The minfi package is described in:

Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA (2014). “Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays.” Bioinformatics, 30(10), 1363–1369. doi:10.1093/bioinformatics/btu049.

SWAN normalization (preprocessSWAN) is described in:

Maksimovic J, Gordon L, Oshlack A (2012). “SWAN: Subset quantile Within-Array Normalization for Illumina Infinium HumanMethylation450 BeadChips.” Genome Biology, 13(6), R44. doi:10.1186/gb-2012-13-6-r44.

Funnorm normalization (preprocesFunnorm) is described in:

Fortin J, Labbe A, Lemire M, Zanke BW, Hudson TJ, Fertig EJ, Greenwood CM, Hansen KD (2014). “Functional normalization of 450k methylation array data improves replication in large cancer studies.” Genome Biology, 15(12), 503. doi:10.1186/s13059-014-0503-2.

noob background correction (preprocessNoob) is described in:

Triche TJ, Weisenberger DJ, Van Den Berg D, Laird PW, Siegmund KD (2013). “Low-level processing of Illumina Infinium DNA Methylation BeadArrays.” Nucleic Acids Research, 41(7), e90. doi:10.1093/nar/gkt090.

Reconstruction of A/B compartments (compartments, extractAB) is described in:

Fortin J, Hansen KD (2015). “Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data.” Genome Biology, 16, 180. doi:10.1186/s13059-015-0741-y.

Gap hunting is described in:

Andrews SV, Ladd-Acosta C, Feinberg AP, Hansen KD, Fallin MD (2016). “'Gap hunting' to characterize clustered probe signals in Illumina methylation array data.” Epigenetics & Chromatin, 9, 56. doi:10.1186/s13072-016-0107-z.

Extending minfi to support EPIC arrays is described in:

Fortin J, Triche TJ, Hansen KD (2017). “Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi.” Bioinformatics, 33(4). doi:10.1093/bioinformatics/btw691.

Corresponding BibTeX entries:

  @Article{minfi,
    title = {{Minfi: A flexible and comprehensive Bioconductor package
      for the analysis of Infinium DNA Methylation microarrays}},
    author = {Martin J. Aryee and Andrew E. Jaffe and Hector
      Corrada-Bravo and Christine Ladd-Acosta and Andrew P. Feinberg
      and Kasper D. Hansen and Rafael A. Irizarry},
    year = {2014},
    journal = {Bioinformatics},
    volume = {30},
    number = {10},
    pages = {1363--1369},
    doi = {10.1093/bioinformatics/btu049},
    pubmed = {24478339},
  }

  @Article{SWAN,
    author = {Jovana Maksimovic and Lavinia Gordon and Alicia Oshlack},
    title = {{SWAN: Subset quantile Within-Array Normalization for
      Illumina Infinium HumanMethylation450 BeadChips}},
    journal = {Genome Biology},
    year = {2012},
    volume = {13},
    number = {6},
    pages = {R44},
    doi = {10.1186/gb-2012-13-6-r44},
    pubmed = {22703947},
  }

  @Article{funnorm,
    author = {Jean-Philippe Fortin and Aurelie Labbe and Mathieu Lemire
      and Brent W. Zanke and Thomas J. Hudson and Elana J. Fertig and
      Celia M.T. Greenwood and Kasper D. Hansen},
    title = {Functional normalization of 450k methylation array data
      improves replication in large cancer studies},
    journal = {Genome Biology},
    year = {2014},
    volume = {15},
    number = {12},
    pages = {503},
    doi = {10.1186/s13059-014-0503-2},
    pubmed = {25517394},
  }

  @Article{noob,
    author = {Timothy J. Triche and Daniel J. Weisenberger and David
      {Van Den Berg} and Peter W. Laird and Kimberly D. Siegmund},
    title = {Low-level processing of {Illumina} {Infinium} {DNA}
      {Methylation} {BeadArrays}},
    journal = {Nucleic Acids Research},
    year = {2013},
    volume = {41},
    number = {7},
    pages = {e90},
    doi = {10.1093/nar/gkt090},
    pubmed = {23476028},
  }

  @Article{compartments,
    author = {Jean-Philippe Fortin and Kasper D. Hansen},
    title = {Reconstructing A/B compartments as revealed by Hi-C using
      long-range correlations in epigenetic data},
    journal = {Genome Biology},
    year = {2015},
    volume = {16},
    pages = {180},
    doi = {10.1186/s13059-015-0741-y},
    pubmed = {26316348},
  }

  @Article{gaphunter,
    author = {Shan V. Andrews and Christine Ladd-Acosta and Andrew P.
      Feinberg and Kasper D. Hansen and M. Daniele Fallin},
    title = {'Gap hunting' to characterize clustered probe signals in
      Illumina methylation array data},
    journal = {Epigenetics & Chromatin},
    year = {2016},
    volume = {9},
    pages = {56},
    doi = {10.1186/s13072-016-0107-z},
    pubmed = {27980682},
  }

  @Article{minfiEpic,
    author = {Jean-Philippe Fortin and Timothy J. Triche and Kasper D.
      Hansen},
    title = {Preprocessing, normalization and integration of the
      Illumina HumanMethylationEPIC array with minfi},
    journal = {Bioinformatics},
    year = {2017},
    volume = {33},
    number = {4},
    page = {558-560},
    doi = {10.1093/bioinformatics/btw691},
  }