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 yale.edu> BugReports: https://bitbucket.org/kleinstein/scoper/issues License: AGPL-3 URL: https://scoper.readthedocs.io NeedsCompilation: yes Citation: scoper citation info Materials: README NEWS In views: Omics CRAN checks: scoper results Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=scoper to link to this page.
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