Provides a computational framework for B cell clones identification from adaptive immune receptor repertoire sequencing (AIRR-Seq) datasets. Three models are included (identical, hierarchical, and spectral) 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>. Gupta NT, et al. (2017) <doi:10.4049/jimmunol.1601850>.
| Version: | 0.2.0 |
| Depends: | R (≥ 3.1.2), ggplot2 (≥ 3.2.0) |
| Imports: | alakazam (≥ 0.3.0), shazam (≥ 0.2.0), doParallel, foreach, dplyr (≥ 0.8.1), Rcpp (≥ 0.12.12), seqinr, data.table, stringi, stringr, methods, stats, rlang |
| LinkingTo: | Rcpp |
| Suggests: | knitr, rmarkdown, testthat |
| Published: | 2019-08-05 |
| Author: | Nima Nouri [aut, cre], Jason Vander Heiden [ctb], Steven Kleinstein [aut, cph] |
| Maintainer: | Nima Nouri <nima.nouri at yale.edu> |
| BugReports: | https://bitbucket.org/kleinstein/scoper/issues |
| License: | CC BY-SA 4.0 |
| URL: | https://scoper.readthedocs.io |
| NeedsCompilation: | yes |
| SystemRequirements: | C++11 |
| Citation: | scoper citation info |
| Materials: | README NEWS |
| CRAN checks: | scoper results |
| Reference manual: | scoper.pdf |
| Vignettes: |
%\VignetteEngine{knitr::rmarkdown}Identifying clones from high-throughput B cell repertoire sequencing data |
| Package source: | scoper_0.2.0.tar.gz |
| Windows binaries: | r-devel: scoper_0.2.0.zip, r-devel-gcc8: scoper_0.2.0.zip, r-release: scoper_0.2.0.zip, r-oldrel: scoper_0.2.0.zip |
| OS X binaries: | r-release: scoper_0.2.0.tgz, r-oldrel: scoper_0.2.0.tgz |
| Old sources: | scoper archive |
Please use the canonical form https://CRAN.R-project.org/package=scoper to link to this page.