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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "knowYourCG" in publications use:'
type: software
license: AGPL-3.0-only
title: 'knowYourCG: Functional analysis of DNA methylome datasets'
version: 1.8.0
doi: 10.1126/sciadv.adw3027
identifiers:
- type: doi
  value: 10.32614/CRAN.package.knowYourCG
abstract: 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 (<https://doi.org/10.1126/sciadv.adw3027>).
authors:
- family-names: Zhou
  given-names: Wanding
  email: zhouwanding@gmail.com
  orcid: https://orcid.org/0000-0001-9126-1932
- family-names: Goldberg
  given-names: David
  email: golddc72@pennmedicine.upenn.edu
  orcid: https://orcid.org/0000-0002-9622-4708
preferred-citation:
  type: article
  title: 'KnowYourCG: Facilitating base-level sparse methylome interpretation'
  authors:
  - family-names: Goldberg
    given-names: David C.
  - family-names: Fu
    given-names: Hongxiang
  - family-names: Atkins
    given-names: Daniel
  - family-names: Moyer
    given-names: Ethan
  - family-names: Lee
    given-names: Chin Nien
  - family-names: Deng
    given-names: Yanxiang
  - family-names: Zhou
    given-names: Wanding
    email: zhouwanding@gmail.com
    orcid: https://orcid.org/0000-0001-9126-1932
  journal: Science Advances
  year: '2025'
  volume: '11'
  issue: '43'
  doi: 10.1126/sciadv.adw3027
  start: eadw3027
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/zhou-lab/knowYourCG
commit: d476d427e3d5d8a962d7102f0a49039d45269485
url: https://github.com/zhou-lab/knowYourCG
date-released: '2026-04-28'
contact:
- family-names: Goldberg
  given-names: David
  email: golddc72@pennmedicine.upenn.edu
  orcid: https://orcid.org/0000-0002-9622-4708