-methylation-analysis covers measuring and analyzing DNA methylation (5mC): Illumina arrays
(450K/EPIC) and bisulfite sequencing (WGBS/RRBS), processing pipelines (minfi, Bismark),
differential methylation (DMPs/DMRs), cell-type deconvolution, and epigenetic clocks. Methylation
is tissue- and cell-type-specific — every analysis must reckon with cellular heterogeneity.
## When to use
- Platform choice: EPIC arrays vs WGBS vs RRBS vs targeted bisulfite-seq.
- Array processing: minfi pipeline — QC, normalization (functional/BMIQ), probe filtering.
- Bisulfite-seq: Bismark alignment, methylation calling, coverage requirements.
- DMP/DMR analysis: limma-based, bumphunter, DMRcate.
- Cell-type heterogeneity: reference-based deconvolution, ReFACTor.