To cite exact2x2 in publications use:

When using Fisher's exact or Blaker's exact test for 2x2 tables cite:

Fay MP (2010). Confidence intervals that match Fisher's exact or Blaker's exact tests. Biostatistics. 11:373-374

When using the exact McNemar's test (paired=TRUE) cite:

Fay MP (2010). Two-sided Exact Tests and Matching Confidence Intervals for Discrete Data. R Journal 2(1):53-58.

When using binomMeld.test cite:

Fay MP, Proschan, MA, Brittain, E, (2014). Combining one sample confience procedures for inference in the two sample case.

Corresponding BibTeX entries:

  @Article{,
    title = {Confidence intervals that match Fisher's exact or Blaker's
      exact tests},
    author = {Michael P. Fay},
    journal = {Biostatistics},
    year = {2010},
    volume = {11},
    number = {2},
    pages = {373--374},
    url =
      {http://www3.niaid.nih.gov/about/organization/dcr/BRB/staff/michael.htm},
  }
  @Article{,
    title = {Two-sided Exact Tests and Matching Confidence Intervals
      for Discrete Data},
    author = {Michael P. Fay},
    journal = {R Journal},
    year = {2010},
    volume = {2},
    number = {1},
    pages = {53--58},
    url = {http://journal.r-project.org/},
  }
  @Article{,
    title = {Combining one sample confience procedures for inference in
      the two sample case},
    author = {Michael P. Fay and Michael A. Proschan and Erica H.
      Brittain},
    journal = {unpublished manuscript},
    year = {2014},
    url =
      {http://www3.niaid.nih.gov/about/organization/dcr/BRB/staff/michael.htm},
  }