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
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: 2026-07-19 08:22:33 UTC
RemoteUrl: https://github.com/bioc/dnaEPICO
RemoteRef: HEAD
RemoteSha: 24662e69b6d6cbc6bfcff842d99faa82ac96960b
NeedsCompilation: no
Packaged: 2026-07-19 16:06:30 UTC; root
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; ; 2026-07-19 16:23:16 UTC; windows
