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scoper

Spectral Clustering-Based Method for Identifying B Cell Clones

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>.

README

[![](https://www.r-pkg.org/badges/version/scoper)](https://cran.r-project.org/package=scoper)
[![](http://cranlogs.r-pkg.org/badges/grand-total/scoper)](https://www.r-pkg.org/pkg/scoper)
[![](https://cranlogs.r-pkg.org/badges/scoper)](https://www.r-pkg.org/pkg/scoper)
[![](https://img.shields.io/static/v1?label=AIRR-C%20sw-tools%20v1&message=compliant&color=008AFF&labelColor=000000&style=plastic)](https://docs.airr-community.org/en/stable/swtools/airr_swtools_standard.html)
[![](https://img.shields.io/badge/github-repo-blue?logo=github&link=https://github.com/immcantation/scoper)](https://github.com/immcantation/scoper)

SCOPer
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SCOPer (Spectral Clustering for clOne Partitioning) provides a computational framework for the identification of B cell 
clonal relationships from Adaptive Immune Receptor Repertoire sequencing 
(AIRR-Seq) data. It includes methods for assigning clonal identifiers using
sequence identity, hierarchical clustering, and spectral clustering.
SCOPer is part of the [Immcantation](http://immcantation.readthedocs.io) 
analysis framework.

Contact
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If you need help or have any questions, please contact the [Immcantation Group](mailto:immcantation@googlegroups.com).

If you have discovered a bug or have a feature request, you can open an issue using the [issue tracker](https://github.com/immcantation/scoper/issues).

To receive alerts about Immcantation releases, news, events, and tutorials, join the [Immcantation News](https://groups.google.com/g/immcantation-news) Google Group. [Membership settings](https://groups.google.com/g/immcantation-news/membership) can be adjusted to change the frequency of email updates.

Versions across snapshots

VersionRepositoryFileSize
1.4.0 rolling linux/jammy R-4.5 scoper_1.4.0.tar.gz 387.1 KiB
1.4.0 rolling linux/noble R-4.5 scoper_1.4.0.tar.gz 387.1 KiB
1.4.0 rolling source/ R- scoper_1.4.0.tar.gz 387.1 KiB
1.4.0 latest linux/jammy R-4.5 scoper_1.4.0.tar.gz 387.1 KiB
1.4.0 latest linux/noble R-4.5 scoper_1.4.0.tar.gz 387.1 KiB
1.4.0 latest source/ R- scoper_1.4.0.tar.gz 387.1 KiB
1.4.0 2026-04-26 source/ R- scoper_1.4.0.tar.gz 387.1 KiB
1.4.0 2026-04-23 source/ R- scoper_1.4.0.tar.gz 387.1 KiB
1.3.0 2025-04-20 source/ R- scoper_1.3.0.tar.gz 384.3 KiB

Dependencies (latest)

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