# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "sesame" in publications use:'
type: software
license: MIT
title: 'sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips'
version: 1.30.0
doi: 10.1016/j.xgen.2025.100929
identifiers:
- type: doi
  value: 10.32614/CRAN.package.sesame
abstract: 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.
authors:
- family-names: Zhou
  given-names: Wanding
  email: zhouwanding@gmail.com
  orcid: https://orcid.org/0000-0001-9126-1932
- family-names: Shen
  given-names: Hui
  email: Hui.Shen@vai.org
preferred-citation:
  type: article
  title: Scalable screening of ternary-code DNA methylation dynamics associated with
    human traits
  authors:
  - family-names: Goldberg
    given-names: David C
  - family-names: Cloud
    given-names: Cameron
  - family-names: Lee
    given-names: Sol Moe
  - family-names: Barnes
    given-names: Bret
  - family-names: Gruber
    given-names: Steven
  - family-names: Kim
    given-names: Elliot
  - family-names: Pottekat
    given-names: Anita
  - family-names: Westphal
    given-names: Maximillian S
  - family-names: McAuliffe
    given-names: Luana
  - family-names: Majounie
    given-names: Elisa
  - family-names: Manian
    given-names: Manesh Kalayil
  - family-names: Zhu
    given-names: Qingdi
  - family-names: Tran
    given-names: Christine
  - family-names: Hansen
    given-names: Mark
  - family-names: Stojakovic
    given-names: Jelena
  - family-names: Parker
    given-names: Jared B
  - family-names: Kohli
    given-names: Rahul M
  - family-names: Porecha
    given-names: Rishi
  - family-names: Renke
    given-names: Nicole
  - family-names: Zhou
    given-names: Wanding
    email: zhouwanding@gmail.com
    orcid: https://orcid.org/0000-0001-9126-1932
  year: '2025'
  month: '9'
  journal: Cell Genomics
  volume: '5'
  issue: '9'
  doi: 10.1016/j.xgen.2025.100929
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/zwdzwd/sesame
commit: 0c12d47bde070cdf178010b006431df721d935c9
url: https://github.com/zwdzwd/sesame
date-released: '2026-04-28'
contact:
- family-names: Zhou
  given-names: Wanding
  email: zhouwanding@gmail.com
  orcid: https://orcid.org/0000-0001-9126-1932
references:
- type: article
  title: 'mLiftOver: harmonizing data across Infinium DNA methylation platforms'
  authors:
  - family-names: Chen
    given-names: Brian H
  - family-names: Zhou
    given-names: Wanding
  year: '2024'
  month: '7'
  journal: Bioinformatics
  volume: '40'
  issue: '7'
  doi: 10.1093/bioinformatics/btae423
  issn: 1367-4811
- type: article
  title: Low-input and single-cell methods for Infinium DNA methylation BeadChips
  authors:
  - family-names: Lee
    given-names: Sol Moe
  - family-names: Loo
    given-names: Christian
  - family-names: Prasasya
    given-names: Rexxi
  - family-names: Bartolomei
    given-names: Marisa
  - family-names: Kohli
    given-names: Rahul
  - family-names: Zhou
    given-names: Wanding
  year: '2024'
  month: '2'
  journal: Nucleic acids research
  doi: 10.1093/nar/gkae127
  issn: 1362-4962
- type: article
  title: Comparative epigenome analysis using Infinium DNA methylation BeadChips
  authors:
  - family-names: Ding
    given-names: Wubin
  - family-names: Kaur
    given-names: Diljeet
  - family-names: Horvath
    given-names: Steve
  - family-names: Zhou
    given-names: Wanding
  year: '2023'
  month: '1'
  journal: Briefings in bioinformatics
  volume: '24'
  issue: '1'
  doi: 10.1093/bib/bbac617
  issn: 1477-4054
- type: article
  title: DNA methylation dynamics and dysregulation delineated by high-throughput
    profiling in the mouse
  authors:
  - family-names: Zhou
    given-names: Wanding
  - family-names: Hinoue
    given-names: Toshinori
  - family-names: Barnes
    given-names: Bret
  - family-names: Mitchell
    given-names: Owen
  - family-names: Iqbal
    given-names: Waleed
  - family-names: Lee
    given-names: Sol Moe
  - family-names: Foy
    given-names: Kelly K
  - family-names: Lee
    given-names: Kwang-Ho
  - family-names: Moyer
    given-names: Ethan J
  - family-names: VanderArk
    given-names: Alexandra
  - family-names: Koeman
    given-names: Julie M
  - family-names: Ding
    given-names: Wubin
  - family-names: Kalkat
    given-names: Manpreet
  - family-names: Spix
    given-names: Nathan J
  - family-names: Eagleson
    given-names: Bryn
  - family-names: Pospisilik
    given-names: John Andrew
  - family-names: Szabó
    given-names: Piroska E
  - family-names: Bartolomei
    given-names: Marisa S
  - family-names: Schaaf
    given-names: Nicole A Vander
  - family-names: Kang
    given-names: Liang
  - family-names: Wiseman
    given-names: Ashley K
  - family-names: Jones
    given-names: Peter A
  - family-names: Krawczyk
    given-names: Connie M
  - family-names: Adams
    given-names: Marie
  - family-names: Porecha
    given-names: Rishi
  - family-names: Chen
    given-names: Brian H
  - family-names: Shen
    given-names: Hui
  - family-names: Laird
    given-names: Peter W
  year: '2022'
  month: '7'
  journal: Cell genomics
  volume: '2'
  issue: '7'
  doi: 10.1016/j.xgen.2022.100144
  issn: 2666-979X
- type: article
  title: 'SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips
    in genomic deletions'
  authors:
  - family-names: Zhou
    given-names: Wanding
  - family-names: Triche
    given-names: Timothy J.
  - family-names: Laird
    given-names: Peter W.
  - family-names: Shen
    given-names: Hui
  year: '2018'
  journal: Nucleic Acids Research
  volume: gky691
  doi: 10.1093/nar/gky691
- type: article
  title: Low-level processing of Illumina Infinium DNA Methylation BeadArrays
  authors:
  - family-names: Triche
    given-names: Timothy J.
  - family-names: Weisenberger
    given-names: Daniel J.
  - family-names: Van Den Berg
    given-names: David
  - family-names: Laird
    given-names: Peter W.
  - family-names: Siegmund
    given-names: Kimberly D.
  journal: Nucleic Acids Research
  year: '2013'
  volume: '41'
  issue: '7'
  doi: 10.1093/nar/gkt090
  start: e90