To cite the scoper package or spectral clustering-based model in publications, please use:

Nouri N, Kleinstein S (2018). “A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data.” Bioinformatics, i341-i349. doi:10.1093/bioinformatics/bty235.

Nouri N, Kleinstein S (2020). “Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data.” PLOS Computational Biology, 16(6), e1007977. doi:10.1371/journal.pcbi.1007977.

To cite the hierarchical clustering-based model in publications, please use:

Gupta N, Adams K, Briggs A, Timberlake S, Vigneault F, Kleinstein S (2017). “Hierarchical clustering can identify B cell clones with high confidence in Ig repertoire sequencing data.” The Journal of Immunology, 2489-2499. doi:10.4049/jimmunol.1601850.

Corresponding BibTeX entries:

  @Article{,
    style = {citation},
    title = {A spectral clustering-based method for identifying clones
      from high-throughput B cell repertoire sequencing data.},
    author = {Nima Nouri and Steven H. Kleinstein},
    year = {2018},
    journal = {Bioinformatics},
    pages = {i341-i349},
    doi = {10.1093/bioinformatics/bty235},
  }

  @Article{,
    style = {citation},
    title = {Somatic hypermutation analysis for improved identification
      of B cell clonal families from next-generation sequencing data.},
    author = {Nima Nouri and Steven H. Kleinstein},
    year = {2020},
    journal = {PLOS Computational Biology},
    volume = {16},
    number = {6},
    pages = {e1007977},
    doi = {10.1371/journal.pcbi.1007977},
  }

  @Article{,
    style = {citation},
    title = {Hierarchical clustering can identify B cell clones with
      high confidence in Ig repertoire sequencing data.},
    author = {Namita T. Gupta and Kristofor D. Adams and Adrian W.
      Briggs and Sonia C. Timberlake and Francois Vigneault and Steven
      H. Kleinstein},
    year = {2017},
    journal = {The Journal of Immunology},
    pages = {2489-2499},
    doi = {10.4049/jimmunol.1601850},
  }