Package: mesa
Title: Methylation Enrichment Sequencing Analysis
Version: 0.99.1
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-3
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
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,
        GenomicAlignments, 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, MEDIPS, 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
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
BugReports: https://github.com/cruk-mi/mesa
NeedsCompilation: no
Packaged: 2026-05-04 17:26:02 UTC; pkgbuild
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>
