scoper: Spectral Clustering-Based Method for Identifying B Cell Clones

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>.

Version: 1.3.0
Depends: R (≥ 4.0), ggplot2 (≥ 3.4.0)
Imports: alakazam (≥ 1.3.0), shazam (≥ 1.2.0), data.table, doParallel, dplyr (≥ 1.0), foreach, methods, Rcpp (≥ 0.12.12), rlang, scales, stats, stringi, tidyr (≥ 1.0)
LinkingTo: Rcpp
Suggests: knitr, rmarkdown, testthat
Published: 2023-10-06
DOI: 10.32614/CRAN.package.scoper
Author: Nima Nouri [aut], Edel Aron [ctb], Gisela Gabernet [ctb], Susanna Marquez [ctb, cre], Jason Vander Heiden [aut], Steven Kleinstein [aut, cph]
Maintainer: Susanna Marquez <susanna.marquez at>
License: AGPL-3
NeedsCompilation: yes
Citation: scoper citation info
Materials: README NEWS
In views: Omics
CRAN checks: scoper results


Reference manual: scoper.pdf
Vignettes: Inferring B cell clonal relationships


Package source: scoper_1.3.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): scoper_1.3.0.tgz, r-oldrel (arm64): scoper_1.3.0.tgz, r-release (x86_64): scoper_1.3.0.tgz, r-oldrel (x86_64): scoper_1.3.0.tgz
Old sources: scoper archive


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