Package: knowYourCG
Type: Package
Title: Functional analysis of DNA methylome datasets
Version: 1.7.11
Authors@R: c(
    person("Wanding", "Zhou",
        role = c("aut", "fnd"),
        email = "zhouwanding@gmail.com",
        comment = c(ORCID = "0000-0001-9126-1932")
    ),
    person("David", "Goldberg",
        role = c("aut", "cre"),
        email = "golddc72@pennmedicine.upenn.edu",
        comment = c(ORCID = "0000-0002-9622-4708")
    ),
    person("Hongxiang", "Fu",
        role = "ctb",
        email = "fhx@seas.upenn.edu"
    ))
Description: KnowYourCG (KYCG) is a supervised learning framework designed for
    the functional analysis of DNA methylation data. Unlike existing tools
    that focus on genes or genomic intervals, KnowYourCG directly targets CpG
    dinucleotides, featuring automated supervised screenings of diverse
    biological and technical influences, including sequence motifs,
    transcription factor binding, histone modifications, replication timing,
    cell-type-specific methylation, and trait-epigenome associations.
    KnowYourCG addresses the challenges of data sparsity in various methylation
    datasets, including low-pass Nanopore sequencing, single-cell DNA
    methylomes, 5-hydroxymethylation profiles, spatial DNA methylation maps,
    and array-based datasets for epigenome-wide association studies and
    epigenetic clocks (<doi:10.1126/sciadv.adw3027>).
Depends: R (>= 4.4.0)
URL: https://github.com/zhou-lab/knowYourCG
BugReports: https://github.com/zhou-lab/knowYourCG/issues
License: AGPL-3
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 7.3.3
Imports: sesameData, ExperimentHub, AnnotationHub, dplyr, methods,
        rlang, GenomicRanges, IRanges, reshape2, S4Vectors, stats,
        stringr, utils, ggplot2, ggrepel, tibble, wheatmap, magrittr,
        readr
biocViews: Epigenetics, DNAMethylation, Sequencing, SingleCell,
        Spatial, Transcription, MethylationArray
Suggests: testthat (>= 3.0.0), SummarizedExperiment, rmarkdown, knitr,
        sesame, gprofiler2, ggrastr
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/knowYourCG
git_branch: devel
git_last_commit: 51b323e
git_last_commit_date: 2026-01-07
Repository: Bioconductor 3.23
Date/Publication: 2026-01-08
NeedsCompilation: yes
Packaged: 2026-01-08 21:48:18 UTC; biocbuild
Author: Wanding Zhou [aut, fnd] (ORCID:
    <https://orcid.org/0000-0001-9126-1932>),
  David Goldberg [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-9622-4708>),
  Hongxiang Fu [ctb]
Maintainer: David Goldberg <golddc72@pennmedicine.upenn.edu>
Built: R 4.6.0; aarch64-apple-darwin20; 2026-01-09 04:39:46 UTC; unix
