Package: dnaEPICO
Title: dnaEPICO: Analysis Pipeline for Illumina DNA Methylation Array
        Data
Version: 0.99.30
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, 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: 2026-06-09 11:44:07 UTC
RemoteUrl: https://github.com/bioc/dnaEPICO
RemoteRef: HEAD
RemoteSha: 743b72b2584cc2fb7876e88c6d7bda913c1c06dc
NeedsCompilation: no
Packaged: 2026-06-09 17:00:46 UTC; root
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>