Package: VDJdive
Title: Analysis Tools for 10X V(D)J Data
Version: 1.15.1
Authors@R: c(
    person("Kelly", "Street", role = c("aut", "cre"), email = "street.kelly@gmail.com", comment = c(ORCID = "0000-0001-6379-5013")),
    person("Mercedeh", "Movassagh", role = "aut", email = "mercedeh@ds.dfci.harvard.edu", comment = c(ORCID = "0000-0001-7690-0230")),
    person("Jill", "Lundell", role = "aut", email = "jflundell@gmail.com", comment = c(ORCID = "0000-0002-6048-4700")),
    person("Jared", "Brown", role = "ctb"),
    person("Linglin", "Huang", role = "ctb"),
    person("Mingzhi", "Ye", role = "ctb"))
Description: This package provides functions for handling and analyzing
        immune receptor repertoire data, such as produced by the
        CellRanger V(D)J pipeline. This includes reading the data into
        R, merging it with paired single-cell data, quantifying
        clonotype abundances, calculating diversity metrics, and
        producing common plots. It implements the E-M Algorithm for
        clonotype assignment, along with other methods, which makes use
        of ambiguous cells for improved quantification.
Depends: R (>= 4.2)
Imports: BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix,
        methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment,
        stats, SummarizedExperiment, utils
Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle
LinkingTo: Rcpp
License: Artistic-2.0
URL: https://github.com/kstreet13/VDJdive
BugReports: https://github.com/kstreet13/VDJdive/issues
biocViews: Software, ImmunoOncology, SingleCell, Annotation, RNASeq,
        TargetedResequencing
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
StagedInstall: no
VignetteBuilder: knitr
Collate: 'RcppExports.R' 'clonoStats_class.R' 'abundanceVDJ.R'
        'barVDJ.R' 'boxVDJ.R' 'calculateDiversity.R'
        'clonoStats_helpers.R' 'clonoStats.R' 'contigs.R' 'pieVDJ.R'
        'runBreakaway.R' 'runVDJPCA.R' 'scatterVDJ.R' 'setup.R'
        'utils.R'
Config/Bioconductor/UnsupportedPlatforms: windows
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-05-29 18:37:27 UTC
RemoteUrl: https://github.com/bioc/VDJdive
RemoteRef: HEAD
RemoteSha: e6b1f6bd749238aaec49033f84304d66c13eca6a
NeedsCompilation: yes
Packaged: 2026-06-11 11:12:21 UTC; root
Author: Kelly Street [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-6379-5013>),
  Mercedeh Movassagh [aut] (ORCID:
    <https://orcid.org/0000-0001-7690-0230>),
  Jill Lundell [aut] (ORCID: <https://orcid.org/0000-0002-6048-4700>),
  Jared Brown [ctb],
  Linglin Huang [ctb],
  Mingzhi Ye [ctb]
Maintainer: Kelly Street <street.kelly@gmail.com>