To cite package ‘muscat’ in publications use:

  Crowell, L H, Soneson, Charlotte, Germain, Pierre-Luc, Calini,
  Daniela, Collin, Ludovic, Raposo, Catarina, Malhotra, Dheeraj,
  Robinson, D M (2020). “muscat detects subpopulation-specific state
  transitions from multi-sample multi-condition single-cell
  transcriptomics data.” _Nature Communications_, *11*(1), 6077.
  doi:10.1038/s41467-020-19894-4
  <https://doi.org/10.1038/s41467-020-19894-4>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {muscat detects subpopulation-specific state transitions from
             multi-sample multi-condition single-cell transcriptomics data},
    author = {{Crowell} and Helena L and {Soneson} and {Charlotte} and {Germain} and {Pierre-Luc} and {Calini} and {Daniela} and {Collin} and {Ludovic} and {Raposo} and {Catarina} and {Malhotra} and {Dheeraj} and {Robinson} and Mark D},
    journal = {Nature Communications},
    volume = {11},
    number = {1},
    pages = {6077},
    year = {2020},
    doi = {10.1038/s41467-020-19894-4},
  }

  Gilis, Jeroen, Perin, Laura, Malfait, Milan, Crowell, L H, Van den
  Berge, Koen, Assefa, Takele A, Verbist, Bie, Risso, Davide, Clement,
  Lieven (2025). “Differential detection workflows for multi-sample
  single-cell RNA-seq data.” _BMC Genomics_, *26*(1), 886.
  doi:10.1186/s12864-025-12102-x
  <https://doi.org/10.1186/s12864-025-12102-x>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {{Differential detection workflows for multi-sample single-cell
               RNA-seq data}},
    author = {{Gilis} and {Jeroen} and {Perin} and {Laura} and {Malfait} and {Milan} and {Crowell} and Helena L and {Van den Berge} and {Koen} and {Assefa} and Alemu Takele and {Verbist} and {Bie} and {Risso} and {Davide} and {Clement} and {Lieven}},
    journal = {BMC Genomics},
    volume = {26},
    number = {1},
    pages = {886},
    year = {2025},
    doi = {10.1186/s12864-025-12102-x},
  }

  Germain, Pierre-Luc, Wang, Jiayi, Robinson, D M (2025). “Bulk-based
  hypothesis weighing increases power in single-cell differential
  expression analysis.” _Peer Community Journal_, *5*(e136).
  doi:10.24072/pcjournal.663 <https://doi.org/10.24072/pcjournal.663>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Bulk-based hypothesis weighing increases power in single-cell
               differential expression analysis},
    author = {{Germain} and {Pierre-Luc} and {Wang} and {Jiayi} and {Robinson} and Mark D},
    journal = {Peer Community Journal},
    year = {2025},
    volume = {5},
    number = {e136},
    doi = {10.24072/pcjournal.663},
  }