Package: knowYourCG
Type: Package
Title: Functional analysis of DNA methylome datasets
Version: 1.9.0
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
Config/pak/sysreqs: libicu-dev libpng-dev libssl-dev libx11-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:02:45 UTC
RemoteUrl: https://github.com/bioc/knowYourCG
RemoteRef: HEAD
RemoteSha: a93c3a93a6cb339b84de66972a7a4cfd9f8586a3
NeedsCompilation: yes
Packaged: 2026-06-22 10:49:38 UTC; root
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>