ENmix R pacakge

  list(author = list(list(given = "Zongli", family = "Xu", role = NULL,
  email = NULL, comment = NULL), list(given = "Liang", family = "Niu",
  role = NULL, email = NULL, comment = NULL), list(given = "Jack,A.",
  family = "Taylor", role = NULL, email = NULL, comment = NULL)), title
  = "Comprehensive evaluation of DNA methylation analysis pipelines for
  Illumina BeadChip", journal = "In review", year = "2021", pubmed =
  "---")

A BibTeX entry for LaTeX users is

  @Article{ENmix,
    title = {ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip},
    author = {Zongli Xu and Liang Niu and Leping Li and Jack,A. Taylor},
    year = {2016},
    journal = {Nucleic Acids Research},
    pubmed = {26384415},
  }

methylation pipeline evaluation

  Xu Z, Niu L, Sandler D, Taylor J (2022). “The ENmix DNA methylation
  analysis pipeline for Illumina BeadChip and comparisons to 7 other
  preprocessing pipelines.” _Clinical Epigenetics_.

A BibTeX entry for LaTeX users is

  @Article{methylation pipeline evaluation,
    author = {Zongli Xu and Liang Niu and Dale,P. Sandler and Jack,A. Taylor},
    title = {The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons to 7 other preprocessing pipelines},
    journal = {Clinical Epigenetics},
    year = {2022},
    pubmed = {---},
  }

RCP probe type bias correction

  Niu L, Xu Z, Taylor J (2016). “RCP: a novel probe design bias
  correction method for Illumina Methylation BeadChip.”
  _Bioinformatics_.

A BibTeX entry for LaTeX users is

  @Article{RCP,
    author = {Liang Niu and Zongli Xu and Jack,A. Taylor},
    title = {RCP: a novel probe design bias correction method for Illumina Methylation BeadChip},
    journal = {Bioinformatics},
    year = {2016},
    pubmed = {27153672},
  }

oxBS-MLE to estimate 5-hydroxymethylcytosine

  Xu Z, Taylor J, Leung Y, Ho S, Niu L (2016). “oxBS-MLE: An efficient
  method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in
  paired bisulfite and oxidative bisulfite treated DNA.”
  _Bioinformatics_.

A BibTeX entry for LaTeX users is

  @Article{oxBS-MLE,
    author = {Zongli Xu and Jack,A. Taylor and Yuet-Kin Leung and Shuk-Mei Ho and Liang Niu},
    title = {oxBS-MLE: An efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA},
    journal = {Bioinformatics},
    year = {2016},
    pubmed = {27522082},
  }

RELIC dye-bias correction

  Xu Z, Taylor J, Langie S, Boever P, Niu L (2017). “RELIC: a novel
  dye-bias correction method for Illumina Methylation BeadChip.” _BMC
  Genomics_.

A BibTeX entry for LaTeX users is

  @Article{RELIC,
    author = {Zongli Xu and Jack,A. Taylor and Sabine,A.S. Langie and Patrick,De Boever and Liang Niu},
    title = {RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip},
    journal = {BMC Genomics},
    year = {2017},
    pubmed = {28049437},
  }

Intraclass correlation

  Xu Z, Taylor J (2020). “Reliability of DNA methylation measures using
  Illumina methylation BeadChip.” _Epigenetics_.

A BibTeX entry for LaTeX users is

  @Article{dupicc,
    author = {Zongli Xu and Jack,A. Taylor},
    title = {Reliability of DNA methylation measures using Illumina methylation BeadChip},
    journal = {Epigenetics},
    year = {2020},
    pubmed = {32749174},
  }

DMR analysis

  Xu Z, Xie C, Taylor J, Niu L (2020). “ipDMR: Identification of
  differentially methyl-ated regions with interval P values.”
  _Bioinformatics_.

A BibTeX entry for LaTeX users is

  @Article{ipDMR,
    author = {Zongli Xu and Changchun Xie and Jack,A. Taylor and Liang Niu},
    title = {ipDMR: Identification of differentially methyl-ated regions with interval P values},
    journal = {Bioinformatics},
    year = {2020},
    pubmed = {32805005},
  }

methscore

  Xu Z, Niu L, Kresovich J, Taylor J (2024). “Methscore: a
  comprehensive R function for DNA methylation-based health
  predictors.” _Bioinformatics_.

A BibTeX entry for LaTeX users is

  @Article{methscore,
    author = {Zongli Xu and Liang Niu and Jacob,K. Kresovich and Jack,A. Taylor},
    title = {Methscore: a comprehensive R function for DNA methylation-based health predictors},
    journal = {Bioinformatics},
    year = {2024},
    pubmed = {38702768},
  }