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 |