Package: dnaEPICO
Title: dnaEPICO: Analysis Pipeline for Illumina DNA Methylation Array
        Data
Version: 0.99.38
Date: 2026-08-18
Authors@R: person("Paul", "Ruiz Pinto", 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. It supports quality control, probe
        filtering, cell-type deconvolution, phenotype preparation,
        CpG-wise generalised linear models with optional term-level
        omnibus F tests, longitudinal mixed-effects models using
        'lmerTest'/'lme4' or 'nlme', optional 'nlme' residual
        correlation structures, and automated reports. The workflow
        uses established Bioconductor tools, including 'minfi',
        'ENmix', and 'wateRmelon', and runs locally or in
        high-performance computing environments.
License: AGPL-3 + file LICENSE
URL: https://github.com/paulYRP/dnaEPICO
BugReports: https://github.com/paulYRP/dnaEPICO/issues
Depends: R (>= 4.4.0)
Imports: AnnotationHub, Biobase, BiocGenerics, car, RColorBrewer,
        data.table, ggplot2, grid, methods, minfi, openxlsx, limma,
        wateRmelon, ENmix, ggrepel, glm2, GenomeInfoDb, GenomicRanges,
        IRanges, parallel, lme4, lmerTest, nlme, quadprog, S4Vectors,
        SummarizedExperiment, utils, stats
Suggests: IlluminaHumanMethylation450kmanifest,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylationEPICv2anno.20a1.hg38,
        IlluminaHumanMethylationEPICv2manifest,
        IlluminaHumanMethylationEPICmanifest,
        IlluminaHumanMethylationEPICanno.ilm10b4.hg19, minfiData,
        remotes, BiocManager, BiocStyle, RefManageR, sessioninfo,
        devtools, testthat, ggVennDiagram, tiff, magick, knitr,
        rmarkdown, covr, withr, tinytex, FlowSorted.Blood.EPIC,
        FlowSorted.Blood.450k, BeadSorted.Saliva.EPIC, pbkrtest
VignetteBuilder: knitr
SystemRequirements: Quarto command-line interface (optional, for
        website report generation), GNU make (optional, for Make-based
        workflows)
biocViews: Software, Preprocessing, MethylationArray, QualityControl,
        Epigenetics, Microarray, StatisticalMethod, ChipOnChip
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 8.0.0
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev libx11-dev xz-utils
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-08-18 09:14:34 UTC
RemoteUrl: https://github.com/bioc/dnaEPICO
RemoteRef: HEAD
RemoteSha: 3e3fbe36e1bdd6cba42f5a55fde75df7dec3c012
NeedsCompilation: no
Packaged: 2026-10-17 09:23:07 UTC; root
Author: Paul Ruiz Pinto [aut, cre] (ORCID:
    <https://orcid.org/0009-0007-6714-3566>)
Maintainer: Paul Ruiz Pinto <ruizpint@qut.edu.au>