scoper

MaRDI QIDQ95984CRANFDO

Authors Jason vander Heiden, Nima Nouri, Steven H. Kleinstein

Last update 6 October 2023

Copyright license GNU Affero General Public License, version 3.0

Software version identifier 1.2.1, 0.1.0, 0.2.0, 1.0.0, 1.0.1, 1.1.0, 1.2.0, 1.3.0

Description

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>.

Cites work

• A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data
• Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data
• Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data

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