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 ethnicity, sex and advanced quality
        control routines.
Version: 1.28.1
Authors@R: c(person("Wanding", "Zhou", role = c("aut","cre"), 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"), email = "Hui.Shen@vai.org"))
Depends: R (>= 4.4.0), sesameData
License: MIT + file LICENSE
RoxygenNote: 7.3.3
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, 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/pak/sysreqs: libicu-dev libpng-dev libssl-dev libx11-dev
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-11-23 00:18:29 UTC
RemoteUrl: https://github.com/bioc/sesame
RemoteRef: RELEASE_3_22
RemoteSha: 3fa12279a56279c9edf3a82fa9b646fb0e3abaef
NeedsCompilation: no
Packaged: 2026-02-22 05:40:42 UTC; root
Author: Wanding Zhou [aut, cre] (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]
Maintainer: Wanding Zhou <zhouwanding@gmail.com>
Built: R 4.5.2; ; 2026-02-22 05:42:50 UTC; windows
