scoper: Spectral Clustering-Based Method for Identifying B Cell Clones

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

Downloads:

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-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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=scoper to link to this page.