dnaEPICO

dnaEPICO: Analysis Pipeline for Illumina DNA Methylation Array Data

Bioconductor version: 3.24 · Package version: 0.99.38

A modular and reproducible workflow for preprocessing and analysing Illumina DNA methylation array data from the EPICv2, EPIC, and 450K platforms. It supports quality control, probe filtering, cell-type deconvolution, phenotype preparation, CpG-wise generalised linear models with optional term-level omnibus F tests, longitudinal mixed-effects models using 'lmerTest'/'lme4' or 'nlme', optional 'nlme' residual correlation structures, and automated reports. The workflow uses established Bioconductor tools, including 'minfi', 'ENmix', and 'wateRmelon', and runs locally or in high-performance computing environments.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("dnaEPICO")