DESCRIPTION

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: 1.25.2
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 (>= 4.5.0),
          sesameData
License: MIT + file LICENSE
RoxygenNote: 7.3.2
Imports:
    graphics,
    BiocParallel,
    utils,
    methods,
    stringr,
    readr,
    tibble,
    MASS,
    wheatmap (>= 0.2.0),
    GenomicRanges,
    IRanges,
    grid,
    preprocessCore,
    S4Vectors,
    ggplot2,
    BiocFileCache,
    GenomeInfoDb,
    stats,
    SummarizedExperiment,
    dplyr,
    reshape2
Suggests: scales,
          BiocManager,
          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'