scoper: Spectral Clustering-Based Method for Identifying B Cell Clones (original) (raw)
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 |
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