Package: sesame
Type: Package
Title: SEnsible Step-wise Analysis of DNA MEthylation BeadChips
Description: Tools For analyzing Illumina Infinium DNA methylation
        arrays. SeSAMe provides utilities to support analyses of
        multiple generations of Infinium DNA methylation BeadChips,
        including preprocessing, quality control, visualization and
        inference. SeSAMe features accurate detection calling,
        intelligent inference of sex, age, species and strain, and
        advanced quality control routines.
Version: 1.31.12
Authors@R: c(person("Wanding", "Zhou", role = c("aut","cre","fnd"), email = "zhouwanding@gmail.com", comment = c(ORCID = "0000-0001-9126-1932")),
             person("Wubin", "Ding", role = "ctb"),
             person("David", "Goldberg", role = "ctb"),
             person("Ethan", "Moyer", role = "ctb"),
             person("Bret", "Barnes", role = "ctb"),
             person("Timothy", "Triche", role = "ctb"),
             person("Hui", "Shen", role = c("aut","fnd"), email = "Hui.Shen@vai.org"))
Depends: R (>= 4.5.0), sesameData (>= 1.31.1)
License: MIT + file LICENSE
Imports: graphics, BiocParallel, utils, methods, stringr, readr,
        tibble, MASS, wheatmap (>= 0.2.0), GenomicRanges (>= 1.61.1),
        IRanges, grid, preprocessCore, S4Vectors, ggplot2,
        BiocFileCache, Seqinfo, stats, SummarizedExperiment (>=
        1.39.1), dplyr, reshape2
Suggests: scales, BiocManager, biomaRt, GenomeInfoDb, knitr, DNAcopy,
        e1071, randomForest, RPMM, rmarkdown, testthat, tidyr,
        BiocStyle, ggrepel, grDevices, KernSmooth, pals
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://github.com/zwdzwd/sesame
BugReports: https://github.com/zwdzwd/sesame/issues
biocViews: DNAMethylation, MethylationArray, Preprocessing,
        QualityControl
Collate: 'readIDAT.R' 'sex.R' 'species.R' 'QC.R' 'GEO.R'
        'SigDFMethods.R' 'sesame.R' 'age.R' 'background.R'
        'cell_composition.R' 'channel_inference.R' 'cnv.R' 'impute.R'
        'mLiftOver.R' 'ethnicity.R' 'deidentify.R' 'detection.R' 'dm.R'
        'dye_bias.R' 'feature_selection.R' 'fileSet.R' 'mask.R'
        'sesameAnno.R' 'open.R' 'strain.R' 'tissue.R' 'track.R'
        'match_design.R' 'utils.R' 'vcf.R' 'visualize.R'
        'visualizeHelper.R' 'zzz.R' 'palgen.R'
Config/roxygen2/version: 8.0.0
RoxygenNote: 7.3.3
Config/pak/sysreqs: libicu-dev libpng-dev libssl-dev libx11-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-11-01 22:48:13 UTC
RemoteUrl: https://github.com/bioc/sesame
RemoteRef: HEAD
RemoteSha: 8b1fcfaed89b28e0def8b031a81611a0a770053c
NeedsCompilation: no
Packaged: 2026-11-02 07:55:12 UTC; root
Author: Wanding Zhou [aut, cre, fnd] (ORCID:
    <https://orcid.org/0000-0001-9126-1932>),
  Wubin Ding [ctb],
  David Goldberg [ctb],
  Ethan Moyer [ctb],
  Bret Barnes [ctb],
  Timothy Triche [ctb],
  Hui Shen [aut, fnd]
Maintainer: Wanding Zhou <zhouwanding@gmail.com>