Package: methodical
Title: Discovering genomic regions where methylation is strongly
        associated with transcriptional activity
Version: 1.6.0
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, annotatr, BiocCheck, BiocManager, BiocParallel,
        BiocStyle, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19,
        BSgenome.Hsapiens.UCSC.hg38, 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, TumourMethData, usethis
Suggests: BSgenome.Athaliana.TAIR.TAIR9, DESeq2, methrix, rmarkdown
VignetteBuilder: knitr
SystemRequirements: kallisto
URL: https://github.com/richardheery/methodical
Config/pak/sysreqs: libfontconfig1-dev libfreetype6-dev libfribidi-dev
        git make libharfbuzz-dev libbz2-dev libgit2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libtiff-dev libwebp-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:27:18 UTC
RemoteUrl: https://github.com/bioc/methodical
RemoteRef: RELEASE_3_22
RemoteSha: ebf4ab4fee5595a542426ac2c7b6cf2edd7cce39
NeedsCompilation: no
Packaged: 2026-02-24 09:34:33 UTC; root
Author: Richard Heery [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8067-3114>)
Maintainer: Richard Heery <richardheery@gmail.com>
Built: R 4.5.2; ; 2026-02-24 09:39:19 UTC; windows
