Package: mesa
Title: Methylation Enrichment Sequencing Analysis
Version: 0.99.8
Authors@R: c(
    person(given = "Simon",
           family = "Pearce",
           role = c("aut"),
           comment = c(ORCID = "0000-0002-1680-5538")),
    person(given = "Steven",
           family = "Hill",
           role = c("aut", "cre"),
           email = "stevenhill.work@gmail.com",
           comment = c(ORCID = "0000-0002-5909-692X")),
    person(given = "Paddy",
           family = "Harker",
           role = "ctb",
           comment = c(ORCID = "0000-0002-2531-8774")),
    person(given = "Kevin",
           family = "Brennan",
           role = "ctb",
           email = "kevin.brennan@cruk.manchester.ac.uk",
           comment = c(ORCID = "0000-0001-9018-9852")),           
    person(given = "Katarzyna",
           family = "Kamieniecka",
           role = "ctb"),
    person(given = "Felipe",
           family = "Perez Martinez",
           role = "ctb",
           email = "felipe.perezmartinez@cruk.manchester.ac.uk",
           comment = c(ORCID = "0009-0007-9138-3674")),
    person(given = "Cancer Research UK National Biomarker Centre", 
           role = c("cph", "fnd"))
           )
Description: A package for the analysis of methylation enrichment
        sequencing data (e.g. MBD-seq or MEDIP-seq). This allows for
        the window-based evaluation of methylation levels (using the
        'qsea' package), including functions for determining
        differentially methylated regions. Many functions are provided
        for tidyverse style modification of the qseaSet objects
        originally defined in 'qsea'.
License: GPL (>=2)
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Roxygen: list(markdown = TRUE)
Imports: plyranges, magrittr, limma, glue, ChIPseeker, purrr, progress,
        tidyselect, rlang, GenomeInfoDb, GenomicRanges, BiocGenerics,
        Biostrings, gtools, RColorBrewer, pheatmap, HMMcopy, ggplot2,
        janitor, stats, stringr, methods, graphics, grDevices, tibble,
        tidyr, BSgenome, BiocParallel, matrixStats, IRanges, cigarillo,
        data.table, Rsamtools, tools, ComplexHeatmap, readr, memoise,
        biomaRt, hues, circlize, scales
Depends: qsea, R (>= 4.5.0), dplyr
Suggests: rmarkdown, knitr, openxlsx, testthat (>= 3.0.0), UpSetR,
        rtracklayer, ggrepel, workflows, MEDIPSData, uwot,
        BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.UCSC.hg19,
        BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, org.Mm.eg.db,
        TxDb.Hsapiens.UCSC.hg38.knownGene,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Mmusculus.UCSC.mm10.knownGene, plotly, ragg
VignetteBuilder: knitr
biocViews: Sequencing, DNAMethylation, CpGIsland, Preprocessing,
        Normalization, QualityControl, Visualization,
        CopyNumberVariation, DifferentialMethylation, Coverage,
        ChIPSeq, ChipOnChip
Config/testthat/edition: 3
URL: https://github.com/cruk-mi/mesa, https://cruk-mi.github.io/mesa/
BugReports: https://github.com/cruk-mi/mesa/issues
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libbz2-dev libicu-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev perl
        libx11-dev xz-utils zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-16 11:33:23 UTC
RemoteUrl: https://github.com/BiocStaging/mesa
RemoteRef: HEAD
RemoteSha: dc949639e71a62a141a068b2e978ea298084095b
NeedsCompilation: no
Packaged: 2026-10-16 12:47:27 UTC; root
Author: Simon Pearce [aut] (ORCID: <https://orcid.org/0000-0002-1680-5538>),
  Steven Hill [aut, cre] (ORCID: <https://orcid.org/0000-0002-5909-692X>),
  Paddy Harker [ctb] (ORCID: <https://orcid.org/0000-0002-2531-8774>),
  Kevin Brennan [ctb] (ORCID: <https://orcid.org/0000-0001-9018-9852>),
  Katarzyna Kamieniecka [ctb],
  Felipe Perez Martinez [ctb] (ORCID:
    <https://orcid.org/0009-0007-9138-3674>),
  Cancer Research UK National Biomarker Centre [cph, fnd]
Maintainer: Steven Hill <stevenhill.work@gmail.com>