DESCRIPTION

Package: knowYourCG
Type: Package
Title: Functional analysis of DNA methylome datasets
Version: 1.3.15
Authors@R: c(person("Zhou", "Wanding", role=c("aut"), email = "zhouwanding@gmail.com", comment = c(ORCID = "0000-0001-9126-1932")),
             person("Goldberg", "David", role=c("aut","cre"), email="golddc72@pennmedicine.upenn.edu", comment=c(ORCID="0000-0002-9622-4708")),
             person("Fu","Hongxiang",role=c("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.
Depends: R (>= 4.4.0)
URL: https://github.com/zhou-lab/knowYourCG
BugReports: https://github.com/zhou-lab/knowYourCG/issues
License: MIT + file LICENSE
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.2
Imports:
    sesameData,
    dplyr,
    methods,
    rlang,
    GenomicRanges,
    IRanges,
    reshape2,
    S4Vectors,
    stats,
    stringr,
    utils,
    ggplot2,
    ggrepel,
    tibble,
    wheatmap,
    magrittr
biocViews:
    Epigenetics, 
    DNAMethylation,
    Sequencing,
    SingleCell,
    Spatial,
    MethylationArray
Suggests: 
    testthat (>= 3.0.0),
    SummarizedExperiment,
    rmarkdown,
    knitr,
    sesame,
    gprofiler2,
    ggrastr
Config/testthat/edition: 3