dnaEPICO

dnaEPICO provides a modular and reproducible pipeline for preprocessing and statistically analysing Illumina DNA methylation array data from the EPICv2, EPIC, and 450K platforms.

The package supports CpG-wise generalised linear models and longitudinal mixed-effects models using lmerTest/lme4 or nlme. It also integrates preprocessing, quality control, phenotype preparation, and automated report generation for local and High-Performance Computing (HPC) environments through a GNU Make-based workflow.

For lmerTest/lme4 analyses, optional omnibus F tests jointly evaluate complete phenotype main effects or phenotype-by-interaction terms while retaining the participant-level random-intercept model.

Installation instructions

Get the latest stable R release from CRAN. Then install dnaEPICO from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("dnaEPICO")

And the development version from GitHub with:

BiocManager::install("paulYRP/dnaEPICO")

Alternatively, install directly from GitHub:

install.packages('devtools')
devtools::install_github('paulYRP/dnaEPICO')

Articles:

• A Pilot Epigenome-Wide Study of Posttraumatic Growth: Identifying Novel Candidates for Future Research

Tutorials:

• DNA Methylation Tutorial
• Getting Started
• Requirements

Citation

Below is the citation output from using citation('dnaEPICO') in R. Please run this yourself to check for any updates on how to cite dnaEPICO.

print(citation("dnaEPICO"), bibtex = TRUE)

## dnaEPICO: Analysis Pipeline for Illumina DNA Methylation Array Data,
## generated as part of 10.3390/epigenomes9040039
## 
##   Ruiz P (2026). "dnaEPICO: Analysis Pipeline for Illumina DNA
##   Methylation Array Data." _Epigenomes_. doi:10.3390/epigenomes9040039
##   <https://doi.org/10.3390/epigenomes9040039>,
##   <https://bioconductor.org/packages/dnaEPICO>.
## 
## A BibTeX entry for LaTeX users is
## 
##   @Article{,
##     title = {dnaEPICO: Analysis Pipeline for Illumina DNA Methylation Array Data},
##     doi = {10.3390/epigenomes9040039},
##     journal = {Epigenomes},
##     author = {Paul Ruiz},
##     year = {2026},
##     url = {https://bioconductor.org/packages/dnaEPICO},
##   }

Please note that the dnaEPICO was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the dnaEPICO project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

• Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
• Code coverage assessment is possible thanks to codecov and covr.
• The documentation website is automatically updated thanks to pkgdown.
• The code is styled automatically thanks to styler.
• The documentation is formatted thanks to devtools and roxygen2.

For more details, check the dev directory.

This package was developed using biocthis.