dnaEPICO

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

The package integrates preprocessing, quality control, phenotype merging, generalised linear models (GLM), linear mixed-effects models (LME), and automated report generation. It is designed to operate on both local machines and High-Performance Computing (HPC) environments through a GNU Make–based workflow.

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, Mehta D (2025). "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 and Divya Mehta},
#>     year = {2025},
#>     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.