To cite package ‘FLAMES’ in publications use:

  Changqing, W., Yair, D. J. P., et al. (2025). Igniting Full-Length
  Isoform Analysis in Single-Cell and Spatial {{RNA-seq}} Data with
  {{FLAMESv2}}. _bioRxiv_. doi:10.1101/2025.10.19.683327
  <https://doi.org/10.1101/2025.10.19.683327>

A BibTeX entry for LaTeX users is

  @Article{,
    journal = {bioRxiv},
    author = {Changqing Wang and Yair D J Prawer and Oliver Voogd and Jakob Schuster and Ricardo De Paoli-Iseppi and Anran Li and Jeannette Hallab and Luyi Tian and Hongke Peng and Margaux David and Mei R M Du and Silvia Velasco and Maria G Garone and Xueyi Dong and Kathleen Zeglinski and Chiara Pavan and Kevin C L Law and Kwaku Dad Abu-Bonsrah and Cameron P J Hunt and Clare L Parish and Quentin Gouil and Rachel Thijssen and Nadia M Davidson and Matthew E Ritchie and Michael B Clark and Yupei You},
    title = {Igniting Full-Length Isoform Analysis in Single-Cell and Spatial {\{}{\{}RNA-seq{\}}{\}} Data with {\{}{\{}FLAMESv2{\}}{\}}},
    year = {2025},
    month = {oct},
    publisher = {bioRxiv},
    pages = {2025.10.19.683327},
    doi = {10.1101/2025.10.19.683327},
    url = {https://doi.org/10.1101/2025.10.19.683327},
  }

  Tian, L., Jabbari, J. S., Thijssen, R., et al. (2021). Comprehensive
  characterization of single-cell full-length isoforms in human and
  mouse with long-read sequencing. Genome Biology, 22(1), 310.
  https://doi.org/10.1186/s13059-021-02525-6

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Luyi Tian and Jafar S Jabbari and Rachel Thijssen and {et al.}},
    title = {Comprehensive Characterization of Single-Cell Full-Length Isoforms in Human and Mouse with Long-Read Sequencing},
    journal = {Genome Biology},
    year = {2021},
    volume = {22},
    number = {1},
    pages = {310},
    doi = {10.1186/s13059-021-02525-6},
  }