Package: scoper 1.3.1.999

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>.

Authors:Nima Nouri [aut], Edel Aron [ctb], Gisela Gabernet [ctb], Susanna Marquez [ctb, cre], Jason Vander Heiden [aut], Steven Kleinstein [aut, cph]

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NEWS

# Install 'scoper' in R:
install.packages('scoper', repos = c('https://ssnn-airr.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/immcantation/scoper/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

cpp

5.43 score 89 scripts 468 downloads 8 exports 103 dependencies

Last updated 1 months agofrom:a170d88c8b. Checks:1 OK, 8 WARNING, 1 FAILURE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 17 2025
R-4.5-win-x86_64WARNINGFeb 17 2025
R-4.5-mac-x86_64WARNINGFeb 17 2025
R-4.5-mac-aarch64WARNINGFeb 17 2025
R-4.5-linux-x86_64WARNINGFeb 17 2025
R-4.4-win-x86_64WARNINGFeb 17 2025
R-4.4-mac-x86_64WARNINGFeb 17 2025
R-4.4-mac-aarch64WARNINGFeb 17 2025
R-4.3-win-x86_64OUTDATEDDec 04 2024
R-4.3-mac-x86_64WARNINGFeb 17 2025

Exports:as.data.framehierarchicalClonesidenticalClonesplotplotCloneSummaryprintspectralClonessummary

Dependencies:abindade4airralakazamapeaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsclicliprcodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydigestdiptestdoParalleldplyrfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehmshttrigraphIRangesisobanditeratorsjsonliteKernSmoothlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpixmappkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloreadrRhtslibrlangRsamtoolsS4ArraysS4VectorsscalessegmentedseqinrshazamsnowspSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXVectoryaml

Identifying clones from high-throughput B cell repertoire sequencing data

Nima Nouri, Jason Vander Heiden, Edel Aron, and Susanna Marquez

Rendered fromScoper-Vignette.Rmdusingknitr::rmarkdownon Feb 17 2025.

Last update: 2022-05-09
Started: 2018-10-04