To cite WGCNA in publications use:

Langfelder P and Horvath S, WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008, 9:559 doi:10.1186/1471-2105-9-559
Peter Langfelder, Steve Horvath (2012). Fast R Functions for Robust Correlations and Hierarchical Clustering. Journal of Statistical Software, 46(11), 1-17. URL http://www.jstatsoft.org/v46/i11/.

We have invested a lot of time and effort in creating the package, please cite it when using it for data analysis.

Corresponding BibTeX entries:

  @Article{,
    author = {Peter Langfelder and Steve Horvath},
    title = {WGCNA: an R package for weighted correlation network
      analysis},
    journal = {BMC Bioinformatics},
    year = {2008},
    number = {1},
    pages = {559},
    pubmedid = {19114008},
  }
  @Article{,
    title = {Fast {R} Functions for Robust Correlations and
      Hierarchical Clustering},
    author = {Peter Langfelder and Steve Horvath},
    journal = {Journal of Statistical Software},
    year = {2012},
    volume = {46},
    number = {11},
    pages = {1--17},
    url = {http://www.jstatsoft.org/v46/i11/},
  }