Please cite the paper below for the qusage software itself.  Please
also try to cite the appropriate methodology articles when using either
the QGen mixed model framework or the gene set meta-analysis pipeline.
To cite QuSAGE, use the following publication: To cite the QGen mixed
model framework, use the following publication: To cite the QuSAGE
meta-analysis framework, use the following publication:

  Yaari G, Bolen CR, Thakar J, Kleinstein SH. Quantitative set analysis
  for gene expression: a method to quantify gene set differential
  expression including gene-gene correlations. Nucleic Acids Res. 2013
  Aug 5.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations.},
    author = {Gur Yaari and Christopher R. Bolen and Juilee Thakar and Steven H. Kleinstein},
    journal = {Nucleic Acids Res.},
    year = {2013},
  }

  Turner JA, Bolen CR, Blankenship DM. Quantitative gene set analysis
  generalized for repeated measures, confounder adjustment, and
  continuous covariates. BMC Bioinformatics. 2015 Aug 28

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Quantitative gene set analysis generalized for repeated measures, confounder adjustment, and continuous covariates.},
    author = {Jacob A. Turner and Christopher R. Bolen and Derek M. Blankenship},
    journal = {BMC Bioinformatics.},
    year = {2015},
  }

  Meng H, Yaari G, Bolen CR, Avey S, Kleinstein SH. Gene set
  meta-analysis with Quantitative Set Analysis for Gene Expression
  (QuSAGE). PLoS Comput Biol. 2019

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE).
.},
    author = {Hailong Meng and Gur Yaari and Christopher R. Bolen and Stefan Avey and Steven H. Kleinstein},
    journal = {PLoS Computat Biol.},
    year = {2019},
  }