SCOPer

SCOPer provides a computational framework for the identification of B cell clonal relationships from Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data. It includes methods for assigning clonal identifiers using sequence identity, hierarchical clustering, and spectral clustering. SCOPer is part of the Immcantation analysis framework.

Contact

For help and questions please contact the Immcantation Group

Dependencies

Depends: ggplot2
Imports: alakazam, shazam, data.table, doParallel, dplyr, foreach, magrittr, methods, Rcpp, rlang, scales, stats, stringi
Suggests: knitr, rmarkdown, testthat

Authors

Nima Nouri (aut)
Edel Aron (ctb)
Jason Vander Heiden (aut, cre)
Steven Kleinstein (aut, cph)

Citing

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 (URL: https://doi.org/10.1093/bioinformatics/bty235).

Nouri N, Kleinstein S (2019). “Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data.” bioRxiv. doi: 10.1101/788620 (URL: https://doi.org/10.1101/788620).

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 (URL: https://doi.org/10.4049/jimmunol.1601850).

License

AGPL-3