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
  <https://doi.org/10.1093/bioinformatics/btu049>.

A BibTeX entry for LaTeX users is

  @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},
  }

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
  <https://doi.org/10.1186/gb-2012-13-6-r44>.

A BibTeX entry for LaTeX users is

  @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},
  }

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
  <https://doi.org/10.1186/s13059-014-0503-2>.

A BibTeX entry for LaTeX users is

  @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},
  }

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 <https://doi.org/10.1093/nar/gkt090>.

A BibTeX entry for LaTeX users is

  @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},
  }

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
  <https://doi.org/10.1186/s13059-015-0741-y>.

A BibTeX entry for LaTeX users is

  @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},
  }

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
  <https://doi.org/10.1186/s13072-016-0107-z>.

A BibTeX entry for LaTeX users is

  @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},
  }

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
  <https://doi.org/10.1093/bioinformatics/btw691>.

A BibTeX entry for LaTeX users is

  @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},
  }