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SCOPer¶

SCOPer (Spectral Clustering for clOne Partitioning) 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¶

If you need help or have any questions, please contact the Immcantation Group.

If you have discovered a bug or have a feature request, you can open an issue using the issue tracker.

To receive alerts about Immcantation releases, news, events, and tutorials, join the Immcantation News Google Group. Membership settings can be adjusted to change the frequency of email updates.

Dependencies¶

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

Authors¶

Nima Nouri (aut)
Edel Aron (ctb)
Robert Bjornson (ctb)
Gisela Gabernet (ctb)
Cole Jensen (ctb)
Huimin Lyu (ctb)
Susanna Marquez (ctb, cre)
Jason Vander Heiden (aut)
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 https://doi.org/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 https://doi.org/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 https://doi.org/10.4049/jimmunol.1601850.

License¶

AGPL-3