To cite the fastTopics package, please use:

Kushal K. Dey, Chiaowen Joyce Hsiao and Matthew Stephens (2017). Visualizing the structure of RNA-seq expression data using grade of membership models. PLoS Genetics 13(3), e1006599,<doi:10.1371/journal.pgen.1006599>

Peter Carbonetto, Abhishek Sarkar, Zihao Wang and Matthew Stephens (2021). Non-negative matrix factorization algorithms greatly improve topic model fits. arXiv 2105.13440.

If de_analysis is used, please also cite:

Peter Carbonetto, Kaixuan Luo, Abhishek Sarkar, Anthony Hung, Karl Tayeb, Sebastian Pott and Matthew Stephens. GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership. Genome Biology 24: 236 (2023). https://doi.org/10.1186/s13059-023-03067-9

Corresponding BibTeX entries:

  @Article{,
    title = {Visualizing the structure of RNA-seq expression data using
      grade of membership models},
    author = {{Kushal K. Dey} and {Chiaowen Joyce Hsiao} and {Matthew
      Stephens}},
    journal = {PLoS Genetics},
    volume = {13},
    number = {3},
    pages = {e1006599},
    year = {2017},
    url = {https://doi.org/10.1371/journal.pgen.1006599},
  }

  @Article{,
    title = {Non-negative matrix factorization algorithms greatly
      improve topic model fits},
    author = {{Peter Carbonetto} and {Abhishek Sarkar} and {Zihao Wang}
      and {Matthew Stephens}},
    journal = {arXiv},
    volume = {2105.13440},
    eprint = {2105.13440},
    year = {2021},
    archiveprefix = {arXiv},
    url = {https://arxiv.org/abs/2105.13440},
  }

  @Article{,
    title = {Interpreting structure in sequence count data with
      differential expression analysis allowing for grades of
      membership},
    author = {{Peter Carbonetto} and {Kaixuan Luo} and {Abhishek
      Sarkar} and {Anthony Hung} and {Karl Tayeb} and {Sebastian Pott}
      and {Matthew Stephens}},
    journal = {Genome Biology},
    doi = {10.1186/s13059-023-03067-9},
    volume = {24},
    pages = {236},
    year = {2023},
  }