Package: dnaEPICO
Title: dnaEPICO: Analysis Pipeline for Illumina DNA Methylation Array
        Data
Version: 0.99.14
Date: 2026-01-18
Authors@R: c(person("Paul", "Ruiz", role = c("aut", "cre"),
            email = "ruizpint@qut.edu.au", comment = c(ORCID = "0009-0007-6714-3566")),
            person("Divya", "Mehta", role = "aut",
            comment = c(ORCID = "0000-0001-7971-7255")))
Description: 
    A modular and reproducible workflow for preprocessing and analysing
    Illumina DNA methylation array data from the EPICv2, EPIC, and
    450K platforms. The package integrates quality control, probe
    filtering, cell-type deconvolution, phenotype preparation,
    generalised linear models, linear mixed-effects models, and
    automated report generation. It builds on established Bioconductor
    infrastructure and wraps commonly used tools including 'minfi',
    'ENmix', and 'wateRmelon', with support for both local execution
    and high-performance computing workflows.
License: AGPL-3 + file LICENSE
URL: https://github.com/paulYRP/dnaEPICO
BugReports: https://github.com/paulYRP/dnaEPICO/issues
Depends: R (>= 4.4)
Imports: Biobase, RColorBrewer, data.table, ggplot2, MASS, methods,
        minfi, limma, wateRmelon, ENmix, ggrepel, glm2, parallel, lme4,
        lmerTest, quadprog, rmarkdown, SummarizedExperiment, utils,
        stats
Suggests: IlluminaHumanMethylation450kmanifest,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylationEPICv2anno.20a1.hg38,
        IlluminaHumanMethylationEPICv2manifest,
        IlluminaHumanMethylationEPICmanifest,
        IlluminaHumanMethylationEPICanno.ilm10b4.hg19, minfiData,
        GenomicRanges, S4Vectors, remotes, BiocManager, BiocStyle,
        RefManageR, sessioninfo, devtools, testthat, tiff, knitr, covr,
        withr, tinytex, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k,
        BeadSorted.Saliva.EPIC
VignetteBuilder: knitr
biocViews: Software, Preprocessing, MethylationArray, QualityControl,
        Epigenetics, Microarray, StatisticalMethod, ChipOnChip
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-04-23 01:03:56 UTC; pkgbuild
Author: Paul Ruiz [aut, cre] (ORCID: <https://orcid.org/0009-0007-6714-3566>),
  Divya Mehta [aut] (ORCID: <https://orcid.org/0000-0001-7971-7255>)
Maintainer: Paul Ruiz <ruizpint@qut.edu.au>
