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: 1.1.0
Depends: R (≥ 3.5.0), ggplot2 (≥ 3.2.0)
Imports: alakazam (≥ 1.0.2), shazam (≥ 1.0.1), data.table, doParallel, dplyr (≥ 0.8.1), foreach, methods, Rcpp (≥ 0.12.12), rlang, scales, stats, stringi, tidyr (≥ 1.0.0)
LinkingTo: Rcpp
Suggests: knitr, rmarkdown, testthat
Published: 2020-08-10
Author: Nima Nouri [aut], Edel Aron [ctb], Jason Vander Heiden [aut, cre], Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden at gmail.com>
BugReports: https://bitbucket.org/kleinstein/scoper/issues
License: AGPL-3
URL: https://scoper.readthedocs.io
NeedsCompilation: yes
SystemRequirements: C++11
Citation: scoper citation info
Materials: README NEWS
CRAN checks: scoper results

Downloads:

Reference manual: scoper.pdf
Vignettes: Inferring B cell clonal relationships
Package source: scoper_1.1.0.tar.gz
Windows binaries: r-devel: scoper_1.1.0.zip, r-release: scoper_1.0.1.zip, r-oldrel: scoper_1.0.1.zip
macOS binaries: r-release: scoper_1.0.1.tgz, r-oldrel: scoper_1.1.0.tgz
Old sources: scoper archive

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