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:	1.3.0
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
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

Documentation:

Reference manual:	scoper.pdf
Vignettes:	Inferring B cell clonal relationships

Downloads:

Package source:	scoper_1.3.0.tar.gz
Windows binaries:	r-devel: scoper_1.3.0.zip, r-release: scoper_1.3.0.zip, r-oldrel: scoper_1.3.0.zip
macOS binaries:	r-release (arm64): scoper_1.3.0.tgz, r-oldrel (arm64): scoper_1.3.0.tgz, r-release (x86_64): scoper_1.3.0.tgz, r-oldrel (x86_64): scoper_1.3.0.tgz
Old sources:	scoper archive

Linking:

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