Package: scoper
Type: Package
Version: 1.5.0.999
Date: 2026-05-25
Authors@R: c(person("Nima", "Nouri", role=c("aut"), 
                    email="nima.nouri@yale.edu"),
             person("Edel", "Aron", role=c("ctb"),
                    email="edel.aron@yale.edu"),
             person("Robert", "Bjornson", role=c("ctb"),
                    email="robert.bjornson@yale.edu"),
             person("Gisela", "Gabernet", role=c("ctb"),
                    email="gisela.gabernet@yale.edu"),                 
             person("Cole", "Jensen", role=c("ctb"),
                    email="cole.jensen@yale.edu"),
             person("Huimin", "Lyu", role=c("ctb"),
                    email="huimin.lyu@yale.edu"),
             person("Susanna", "Marquez", role=c("ctb", "cre"),
                    email="susanna.marquez@yale.edu"),
             person("Jason", "Vander Heiden", role=c("aut"),
                    email="jason.vanderheiden@gmail.com"),
             person("Steven", "Kleinstein", role=c("aut", "cph"),
                    email="steven.kleinstein@yale.edu"))
Title: Spectral Clustering-Based Method for Identifying B Cell Clones
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>.
License: AGPL-3
URL: https://scoper.readthedocs.io
BugReports: https://github.com/immcantation/scoper/issues
LazyData: true
BuildVignettes: true
VignetteBuilder: knitr
Encoding: UTF-8
LinkingTo: Rcpp
Depends: R (>= 4.0), ggplot2 (>= 3.4.0)
Imports: alakazam (>= 1.4.1), shazam (>= 1.3.0), data.table,
        doParallel, dplyr (>= 1.0), fastcluster, foreach, methods, Rcpp
        (>= 0.12.12), rlang, scales, stats, stringi, tidyr (>= 1.0)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
RoxygenNote: 7.3.3
Collate: 'Data.R' 'Scoper.R' 'Functions.R' 'RcppExports.R'
Config/pak/sysreqs: libglpk-dev libbz2-dev libicu-dev liblzma-dev
        libxml2-dev libx11-dev xz-utils zlib1g-dev
Repository: https://immcantation.r-universe.dev
Date/Publication: 2026-05-25 17:15:59 UTC
RemoteUrl: https://github.com/immcantation/scoper
RemoteRef: HEAD
RemoteSha: 810ad5a174a0fa8a40d73318cd5dfdcfcff31bf8
NeedsCompilation: yes
Packaged: 2026-07-03 17:01:19 UTC; root
Author: Nima Nouri [aut],
  Edel Aron [ctb],
  Robert Bjornson [ctb],
  Gisela Gabernet [ctb],
  Cole Jensen [ctb],
  Huimin Lyu [ctb],
  Susanna Marquez [ctb, cre],
  Jason Vander Heiden [aut],
  Steven Kleinstein [aut, cph]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>