Spectral Clustering-Based Method for Identifying B Cell Clones R package scoper version 1.5.0 CRAN Task View: Omics (https://CRAN.R-project.org/view=Omics) 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) <doi: 10.1093/bioinformatics/bty235>. Nouri N and Kleinstein SH (2019) <doi: 10.1101/788620>. Gupta NT, et al. (2017) <doi: 10.4049/jimmunol.1601850>. Software Depends: R (>= 4.0), ggplot2 (>= 3.4.0) Imports: alakazam (>= 1.4.1), shazam (>= 1.3.0), data.table, doParallel, dplyr (>= 1.0), fastcluster, foreach, methods, Rcpp (>= 0.12.12), rlang, scales, stats, stringi, tidyr (>= 1.0) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat (>= 3.0.0) Susanna Marquez <susanna.marquez@yale.edu> Comprehensive R Archive Network (CRAN) 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] AGPL-3 2026-05-05 application/tgz https://CRAN.R-project.org/package=scoper doi:10.32614/CRAN.package.scoper