Package: methylationArrayAnalysis
Title: A cross-package Bioconductor workflow for analysing methylation
        array data
Version: 1.37.1
Authors@R: person(role=c("aut", "cre"), "Jovana Maksimovic",
        "Maintainer", email = "jovana.maksimovic@petermac.org")
Description: Methylation in the human genome is known to be associated
        with development and disease. The Illumina Infinium methylation
        arrays are by far the most common way to interrogate
        methylation across the human genome. This Bioconductor workflow
        uses multiple packages for the analysis of methylation array
        data. Specifically, we demonstrate the steps involved in a
        typical differential methylation analysis pipeline including:
        quality control, filtering, normalization, data exploration and
        statistical testing for probe-wise differential methylation. We
        further outline other analyses such as differential methylation
        of regions, differential variability analysis, estimating cell
        type composition and gene ontology testing. Finally, we provide
        some examples of how to visualise methylation array data.
Depends: R (>= 3.3.0), knitr, rmarkdown, BiocStyle, limma, minfi,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylation450kmanifest, RColorBrewer, missMethyl,
        matrixStats, minfiData, Gviz, DMRcate, stringr,
        FlowSorted.Blood.450k
License: Artistic-2.0
Encoding: UTF-8
VignetteBuilder: knitr
biocViews: Workflow, EpigeneticsWorkflow
NeedsCompilation: no
Author: Jovana Maksimovic [aut, cre]
Maintainer: Jovana Maksimovic <jovana.maksimovic@petermac.org>
RoxygenNote: 7.3.3
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev libjpeg-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-08-17 04:07:47 UTC
RemoteUrl: https://github.com/bioc/methylationArrayAnalysis
RemoteRef: HEAD
RemoteSha: f2f5edef895add108b89247a9e7028b16f11dbe7
Packaged: 2026-10-07 14:43:39 UTC; root
