SCOPer

SCOPer provides a computational framework for B cell clones identification from adaptive immune receptor repertoire sequencing (AIRR-Seq) datasets. Three models are included (identical, hierarchical, and spectral) that perform clustering among sequences of BCRs/IGs (B cell receptors/immunoglobulins) which share the same V gene, J gene and junction length. SCOPer is part of the Immcantation analysis framework.

Contact

For help and questions please contact the Immcantation Group

Dependencies

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

Authors

Nima Nouri (aut, cre)
Jason Vander Heiden (ctb)
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).

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).