SCOPer

SCOPer (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. SCOPer is part of the Immcantation analysis framework.

Contact

For help and questions please contact the Immcantation Group

Dependencies

Depends: ggplot2
Imports: alakazam, shazam, doParallel, foreach, dplyr, stringi, methods, stats, iterators, lazyeval
Suggests: knitr, rmarkdown, testthat

Authors

Nima Nouri (aut, cre)
Jason Vander Heiden (ctb)
Steven Kleinstein (aut, cph)

Citing

To cite the scoper package in publications, please use:

Nouri N and Kleinstein S (2018). “A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data.” Bioinformatics, pp. i341-i349. doi: 10.1093/bioinformatics/bty235 (URL: http://doi.org/10.1093/bioinformatics/bty235).

A BibTeX entry for LaTeX users is

@Article{, style = {citation}, title = {A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data.}, author = {Nima Nouri and Steven H. Kleinstein}, year = {2018}, journal = {Bioinformatics}, pages = {i341-i349}, doi = {10.1093/bioinformatics/bty235}, }