Please cite the first paper for the SeqGSEA methodology and the other one for the R package.

Wang X and Cairns MJ (2013). Gene Set Enrichment Analysis of RNA-Seq Data: Integrating Differential Expression and Splicing. BMC Bioinformatics, 14(Suppl 5):S16.

Wang X and Cairns MJ (2014). SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing. Bioinformatics, 30(12):1777-9.

Corresponding BibTeX entries:

  @Article{,
    title = {Gene Set Enrichment Analysis of RNA-Seq Data: Integrating
      Differential Expression and Splicing},
    author = {Xi Wang and Murray J. Cairns},
    journal = {BMC Bioinformatics},
    volume = {14(Suppl 5)},
    pages = {S16},
    year = {2013},
  }

  @Article{,
    title = {SeqGSEA: a Bioconductor package for gene set enrichment
      analysis of RNA-Seq data integrating differential expression and
      splicing},
    author = {Xi Wang and Murray J. Cairns},
    journal = {Bioinformatics},
    volume = {30(12)},
    pages = {1777-9},
    year = {2014},
  }