scoper - The SCOPer package
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) which perform clustering among sequences of B cell receptors (BCRs, also referred to as Immunoglobulins, (Igs)) that share the same V gene, J gene and junction length.
- defineClonesScoper: Clustering sequences into clonal groups.
- Nouri N and Kleinstein SH (2018). A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data. Bioinformatics, 34(13):i341-i349.
- Gupta NT, et al. (2017). Hierarchical clustering can identify B cell clones with high confidence in Ig repertoire sequencing data. The Journal of Immunology, 198(6):2489-2499.