# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "scoper" in publications use:'
type: software
license: AGPL-3.0-only
title: 'scoper: Spectral Clustering-Based Method for Identifying B Cell Clones'
version: 1.3.1.999
doi: 10.1093/bioinformatics/bty235
identifiers:
- type: doi
  value: 10.32614/CRAN.package.scoper
abstract: Provides a computational framework for identification of B cell clones from
  Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data. Three main functions
  are included (identicalClones, hierarchicalClones, and spectralClones) that perform
  clustering among sequences of BCRs/IGs (B cell receptors/immunoglobulins) which
  share the same V gene, J gene and junction length. Nouri N and Kleinstein SH (2018)
  <https://doi.org/ 10.1093/bioinformatics/bty235>. Nouri N and Kleinstein SH (2019)
  <https://doi.org/ 10.1101/788620>. Gupta NT, et al. (2017) <https://doi.org/ 10.4049/jimmunol.1601850>.
authors:
- family-names: Nouri
  given-names: Nima
  email: nima.nouri@yale.edu
- family-names: Marquez
  given-names: Susanna
  email: susanna.marquez@yale.edu
- family-names: Vander Heiden
  given-names: Jason
  email: jason.vanderheiden@gmail.com
- family-names: Kleinstein
  given-names: Steven
  email: steven.kleinstein@yale.edu
preferred-citation:
  type: article
  title: A spectral clustering-based method for identifying clones from high-throughput
    B cell repertoire sequencing data.
  authors:
  - family-names: Nouri
    given-names: Nima
    email: nima.nouri@yale.edu
  - family-names: Kleinstein
    given-names: Steven H.
  year: '2018'
  journal: Bioinformatics
  doi: 10.1093/bioinformatics/bty235
  start: i341-i349
repository: https://ssnn-airr.r-universe.dev
repository-code: https://bitbucket.org/kleinstein/scoper
commit: b930491631cae9a14a778ab73ec9f90e6f09f90e
url: https://scoper.readthedocs.io
date-released: '2024-08-01'
contact:
- family-names: Marquez
  given-names: Susanna
  email: susanna.marquez@yale.edu
references:
- type: article
  title: Somatic hypermutation analysis for improved identification of B cell clonal
    families from next-generation sequencing data.
  authors:
  - family-names: Nouri
    given-names: Nima
  - family-names: Kleinstein
    given-names: Steven H.
  year: '2020'
  journal: PLOS Computational Biology
  volume: '16'
  issue: '6'
  doi: 10.1371/journal.pcbi.1007977
  start: e1007977
- type: article
  title: Hierarchical clustering can identify B cell clones with high confidence in
    Ig repertoire sequencing data.
  authors:
  - family-names: Gupta
    given-names: Namita T.
  - family-names: Adams
    given-names: Kristofor D.
  - family-names: Briggs
    given-names: Adrian W.
  - family-names: Timberlake
    given-names: Sonia C.
  - family-names: Vigneault
    given-names: Francois
  - family-names: Kleinstein
    given-names: Steven H.
  year: '2017'
  journal: The Journal of Immunology
  doi: 10.4049/jimmunol.1601850
  start: 2489-2499