To cite the fastTopics package, please use:

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

Peter Carbonetto, Abhishek Sarkar, Zihao Wang, Matthew Stephens (2021). “Non-negative matrix factorization algorithms greatly improve topic model fits.” arXiv, 2105.13440. 2105.13440, https://arxiv.org/abs/2105.13440.

If de_analysis is used, please also cite:

Peter Carbonetto, Kaixuan Luo, Abhishek Sarkar, Anthony Hung, Karl Tayeb, Sebastian Pott, Matthew Stephens (2023). “Interpreting structure in sequence count data with differential expression analysis allowing for grades of membership.” Genome Biology, 24, 236. doi: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},
  }