ENmix R pacakge

Xu Z, Niu L, Li L, Taylor J (2016). “ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip.” Nucleic Acids Research.

methylation pipeline evaluation

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

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.

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.

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.

Intraclass correlation

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

DMR analysis

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

methscore

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

Corresponding BibTeX entries:

  @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},
  }

  @Article{methylation pipeline evaluation,
    author = {Zongli Xu and Liang Niu 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 = {---},
  }

  @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},
  }

  @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},
  }

  @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},
  }

  @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},
  }

  @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},
  }

  @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},
  }