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 reporting for local and high-performance computing (HPC) environments through a GNU Make-based workflow.
Optional omnibus F tests jointly evaluate complete phenotype main effects or phenotype-by-interaction terms in GLM and lmerTest/lme4 analyses.
Installation
Install a current R release from CRAN, then install the development version of dnaEPICO from GitHub:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("paulYRP/dnaEPICO")Citation
Run citation("dnaEPICO") to obtain the current citation:
## To cite dnaEPICO, use:
##
## Ruiz P (2026). "dnaEPICO: Analysis Pipeline for Illumina DNA
## Methylation Array Data." _Epigenomes_. doi:10.3390/epigenomes9040039
## <https://doi.org/10.3390/epigenomes9040039>.
## <https://github.com/paulYRP/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://github.com/paulYRP/dnaEPICO},
## }dnaEPICO builds on R and bioinformatics software cited in the vignettes and package publications.
Code of Conduct
The dnaEPICO project follows the Bioconductor Code of Conduct. Contributors agree to follow its terms.
Development tools
- GitHub Actions runs package checks with Bioconductor containers and BiocCheck.
- Codecov and covr report code coverage.
- pkgdown builds the documentation website.
- styler formats R code.
- devtools and roxygen2 generate package documentation.
This package was developed using biocthis.
