SCOPe

SCOPe (Spectral Clustering for clOne Partitioning) provides a computational framework for unsupervised identification B cell clones from adaptive immune receptor repertoire sequencing (AIRR-Seq) datasets.

This method performs spectral clustering of the B cell receptor (BCR) junction region within groups of BCR sequences sharing the same V gene, J gene, and junction length. Rather than a fixed threshold, SCOPe uses an adaptive threshold for clustering sequences to determine the local sequence neighborhood, which offers an improvement in both the sensitivity and specificity over a simple fixed threshold for all junction lengths.

Download & Installation

scope is current not available from CRAN and must be installed from the bitbucket repo directly by first cloning the bitbucket repository:

http://bitbucket.org/kleinstein/scope

Then build using the following R commands from the package root:

install.packages(c("devtools", "roxygen2"))
library(devtools)
install_deps(dependencies=T)
document()
install()

Alternatively, you can install directly form the bitbucket repository, but this will not build the documentation:

library(devtools)
install_bitbucket("kleinstein/scope@default")

Documentation

For clustering sequences into clonal groups see:

help("defineClonesScope", package="scope")

For summary statistics an visualization of the clonal clustering results see:

help("clonesAnalysis", package="scope")

How to Cite

Nouri N and Kleinstein SH. A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data. Bioinformatics, (in press).