Package: dnaEPICO
Title: dnaEPICO: Analysis Pipeline for Illumina DNA Methylation Array
        Data
Version: 0.99.34
Date: 2026-01-18
Authors@R: person("Paul", "Ruiz", role = c("aut", "cre"),
            email = "ruizpint@qut.edu.au",
            comment = c(ORCID = "0009-0007-6714-3566"))
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,
    CpG-wise generalised linear models and longitudinal mixed-effects
    models using 'lmerTest'/'lme4' or 'nlme', including optional 'nlme'
    residual correlation structures, 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, methods, minfi,
        openxlsx, limma, wateRmelon, ENmix, ggrepel, glm2, parallel,
        lme4, lmerTest, nlme, quadprog, SummarizedExperiment, utils,
        stats
Suggests: IlluminaHumanMethylation450kmanifest,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylationEPICv2anno.20a1.hg38,
        IlluminaHumanMethylationEPICv2manifest,
        IlluminaHumanMethylationEPICmanifest,
        IlluminaHumanMethylationEPICanno.ilm10b4.hg19, minfiData,
        GenomicRanges, S4Vectors, remotes, BiocManager, BiocStyle,
        AnnotationHub, RefManageR, sessioninfo, devtools, testthat,
        tiff, magick, knitr, rmarkdown, 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
git_url: https://git.bioconductor.org/packages/dnaEPICO
git_branch: devel
git_last_commit: 24662e6
git_last_commit_date: 2026-07-19
Repository: Bioconductor 3.24
Date/Publication: 2026-07-19
NeedsCompilation: no
Packaged: 2026-07-19 20:56:45 UTC; biocbuild
Author: Paul Ruiz [aut, cre] (ORCID: <https://orcid.org/0009-0007-6714-3566>)
Maintainer: Paul Ruiz <ruizpint@qut.edu.au>
Built: R 4.6.1; ; 2026-07-20 05:37:34 UTC; unix
