Package: methodical
Title: Discovering genomic regions where methylation is strongly
        associated with transcriptional activity
Version: 1.9.0
Authors@R: 
    person("Richard", "Heery", , "richardheery@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-8067-3114"))
Description: DNA methylation is generally considered to be associated
        with transcriptional silencing. However, comprehensive,
        genome-wide investigation of this relationship requires the
        evaluation of potentially millions of correlation values
        between the methylation of individual genomic loci and
        expression of associated transcripts in a relatively large
        numbers of samples. Methodical makes this process quick and
        easy while keeping a low memory footprint. It also provides a
        novel method for identifying regions where a number of
        methylation sites are consistently strongly associated with
        transcriptional expression. In addition, Methodical enables
        housing DNA methylation data from diverse sources (e.g. WGBS,
        RRBS and methylation arrays) with a common framework, lifting
        over DNA methylation data between different genome builds and
        creating base-resolution plots of the association between DNA
        methylation and transcriptional activity at transcriptional
        start sites.
License: GPL (>= 3)
BugReports: https://github.com/richardheery/methodical/issues
biocViews: DNAMethylation, MethylationArray, Transcription,
        GenomeWideAssociation, Software
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends: GenomicRanges, ggplot2, R (>= 4.0), SummarizedExperiment
LazyData: false
Imports: AnnotationHub, BiocCheck, BiocManager, BiocParallel,
        BiocStyle, Biostrings, BSgenome, bsseq, cowplot, data.table,
        DelayedArray, devtools, dplyr, ExperimentHub, foreach,
        GenomeInfoDb, HDF5Array, IRanges, knitr, MatrixGenerics,
        R.utils, rcmdcheck, RcppRoll, remotes, rhdf5, rtracklayer,
        S4Vectors, scales, tibble, tidyr, tools, usethis
Suggests: DESeq2, rmarkdown, TumourMethData
VignetteBuilder: knitr
URL: https://github.com/richardheery/methodical
Config/Bioconductor/UnsupportedPlatforms: windows
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev git make libharfbuzz-dev libbz2-dev libgit2-dev
        libicu-dev libjpeg-dev liblzma-dev libpng-dev libtiff-dev
        libuv1-dev libwebp-dev libxml2-dev libssl-dev libx11-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-05-01 14:20:44 UTC
RemoteUrl: https://github.com/bioc/methodical
RemoteRef: HEAD
RemoteSha: 1387d022fab2f4d48fcfec6c589eb3d78d18af42
NeedsCompilation: no
Packaged: 2026-07-04 22:02:30 UTC; root
Author: Richard Heery [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8067-3114>)
Maintainer: Richard Heery <richardheery@gmail.com>