scoper {scoper}

The SCOPer package

Description

scoper is a member of the Immcantation framework and provides computational approaches for the identification of B cell clones from adaptive immune receptor repertoire sequencing (AIRR-Seq) datasets. It includes methods for assigning clonal identifiers using sequence identity, hierarchical clustering, and spectral clustering.

Clonal clustering

• identicalClones: Clonal assignment using sequence identity partitioning.

• hierarchicalClones: Hierarchical clustering approach to clonal assignment.

• spectralClones: Spectral clustering approach to clonal assignment.

Visualization

• plotCloneSummary: Visualize inter- and intra-clone distances.

References

1. 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.

2. Nouri N and Kleinstein SH (2019). Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data. bioRxiv, 10.1101/788620.

3. 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.